Multiple sequence alignment - TraesCS3D01G151100

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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 TraesCS3D01G151100 chr3D 100.000 3767 0 0 1 3767 116021327 116025093 0.000000e+00 6957
1 TraesCS3D01G151100 chr3D 85.855 1732 224 18 1014 2733 116011110 116012832 0.000000e+00 1821
2 TraesCS3D01G151100 chr3B 94.440 3615 125 29 91 3693 169431452 169435002 0.000000e+00 5493
3 TraesCS3D01G151100 chr3B 86.896 786 92 10 1032 1813 169424777 169425555 0.000000e+00 870
4 TraesCS3D01G151100 chr3B 83.041 855 135 7 1887 2733 169425556 169426408 0.000000e+00 767
5 TraesCS3D01G151100 chr3B 96.117 103 3 1 1 103 11017769 11017870 2.330000e-37 167
6 TraesCS3D01G151100 chr3B 97.938 97 1 1 1 96 107961755 107961851 2.330000e-37 167
7 TraesCS3D01G151100 chr3B 95.181 83 1 2 3686 3767 169436134 169436214 1.100000e-25 128
8 TraesCS3D01G151100 chr3A 91.478 2910 151 39 777 3642 112936450 112939306 0.000000e+00 3910
9 TraesCS3D01G151100 chr3A 85.294 1734 231 20 1013 2733 112917991 112919713 0.000000e+00 1768
10 TraesCS3D01G151100 chr3A 91.250 320 25 3 261 578 112935973 112936291 2.080000e-117 433
11 TraesCS3D01G151100 chr3A 90.141 142 9 3 645 781 112936281 112936422 2.990000e-41 180
12 TraesCS3D01G151100 chr6D 78.415 366 53 20 404 764 93436005 93436349 8.200000e-52 215
13 TraesCS3D01G151100 chr1D 98.925 93 1 0 1 93 36612224 36612132 2.330000e-37 167
14 TraesCS3D01G151100 chr7A 95.238 105 3 2 1 104 604387415 604387518 8.370000e-37 165
15 TraesCS3D01G151100 chr2B 96.970 99 2 1 1 98 719520578 719520676 8.370000e-37 165
16 TraesCS3D01G151100 chr1A 96.970 99 2 1 1 99 74253953 74254050 8.370000e-37 165
17 TraesCS3D01G151100 chr7B 96.000 100 3 1 1 100 586306685 586306587 1.080000e-35 161
18 TraesCS3D01G151100 chr2D 96.000 100 2 2 1 100 571949989 571950086 1.080000e-35 161
19 TraesCS3D01G151100 chr2D 94.286 105 4 2 1 104 520357814 520357711 3.890000e-35 159
20 TraesCS3D01G151100 chr6A 81.522 92 15 2 673 764 115339232 115339143 1.450000e-09 75


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 TraesCS3D01G151100 chr3D 116021327 116025093 3766 False 6957.000000 6957 100.000000 1 3767 1 chr3D.!!$F2 3766
1 TraesCS3D01G151100 chr3D 116011110 116012832 1722 False 1821.000000 1821 85.855000 1014 2733 1 chr3D.!!$F1 1719
2 TraesCS3D01G151100 chr3B 169431452 169436214 4762 False 2810.500000 5493 94.810500 91 3767 2 chr3B.!!$F4 3676
3 TraesCS3D01G151100 chr3B 169424777 169426408 1631 False 818.500000 870 84.968500 1032 2733 2 chr3B.!!$F3 1701
