Multiple sequence alignment - TraesCS3D01G070900

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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 TraesCS3D01G070900 chr3D 100.000 3867 0 0 1 3867 31778368 31774502 0.000000e+00 7142.0
1 TraesCS3D01G070900 chr3D 79.487 1716 268 54 1503 3201 31846638 31848286 0.000000e+00 1142.0
2 TraesCS3D01G070900 chr3D 93.976 83 5 0 1421 1503 31776918 31776836 4.060000e-25 126.0
3 TraesCS3D01G070900 chr3D 93.976 83 5 0 1451 1533 31776948 31776866 4.060000e-25 126.0
4 TraesCS3D01G070900 chr3B 95.825 2419 69 6 1451 3867 53952089 53949701 0.000000e+00 3879.0
5 TraesCS3D01G070900 chr3B 93.550 2403 114 16 1473 3867 54304923 54302554 0.000000e+00 3541.0
6 TraesCS3D01G070900 chr3B 79.849 1717 265 45 1503 3201 54500357 54502010 0.000000e+00 1179.0
7 TraesCS3D01G070900 chr3B 93.505 739 38 3 2833 3571 54145160 54145888 0.000000e+00 1090.0
8 TraesCS3D01G070900 chr3B 88.828 913 42 20 238 1106 54308382 54307486 0.000000e+00 1066.0
9 TraesCS3D01G070900 chr3B 93.231 650 32 4 2833 3482 54068965 54069602 0.000000e+00 946.0
10 TraesCS3D01G070900 chr3B 92.037 653 13 10 884 1503 53952653 53952007 0.000000e+00 881.0
11 TraesCS3D01G070900 chr3B 90.167 600 23 14 79 654 53953243 53952656 0.000000e+00 749.0
12 TraesCS3D01G070900 chr3B 88.830 376 25 7 1099 1469 54305227 54304864 2.740000e-121 446.0
13 TraesCS3D01G070900 chr3B 92.958 213 15 0 2833 3045 53996091 53996303 1.040000e-80 311.0
14 TraesCS3D01G070900 chr3B 96.226 53 2 0 1421 1473 53952059 53952007 1.910000e-13 87.9
15 TraesCS3D01G070900 chr1D 81.566 613 75 19 66 656 360280663 360280067 4.520000e-129 472.0
16 TraesCS3D01G070900 chr1D 98.765 81 0 1 3788 3867 63428278 63428358 4.030000e-30 143.0
17 TraesCS3D01G070900 chr1D 97.500 80 2 0 3788 3867 50021694 50021615 1.870000e-28 137.0
18 TraesCS3D01G070900 chr1B 86.634 202 22 2 73 274 482177244 482177048 6.500000e-53 219.0
19 TraesCS3D01G070900 chr4B 100.000 80 0 0 3788 3867 30370069 30369990 8.660000e-32 148.0
20 TraesCS3D01G070900 chr4B 95.349 86 2 2 3784 3867 592354421 592354506 6.740000e-28 135.0
21 TraesCS3D01G070900 chr7B 97.500 80 2 0 3788 3867 104073280 104073359 1.870000e-28 137.0
22 TraesCS3D01G070900 chr5B 97.500 80 2 0 3788 3867 706167800 706167721 1.870000e-28 137.0
23 TraesCS3D01G070900 chr2A 97.531 81 1 1 3788 3867 69385947 69386027 1.870000e-28 137.0


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 TraesCS3D01G070900 chr3D 31774502 31778368 3866 True 2464.666667 7142 95.984000 1 3867 3 chr3D.!!$R1 3866
1 TraesCS3D01G070900 chr3D 31846638 31848286 1648 False 1142.000000 1142 79.487000 1503 3201 1 chr3D.!!$F1 1698