4 TraesCS3D01G151100 chr3A 112917991 112919713 1722 False 1768.000000 1768 85.294000 1013 2733 1 chr3A.!!$F1 1720
5 TraesCS3D01G151100 chr3A 112935973 112939306 3333 False 1507.666667 3910 90.956333 261 3642 3 chr3A.!!$F2 3381

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
864 903 0.478072 TGACATGTGGGCCTGAAACT 59.522 50.0 1.15 0.0 0.0 2.66 F
1908 1968 0.738389 CTGTTTGGCCGTTCACTGTT 59.262 50.0 0.00 0.0 0.0 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2022 2082 1.070445 CCAAAATTGTGCTCCTTGCCA 59.930 47.619 0.0 0.0 42.00 4.92 R
3053 3135 0.593128 ATTGGAACAGACGCAGCAAC 59.407 50.000 0.0 0.0 42.39 4.17 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
33 34 6.578023 AGTGTAGATTCACTCATTTAGCTCC 58.422 40.000 0.00 0.00 44.07 4.70
34 35 5.460419 GTGTAGATTCACTCATTTAGCTCCG 59.540 44.000 0.00 0.00 35.68 4.63
35 36 4.744795 AGATTCACTCATTTAGCTCCGT 57.255 40.909 0.00 0.00 0.00 4.69
36 37 5.854010 AGATTCACTCATTTAGCTCCGTA 57.146 39.130 0.00 0.00 0.00 4.02
37 38 6.412362 AGATTCACTCATTTAGCTCCGTAT 57.588 37.500 0.00 0.00 0.00 3.06
38 39 6.219473 AGATTCACTCATTTAGCTCCGTATG 58.781 40.000 0.00 0.00 0.00 2.39
39 40 5.339008 TTCACTCATTTAGCTCCGTATGT 57.661 39.130 0.00 0.00 0.00 2.29
40 41 6.459670 TTCACTCATTTAGCTCCGTATGTA 57.540 37.500 0.00 0.00 0.00 2.29
41 42 6.073327 TCACTCATTTAGCTCCGTATGTAG 57.927 41.667 0.00 0.00 0.00 2.74
42 43 5.593095 TCACTCATTTAGCTCCGTATGTAGT 59.407 40.000 0.00 0.00 0.00 2.73
43 44 5.915758 CACTCATTTAGCTCCGTATGTAGTC 59.084 44.000 0.00 0.00 0.00 2.59
44 45 5.593095 ACTCATTTAGCTCCGTATGTAGTCA 59.407 40.000 0.00 0.00 0.00 3.41
45 46 5.828747 TCATTTAGCTCCGTATGTAGTCAC 58.171 41.667 0.00 0.00 0.00 3.67
46 47 5.593095 TCATTTAGCTCCGTATGTAGTCACT 59.407 40.000 0.00 0.00 0.00 3.41
47 48 5.909621 TTTAGCTCCGTATGTAGTCACTT 57.090 39.130 0.00 0.00 0.00 3.16
48 49 3.784701 AGCTCCGTATGTAGTCACTTG 57.215 47.619 0.00 0.00 0.00 3.16
49 50 3.090037 AGCTCCGTATGTAGTCACTTGT 58.910 45.455 0.00 0.00 0.00 3.16
50 51 3.510360 AGCTCCGTATGTAGTCACTTGTT 59.490 43.478 0.00 0.00 0.00 2.83
51 52 3.612860 GCTCCGTATGTAGTCACTTGTTG 59.387 47.826 0.00 0.00 0.00 3.33
52 53 4.617530 GCTCCGTATGTAGTCACTTGTTGA 60.618 45.833 0.00 0.00 0.00 3.18
53 54 5.456548 TCCGTATGTAGTCACTTGTTGAA 57.543 39.130 0.00 0.00 35.39 2.69
54 55 5.845103 TCCGTATGTAGTCACTTGTTGAAA 58.155 37.500 0.00 0.00 35.39 2.69
55 56 6.460781 TCCGTATGTAGTCACTTGTTGAAAT 58.539 36.000 0.00 0.00 35.39 2.17
56 57 6.588756 TCCGTATGTAGTCACTTGTTGAAATC 59.411 38.462 0.00 0.00 35.39 2.17
57 58 6.590292 CCGTATGTAGTCACTTGTTGAAATCT 59.410 38.462 0.00 0.00 35.39 2.40