2 TraesCS3D01G070900 chr3B 54302554 54308382 5828 True 1684.333333 3541 90.402667 238 3867 3 chr3B.!!$R2 3629
3 TraesCS3D01G070900 chr3B 53949701 53953243 3542 True 1399.225000 3879 93.563750 79 3867 4 chr3B.!!$R1 3788
4 TraesCS3D01G070900 chr3B 54500357 54502010 1653 False 1179.000000 1179 79.849000 1503 3201 1 chr3B.!!$F4 1698
5 TraesCS3D01G070900 chr3B 54145160 54145888 728 False 1090.000000 1090 93.505000 2833 3571 1 chr3B.!!$F3 738
6 TraesCS3D01G070900 chr3B 54068965 54069602 637 False 946.000000 946 93.231000 2833 3482 1 chr3B.!!$F2 649
7 TraesCS3D01G070900 chr1D 360280067 360280663 596 True 472.000000 472 81.566000 66 656 1 chr1D.!!$R2 590

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
752 806 0.323629 TCAACAGGGCCCGAGTTAAG 59.676 55.0 28.11 19.57 0.0 1.85 F
1501 3859 0.178944 TGAGGAAGACACGGAGGGAA 60.179 55.0 0.00 0.00 0.0 3.97 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1950 4311 0.532573 CGGTGACACAGAGGCTATGT 59.467 55.0 9.36 9.36 0.00 2.29 R
3324 5701 0.110295 ACATAACAGTGGCAGTGGCA 59.890 50.0 25.12 16.56 43.71 4.92 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
19 20 2.399916 AGGTCTTTCAGCTCAGCATC 57.600 50.000 0.00 0.00 0.00 3.91
20 21 1.065564 AGGTCTTTCAGCTCAGCATCC 60.066 52.381 0.00 0.00 0.00 3.51
21 22 1.005340 GTCTTTCAGCTCAGCATCCG 58.995 55.000 0.00 0.00 0.00 4.18
22 23 0.897621 TCTTTCAGCTCAGCATCCGA 59.102 50.000 0.00 0.00 0.00 4.55
23 24 1.276138 TCTTTCAGCTCAGCATCCGAA 59.724 47.619 0.00 0.00 0.00 4.30
24 25 2.079158 CTTTCAGCTCAGCATCCGAAA 58.921 47.619 0.00 1.44 0.00 3.46
25 26 1.730501 TTCAGCTCAGCATCCGAAAG 58.269 50.000 0.00 0.00 0.00 2.62
26 27 0.610174 TCAGCTCAGCATCCGAAAGT 59.390 50.000 0.00 0.00 0.00 2.66
27 28 1.824852 TCAGCTCAGCATCCGAAAGTA 59.175 47.619 0.00 0.00 0.00 2.24
28 29 2.233676 TCAGCTCAGCATCCGAAAGTAA 59.766 45.455 0.00 0.00 0.00 2.24
29 30 3.002791 CAGCTCAGCATCCGAAAGTAAA 58.997 45.455 0.00 0.00 0.00 2.01
30 31 3.003480 AGCTCAGCATCCGAAAGTAAAC 58.997 45.455 0.00 0.00 0.00 2.01
31 32 2.742053 GCTCAGCATCCGAAAGTAAACA 59.258 45.455 0.00 0.00 0.00 2.83
32 33 3.375299 GCTCAGCATCCGAAAGTAAACAT 59.625 43.478 0.00 0.00 0.00 2.71
33 34 4.570772 GCTCAGCATCCGAAAGTAAACATA 59.429 41.667 0.00 0.00 0.00 2.29
34 35 5.502544 GCTCAGCATCCGAAAGTAAACATAC 60.503 44.000 0.00 0.00 0.00 2.39
35 36 4.565166 TCAGCATCCGAAAGTAAACATACG 59.435 41.667 0.00 0.00 0.00 3.06
36 37 4.328983 CAGCATCCGAAAGTAAACATACGT 59.671 41.667 0.00 0.00 0.00 3.57
37 38 4.328983 AGCATCCGAAAGTAAACATACGTG 59.671 41.667 0.00 0.00 0.00 4.49
38 39 4.092383 GCATCCGAAAGTAAACATACGTGT 59.908 41.667 0.00 0.00 41.28 4.49
39 40 5.723135 GCATCCGAAAGTAAACATACGTGTC 60.723 44.000 0.00 0.00 37.67 3.67
40 41 4.236935 TCCGAAAGTAAACATACGTGTCC 58.763 43.478 0.00 0.00 37.67 4.02
41 42 3.989167 CCGAAAGTAAACATACGTGTCCA 59.011 43.478 0.00 0.00 37.67 4.02
42 43 4.448395 CCGAAAGTAAACATACGTGTCCAA 59.552 41.667 0.00 0.00 37.67 3.53
43 44 5.368374 CGAAAGTAAACATACGTGTCCAAC 58.632 41.667 0.00 0.00 37.67 3.77
44 45 5.050904 CGAAAGTAAACATACGTGTCCAACA 60.051 40.000 0.00 0.00 37.67 3.33
45 46 5.917541 AAGTAAACATACGTGTCCAACAG 57.082 39.130 0.00 0.00 37.67 3.16
46 47 3.744426 AGTAAACATACGTGTCCAACAGC 59.256 43.478 0.00 0.00 37.67 4.40
47 48 2.248280 AACATACGTGTCCAACAGCA 57.752 45.000 0.00 0.00 37.67 4.41
48 49 1.508632 ACATACGTGTCCAACAGCAC 58.491 50.000 0.00 0.00 31.41 4.40
49 50 1.202592 ACATACGTGTCCAACAGCACA 60.203 47.619 0.00 0.00 31.41 4.57
50 51 2.076100 CATACGTGTCCAACAGCACAT 58.924 47.619 0.00 0.00 35.51 3.21
51 52 3.258228 CATACGTGTCCAACAGCACATA 58.742 45.455 0.00 0.00 35.51 2.29
52 53 2.472695 ACGTGTCCAACAGCACATAT 57.527 45.000 0.00 0.00 35.51 1.78
53 54 3.603158 ACGTGTCCAACAGCACATATA 57.397 42.857 0.00 0.00 35.51 0.86
54 55 3.521560 ACGTGTCCAACAGCACATATAG 58.478 45.455 0.00 0.00 35.51 1.31
55 56 3.194755 ACGTGTCCAACAGCACATATAGA 59.805 43.478 0.00 0.00 35.51 1.98
56 57 3.551890 CGTGTCCAACAGCACATATAGAC 59.448 47.826 0.00 0.00 35.51 2.59
57 58 3.551890 GTGTCCAACAGCACATATAGACG 59.448 47.826 0.00 0.00 35.81 4.18
58 59 3.445805 TGTCCAACAGCACATATAGACGA 59.554 43.478 0.00 0.00 0.00 4.20
59 60 4.045104 GTCCAACAGCACATATAGACGAG 58.955 47.826 0.00 0.00 0.00 4.18
60 61 2.797156 CCAACAGCACATATAGACGAGC 59.203 50.000 0.00 0.00 0.00 5.03
61 62 3.447742 CAACAGCACATATAGACGAGCA 58.552 45.455 0.00 0.00 0.00 4.26
62 63 3.361794 ACAGCACATATAGACGAGCAG 57.638 47.619 0.00 0.00 0.00 4.24
63 64 2.057316 CAGCACATATAGACGAGCAGC 58.943 52.381 0.00 0.00 0.00 5.25
64 65 1.959985 AGCACATATAGACGAGCAGCT 59.040 47.619 0.00 0.00 0.00 4.24
83 84 2.159599 GCTATGCTATTGCTTCCATCGC 60.160 50.000 0.00 0.00 40.48 4.58
140 145 1.607509 CGAGCCCAGATAGCTTCCATG 60.608 57.143 0.00 0.00 41.75 3.66
141 146 0.769873 AGCCCAGATAGCTTCCATGG 59.230 55.000 4.97 4.97 37.24 3.66
146 156 2.074576 CAGATAGCTTCCATGGCGATG 58.925 52.381 6.96 1.01 34.52 3.84
147 157 0.801251 GATAGCTTCCATGGCGATGC 59.199 55.000 6.96 8.35 34.10 3.91
169 179 1.736645 CAAATGCCTGCTGCTGCAC 60.737 57.895 14.93 6.71 45.31 4.57
334 350 8.604105 TCAGCTATGAACCTTGTGACAAACAAT 61.604 37.037 0.00 0.00 39.23 2.71
376 406 2.127251 TGTATTAGCTTCATCTGCGCG 58.873 47.619 0.00 0.00 35.28 6.86
377 407 1.136502 GTATTAGCTTCATCTGCGCGC 60.137 52.381 27.26 27.26 35.28 6.86
559 599 2.991190 GCATTCAATCAAACTGTGCCTG 59.009 45.455 0.00 0.00 0.00 4.85
642 685 0.324943 AAGTCCTTGGTCGGGATGTG 59.675 55.000 0.00 0.00 35.15 3.21
739 793 5.368256 AGAGCAAACTAAGCAATCAACAG 57.632 39.130 0.00 0.00 0.00 3.16
745 799 0.679640 TAAGCAATCAACAGGGCCCG 60.680 55.000 18.44 14.39 0.00 6.13
746 800 2.361104 GCAATCAACAGGGCCCGA 60.361 61.111 18.44 8.04 0.00 5.14
747 801 2.409870 GCAATCAACAGGGCCCGAG 61.410 63.158 18.44 16.40 0.00 4.63
748 802 1.002134 CAATCAACAGGGCCCGAGT 60.002 57.895 18.44 17.16 0.00 4.18
749 803 0.609131 CAATCAACAGGGCCCGAGTT 60.609 55.000 24.67 24.67 0.00 3.01
750 804 0.988832 AATCAACAGGGCCCGAGTTA 59.011 50.000 28.11 18.98 0.00 2.24
751 805 0.988832 ATCAACAGGGCCCGAGTTAA 59.011 50.000 28.11 19.07 0.00 2.01
752 806 0.323629 TCAACAGGGCCCGAGTTAAG 59.676 55.000 28.11 19.57 0.00 1.85
753 807 0.676782 CAACAGGGCCCGAGTTAAGG 60.677 60.000 28.11 16.45 0.00 2.69
807 861 7.044798 ACCTCATACAAACTCTCTAATCAAGC 58.955 38.462 0.00 0.00 0.00 4.01
824 878 4.864334 CCAAGCGGGGCTAGGCAG 62.864 72.222 19.14 12.30 38.25 4.85
874 928 0.738412 CGATCGCCCCGTTTTACTGT 60.738 55.000 0.26 0.00 0.00 3.55
998 1073 4.147449 CTGCGCCGACCCATCAGA 62.147 66.667 4.18 0.00 0.00 3.27
1017 1092 3.092511 ATGGCCGTGGCTGGATCT 61.093 61.111 11.25 0.00 41.60 2.75
1050 1125 1.890979 CTGGATGATGCTGGACCGC 60.891 63.158 1.90 1.90 0.00 5.68
1243 3595 0.328258 AAAATACGGCTCCAGCACCT 59.672 50.000 0.03 0.00 44.36 4.00
1482 3840 2.047830 ACGGAGGGAACTTCTTCTTGT 58.952 47.619 0.00 0.00 44.43 3.16
1483 3841 2.224305 ACGGAGGGAACTTCTTCTTGTG 60.224 50.000 0.00 0.00 44.43 3.33
1484 3842 2.037251 CGGAGGGAACTTCTTCTTGTGA 59.963 50.000 0.00 0.00 44.43 3.58
1485 3843 3.669536 GGAGGGAACTTCTTCTTGTGAG 58.330 50.000 0.00 0.00 44.43 3.51
1486 3844 3.558109 GGAGGGAACTTCTTCTTGTGAGG 60.558 52.174 0.00 0.00 44.43 3.86
1487 3845 3.318313 AGGGAACTTCTTCTTGTGAGGA 58.682 45.455 0.00 0.00 37.44 3.71
1488 3846 3.716872 AGGGAACTTCTTCTTGTGAGGAA 59.283 43.478 0.00 0.00 37.44 3.36
1494 3852 3.371102 TCTTCTTGTGAGGAAGACACG 57.629 47.619 2.54 0.00 42.59 4.49
1495 3853 2.035961 TCTTCTTGTGAGGAAGACACGG 59.964 50.000 2.54 0.00 42.59 4.94
1496 3854 1.699730 TCTTGTGAGGAAGACACGGA 58.300 50.000 0.00 0.00 40.61 4.69
1497 3855 1.613925 TCTTGTGAGGAAGACACGGAG 59.386 52.381 0.00 0.00 40.61 4.63
1498 3856 0.679505 TTGTGAGGAAGACACGGAGG 59.320 55.000 0.00 0.00 40.61 4.30
1499 3857 1.185618 TGTGAGGAAGACACGGAGGG 61.186 60.000 0.00 0.00 40.61 4.30
1500 3858 0.898789 GTGAGGAAGACACGGAGGGA 60.899 60.000 0.00 0.00 0.00 4.20
1501 3859 0.178944 TGAGGAAGACACGGAGGGAA 60.179 55.000 0.00 0.00 0.00 3.97
1545 3903 2.895372 GGAACCACTATGCGGCGG 60.895 66.667 9.78 0.00 0.00 6.13
1950 4311 6.605119 AGAAAGAGGTTTCCTTGAGATGAAA 58.395 36.000 0.00 0.00 42.84 2.69
1971 4332 1.961180 ATAGCCTCTGTGTCACCGGC 61.961 60.000 16.16 16.16 40.99 6.13
1992 4353 3.664107 CGTTGGAGGTGATCTTCTCAAA 58.336 45.455 14.60 8.99 35.07 2.69
2098 4459 2.159043 AGCATAACGGAGAGTGGTGATG 60.159 50.000 0.00 0.00 0.00 3.07
2216 4580 2.766263 TGAGCATGGACAACCCTAGTAG 59.234 50.000 0.00 0.00 35.38 2.57
3040 5415 5.666969 TGAAGTTTAGATTTCGTGTGTGG 57.333 39.130 0.00 0.00 0.00 4.17
3074 5450 4.570772 TGCTGTGTCAGTCTTGTTAGTTTC 59.429 41.667 0.00 0.00 33.43 2.78
3118 5494 1.066605 TCGTTGGGCGCTAAGAGATAC 59.933 52.381 7.64 0.00 41.07 2.24
3257 5634 1.419387 GCTCAATGCCTCTATCCCAGT 59.581 52.381 0.00 0.00 35.15 4.00
3258 5635 2.158696 GCTCAATGCCTCTATCCCAGTT 60.159 50.000 0.00 0.00 35.15 3.16
3259 5636 3.071602 GCTCAATGCCTCTATCCCAGTTA 59.928 47.826 0.00 0.00 35.15 2.24
3279 5656 9.028284 CCAGTTATTATCATTGAATAGGGCATT 57.972 33.333 0.00 0.00 0.00 3.56
3290 5667 4.889409 TGAATAGGGCATTAGGAAGCAAAG 59.111 41.667 0.00 0.00 0.00 2.77
3291 5668 2.907458 AGGGCATTAGGAAGCAAAGT 57.093 45.000 0.00 0.00 0.00 2.66
3299 5676 5.693814 CATTAGGAAGCAAAGTGAGTTCAC 58.306 41.667 4.09 4.09 46.77 3.18
3323 5700 1.892819 CTGGACAGTCCTCACGCCAT 61.893 60.000 20.82 0.00 37.46 4.40
3324 5701 1.296715 GGACAGTCCTCACGCCATT 59.703 57.895 12.94 0.00 32.53 3.16
3325 5702 1.021390 GGACAGTCCTCACGCCATTG 61.021 60.000 12.94 0.00 32.53 2.82
3326 5703 1.639298 GACAGTCCTCACGCCATTGC 61.639 60.000 0.00 0.00 0.00 3.56
3327 5704 2.045926 AGTCCTCACGCCATTGCC 60.046 61.111 0.00 0.00 0.00 4.52
3328 5705 2.359850 GTCCTCACGCCATTGCCA 60.360 61.111 0.00 0.00 0.00 4.92
3391 5768 3.786635 AGATGTATCAACCGCTTGTCTC 58.213 45.455 0.00 0.00 0.00 3.36
3411 5788 3.921677 TCCTTTTCTCGGTGTATGTGAC 58.078 45.455 0.00 0.00 0.00 3.67
3554 5931 2.133553 CGCTGATAGATGCACTTGAGG 58.866 52.381 0.00 0.00 0.00 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.065564 GGATGCTGAGCTGAAAGACCT 60.066 52.381 5.83 0.00 34.07 3.85
1 2 1.377536 GGATGCTGAGCTGAAAGACC 58.622 55.000 5.83 0.00 34.07 3.85
2 3 1.005340 CGGATGCTGAGCTGAAAGAC 58.995 55.000 5.83 0.00 34.07 3.01
3 4 0.897621 TCGGATGCTGAGCTGAAAGA 59.102 50.000 5.83 0.00 34.07 2.52
4 5 1.730501 TTCGGATGCTGAGCTGAAAG 58.269 50.000 5.83 0.00 0.00 2.62
5 6 2.079158 CTTTCGGATGCTGAGCTGAAA 58.921 47.619 5.83 9.76 0.00 2.69
6 7 1.002430 ACTTTCGGATGCTGAGCTGAA 59.998 47.619 5.83 2.00 0.00 3.02
7 8 0.610174 ACTTTCGGATGCTGAGCTGA 59.390 50.000 5.83 0.00 0.00 4.26
8 9 2.299993 TACTTTCGGATGCTGAGCTG 57.700 50.000 5.83 0.00 0.00 4.24
9 10 3.003480 GTTTACTTTCGGATGCTGAGCT 58.997 45.455 5.83 0.00 0.00 4.09
10 11 2.742053 TGTTTACTTTCGGATGCTGAGC 59.258 45.455 0.00 0.00 0.00 4.26
11 12 5.276395 CGTATGTTTACTTTCGGATGCTGAG 60.276 44.000 0.00 0.00 0.00 3.35
12 13 4.565166 CGTATGTTTACTTTCGGATGCTGA 59.435 41.667 0.00 0.00 0.00 4.26
13 14 4.328983 ACGTATGTTTACTTTCGGATGCTG 59.671 41.667 0.00 0.00 0.00 4.41
14 15 4.328983 CACGTATGTTTACTTTCGGATGCT 59.671 41.667 0.00 0.00 0.00 3.79
15 16 4.092383 ACACGTATGTTTACTTTCGGATGC 59.908 41.667 0.00 0.00 34.46 3.91
16 17 5.220340 GGACACGTATGTTTACTTTCGGATG 60.220 44.000 0.00 0.00 39.95 3.51
17 18 4.866486 GGACACGTATGTTTACTTTCGGAT 59.134 41.667 0.00 0.00 39.95 4.18
18 19 4.236935 GGACACGTATGTTTACTTTCGGA 58.763 43.478 0.00 0.00 39.95 4.55
19 20 3.989167 TGGACACGTATGTTTACTTTCGG 59.011 43.478 0.00 0.00 39.95 4.30
20 21 5.050904 TGTTGGACACGTATGTTTACTTTCG 60.051 40.000 0.00 0.00 39.95 3.46
21 22 6.289745 TGTTGGACACGTATGTTTACTTTC 57.710 37.500 0.00 0.00 39.95 2.62
22 23 5.277634 GCTGTTGGACACGTATGTTTACTTT 60.278 40.000 0.00 0.00 39.95 2.66
23 24 4.212636 GCTGTTGGACACGTATGTTTACTT 59.787 41.667 0.00 0.00 39.95 2.24
24 25 3.744426 GCTGTTGGACACGTATGTTTACT 59.256 43.478 0.00 0.00 39.95 2.24
25 26 3.495377 TGCTGTTGGACACGTATGTTTAC 59.505 43.478 0.00 0.00 39.95 2.01
26 27 3.495377 GTGCTGTTGGACACGTATGTTTA 59.505 43.478 0.00 0.00 39.95 2.01
27 28 2.289547 GTGCTGTTGGACACGTATGTTT 59.710 45.455 0.00 0.00 39.95 2.83
28 29 1.871039 GTGCTGTTGGACACGTATGTT 59.129 47.619 0.00 0.00 39.95 2.71
29 30 1.202592 TGTGCTGTTGGACACGTATGT 60.203 47.619 0.00 0.00 43.71 2.29
30 31 1.507562 TGTGCTGTTGGACACGTATG 58.492 50.000 0.00 0.00 39.59 2.39
31 32 2.472695 ATGTGCTGTTGGACACGTAT 57.527 45.000 0.00 0.00 46.84 3.06
32 33 3.603158 ATATGTGCTGTTGGACACGTA 57.397 42.857 0.00 0.00 46.84 3.57
33 34 2.472695 ATATGTGCTGTTGGACACGT 57.527 45.000 0.00 0.00 46.84 4.49
34 35 3.551890 GTCTATATGTGCTGTTGGACACG 59.448 47.826 0.00 0.00 46.84 4.49
35 36 3.551890 CGTCTATATGTGCTGTTGGACAC 59.448 47.826 0.00 0.00 46.84 3.67
37 38 4.041740 TCGTCTATATGTGCTGTTGGAC 57.958 45.455 0.00 0.00 34.96 4.02
38 39 3.490933 GCTCGTCTATATGTGCTGTTGGA 60.491 47.826 0.00 0.00 0.00 3.53
39 40 2.797156 GCTCGTCTATATGTGCTGTTGG 59.203 50.000 0.00 0.00 0.00 3.77
40 41 3.447742 TGCTCGTCTATATGTGCTGTTG 58.552 45.455 0.00 0.00 33.29 3.33
41 42 3.711086 CTGCTCGTCTATATGTGCTGTT 58.289 45.455 0.00 0.00 33.29 3.16
42 43 2.544694 GCTGCTCGTCTATATGTGCTGT 60.545 50.000 0.00 0.00 34.45 4.40
43 44 2.057316 GCTGCTCGTCTATATGTGCTG 58.943 52.381 0.00 0.00 34.83 4.41
44 45 1.959985 AGCTGCTCGTCTATATGTGCT 59.040 47.619 0.00 0.00 33.29 4.40
45 46 2.430546 AGCTGCTCGTCTATATGTGC 57.569 50.000 0.00 0.00 0.00 4.57
46 47 3.856521 GCATAGCTGCTCGTCTATATGTG 59.143 47.826 4.91 0.00 45.32 3.21
47 48 4.103365 GCATAGCTGCTCGTCTATATGT 57.897 45.455 4.91 0.00 45.32 2.29
60 61 3.124806 CGATGGAAGCAATAGCATAGCTG 59.875 47.826 0.00 0.00 45.49 4.24
61 62 3.332919 CGATGGAAGCAATAGCATAGCT 58.667 45.455 0.00 0.00 45.49 3.32
62 63 2.159599 GCGATGGAAGCAATAGCATAGC 60.160 50.000 0.00 0.00 45.49 2.97
63 64 3.069289 TGCGATGGAAGCAATAGCATAG 58.931 45.455 0.00 0.00 45.49 2.23
64 65 3.069289 CTGCGATGGAAGCAATAGCATA 58.931 45.455 0.00 0.00 44.67 3.14
83 84 2.612672 CACATACTGCTTGATCCTGCTG 59.387 50.000 10.71 10.71 0.00 4.41
163 173 1.709147 GATCATGACGTGGGTGCAGC 61.709 60.000 7.55 7.55 0.00 5.25
169 179 2.330440 TCCATTGATCATGACGTGGG 57.670 50.000 0.00 0.00 34.31 4.61
336 352 4.330250 ACATGAAAGAGTCATCCACAAGG 58.670 43.478 0.00 0.00 44.01 3.61
337 353 7.621428 AATACATGAAAGAGTCATCCACAAG 57.379 36.000 0.00 0.00 44.01 3.16
338 354 7.280876 GCTAATACATGAAAGAGTCATCCACAA 59.719 37.037 0.00 0.00 44.01 3.33
340 356 6.989169 AGCTAATACATGAAAGAGTCATCCAC 59.011 38.462 0.00 0.00 44.01 4.02
376 406 1.985473 TCATGGGCAATCTGGTATGC 58.015 50.000 0.00 0.00 41.82 3.14
377 407 3.559069 ACTTCATGGGCAATCTGGTATG 58.441 45.455 0.00 0.00 0.00 2.39
442 473 4.331168 AGATCTTGCTGTTTTCTACGATGC 59.669 41.667 0.00 0.00 0.00 3.91
642 685 2.787601 TAACTCACTGTCACACGACC 57.212 50.000 0.00 0.00 41.85 4.79
710 753 5.852282 TTGCTTAGTTTGCTCTTCCTTTT 57.148 34.783 0.00 0.00 0.00 2.27
714 757 5.157067 GTTGATTGCTTAGTTTGCTCTTCC 58.843 41.667 0.00 0.00 0.00 3.46
745 799 2.418334 CCTAGAACGTGGGCCTTAACTC 60.418 54.545 4.53 0.00 0.00 3.01
746 800 1.553704 CCTAGAACGTGGGCCTTAACT 59.446 52.381 4.53 0.56 0.00 2.24
747 801 2.019948 CCTAGAACGTGGGCCTTAAC 57.980 55.000 4.53 0.00 0.00 2.01
754 808 1.070289 GATAAGGGCCTAGAACGTGGG 59.930 57.143 6.41 0.00 0.00 4.61
755 809 1.760613 TGATAAGGGCCTAGAACGTGG 59.239 52.381 6.41 0.00 0.00 4.94
756 810 3.536956 TTGATAAGGGCCTAGAACGTG 57.463 47.619 6.41 0.00 0.00 4.49
824 878 3.083293 GACGTCCCAGATCTATCTACCC 58.917 54.545 3.51 0.00 34.85 3.69
853 907 2.101835 GTAAAACGGGGCGATCGCA 61.102 57.895 38.00 15.22 44.11 5.10
913 967 4.865905 AGGGATATCACTGCGAGATAGAT 58.134 43.478 6.71 0.00 32.00 1.98
914 968 4.265893 GAGGGATATCACTGCGAGATAGA 58.734 47.826 13.53 0.00 32.00 1.98
997 1072 3.704231 ATCCAGCCACGGCCATGTC 62.704 63.158 2.24 0.00 43.17 3.06
998 1073 3.704231 GATCCAGCCACGGCCATGT 62.704 63.158 2.24 0.00 43.17 3.21
1191 3543 3.755628 GGCCACCGCACGTAGAGA 61.756 66.667 0.00 0.00 36.38 3.10
1482 3840 0.178944 TTCCCTCCGTGTCTTCCTCA 60.179 55.000 0.00 0.00 0.00 3.86
1483 3841 0.246910 GTTCCCTCCGTGTCTTCCTC 59.753 60.000 0.00 0.00 0.00 3.71
1484 3842 0.178929 AGTTCCCTCCGTGTCTTCCT 60.179 55.000 0.00 0.00 0.00 3.36
1485 3843 0.246910 GAGTTCCCTCCGTGTCTTCC 59.753 60.000 0.00 0.00 0.00 3.46
1486 3844 3.816580 GAGTTCCCTCCGTGTCTTC 57.183 57.895 0.00 0.00 0.00 2.87
1500 3858 2.028020 GTCTTCCTCGGAACATGGAGTT 60.028 50.000 0.00 0.00 44.93 3.01
1501 3859 1.550976 GTCTTCCTCGGAACATGGAGT 59.449 52.381 0.00 0.00 31.51 3.85
1506 3864 0.246635 CCGTGTCTTCCTCGGAACAT 59.753 55.000 0.00 0.00 46.05 2.71
1508 3866 4.573162 CCGTGTCTTCCTCGGAAC 57.427 61.111 0.00 0.00 46.05 3.62
1511 3869 2.711922 CCCTCCGTGTCTTCCTCGG 61.712 68.421 0.00 0.00 44.76 4.63
1950 4311 0.532573 CGGTGACACAGAGGCTATGT 59.467 55.000 9.36 9.36 0.00 2.29
1952 4313 1.961180 GCCGGTGACACAGAGGCTAT 61.961 60.000 23.31 0.00 44.06 2.97
1971 4332 3.319137 TTGAGAAGATCACCTCCAACG 57.681 47.619 10.60 0.00 37.77 4.10
1992 4353 3.120321 TGGCGAACAACAGAAGTGTAT 57.880 42.857 0.00 0.00 35.08 2.29
2098 4459 2.225727 CCCTTTCGTGGAAGCAGTTTAC 59.774 50.000 0.00 0.00 0.00 2.01
2216 4580 4.569966 CCTCAGAGATCAAATAGTGCACAC 59.430 45.833 21.04 0.00 0.00 3.82
2840 5214 4.320057 GCGATCCCTGAAAGCATAAATCAG 60.320 45.833 0.00 0.00 40.17 2.90
2929 5304 6.326064 ACTCTATTCTCCACAGCAGAACATAT 59.674 38.462 0.00 0.00 32.65 1.78
2979 5354 4.326826 TCTCCTCAACAAATCCATGTGAC 58.673 43.478 0.00 0.00 32.81 3.67
3040 5415 5.124776 AGACTGACACAGCAAGTAGATAGAC 59.875 44.000 0.00 0.00 34.37 2.59
3074 5450 1.076350 TGGGGTCCCATACAAGTTTGG 59.924 52.381 10.98 3.08 41.89 3.28
3118 5494 2.972625 TGATCAAACTACAGAAGCCCG 58.027 47.619 0.00 0.00 0.00 6.13
3259 5636 9.471702 CTTCCTAATGCCCTATTCAATGATAAT 57.528 33.333 0.00 0.00 0.00 1.28
3279 5656 3.391296 AGGTGAACTCACTTTGCTTCCTA 59.609 43.478 9.60 0.00 45.73 2.94
3290 5667 1.416401 TGTCCAGGAAGGTGAACTCAC 59.584 52.381 0.98 0.98 45.72 3.51
3291 5668 1.694150 CTGTCCAGGAAGGTGAACTCA 59.306 52.381 0.00 0.00 39.02 3.41
3299 5676 0.610687 GTGAGGACTGTCCAGGAAGG 59.389 60.000 27.48 0.00 39.61 3.46
3301 5678 1.816863 GCGTGAGGACTGTCCAGGAA 61.817 60.000 27.48 8.00 39.61 3.36
3323 5700 1.246649 CATAACAGTGGCAGTGGCAA 58.753 50.000 25.12 5.62 43.71 4.52
3324 5701 0.110295 ACATAACAGTGGCAGTGGCA 59.890 50.000 25.12 16.56 43.71 4.92
3325 5702 0.804989 GACATAACAGTGGCAGTGGC 59.195 55.000 25.12 10.30 40.13 5.01
3326 5703 2.183478 TGACATAACAGTGGCAGTGG 57.817 50.000 25.12 10.56 30.55 4.00
3391 5768 3.679980 CAGTCACATACACCGAGAAAAGG 59.320 47.826 0.00 0.00 0.00 3.11
3430 5807 7.466050 GCATGTTAATTTGCTCCTACACTACTC 60.466 40.741 0.00 0.00 35.95 2.59
3439 5816 6.624423 CAAACTAGCATGTTAATTTGCTCCT 58.376 36.000 15.79 3.35 45.83 3.69
3554 5931 2.297701 TCTGGTTGTTTCACCTTGCTC 58.702 47.619 0.00 0.00 37.75 4.26
3688 6065 3.068732 TGCTGCTGATCCAGAGTACATAC 59.931 47.826 0.00 0.00 34.77 2.39
3761 6138 8.353684 ACACATTTCGTTTTGGACATAACATAA 58.646 29.630 6.48 1.12 0.00 1.90


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

AutoCloner maintained by Alex Coulton.