58 59 7.201444 CCGTATGTAGTCACTTGTTGAAATCTC 60.201 40.741 0.00 0.00 35.39 2.75
59 60 7.542477 CGTATGTAGTCACTTGTTGAAATCTCT 59.458 37.037 0.00 0.00 35.39 3.10
60 61 9.856488 GTATGTAGTCACTTGTTGAAATCTCTA 57.144 33.333 0.00 0.00 35.39 2.43
61 62 8.994429 ATGTAGTCACTTGTTGAAATCTCTAG 57.006 34.615 0.00 0.00 35.39 2.43
62 63 8.178313 TGTAGTCACTTGTTGAAATCTCTAGA 57.822 34.615 0.00 0.00 35.39 2.43
63 64 8.638873 TGTAGTCACTTGTTGAAATCTCTAGAA 58.361 33.333 0.00 0.00 35.39 2.10
64 65 9.477484 GTAGTCACTTGTTGAAATCTCTAGAAA 57.523 33.333 0.00 0.00 35.39 2.52
65 66 8.600449 AGTCACTTGTTGAAATCTCTAGAAAG 57.400 34.615 0.00 0.00 35.39 2.62
66 67 8.424918 AGTCACTTGTTGAAATCTCTAGAAAGA 58.575 33.333 0.00 0.00 35.39 2.52
67 68 8.491950 GTCACTTGTTGAAATCTCTAGAAAGAC 58.508 37.037 0.00 0.00 35.39 3.01
68 69 8.204160 TCACTTGTTGAAATCTCTAGAAAGACA 58.796 33.333 0.00 0.00 0.00 3.41
69 70 8.830580 CACTTGTTGAAATCTCTAGAAAGACAA 58.169 33.333 0.00 0.00 0.00 3.18
70 71 9.396022 ACTTGTTGAAATCTCTAGAAAGACAAA 57.604 29.630 0.00 0.00 0.00 2.83
83 84 9.595823 TCTAGAAAGACAAATATTTAGGAACGG 57.404 33.333 0.00 0.00 0.00 4.44
84 85 9.595823 CTAGAAAGACAAATATTTAGGAACGGA 57.404 33.333 0.00 0.00 0.00 4.69
85 86 8.494016 AGAAAGACAAATATTTAGGAACGGAG 57.506 34.615 0.00 0.00 0.00 4.63
86 87 7.553044 AGAAAGACAAATATTTAGGAACGGAGG 59.447 37.037 0.00 0.00 0.00 4.30
87 88 6.555463 AGACAAATATTTAGGAACGGAGGA 57.445 37.500 0.00 0.00 0.00 3.71
88 89 6.954232 AGACAAATATTTAGGAACGGAGGAA 58.046 36.000 0.00 0.00 0.00 3.36
89 90 7.048512 AGACAAATATTTAGGAACGGAGGAAG 58.951 38.462 0.00 0.00 0.00 3.46
127 128 8.538039 GTTACCTACATTTTATGTTCGTCTAGC 58.462 37.037 0.00 0.00 41.63 3.42
131 132 7.277981 CCTACATTTTATGTTCGTCTAGCTTGT 59.722 37.037 0.00 0.00 41.63 3.16
133 134 6.426937 ACATTTTATGTTCGTCTAGCTTGTGT 59.573 34.615 0.00 0.00 41.63 3.72
180 181 5.014202 TGTCTACTCTTAGTGGCACATACA 58.986 41.667 21.41 3.32 44.52 2.29
227 228 8.620116 ATTAAAATAAACTGCCAGCAATGTTT 57.380 26.923 12.72 12.72 36.69 2.83
257 258 9.916360 TGGTAGATTGTCTACTCTACTATTTCA 57.084 33.333 14.68 0.99 46.44 2.69
334 335 6.459670 TGCTGTGATTTTCATAAGATGCAT 57.540 33.333 0.00 0.00 0.00 3.96
362 363 3.750371 TCCAAATCTGTAGTTGTGTGGG 58.250 45.455 0.00 0.00 0.00 4.61
399 401 8.614814 ACTGGCAGTATATATATTGGGTTTGAT 58.385 33.333 20.61 0.00 0.00 2.57
561 563 1.743394 CCCGGGCATCTTTTCACTAAC 59.257 52.381 8.08 0.00 0.00 2.34
589 591 5.525745 CCGTATTGGCTTTATGTGTATGTGA 59.474 40.000 0.00 0.00 0.00 3.58
753 757 4.623595 GTCTTAGAGAACACTGTTGCTAGC 59.376 45.833 8.10 8.10 0.00 3.42
824 863 4.638865 TGATCTTGTGATTTCCTGATGCAG 59.361 41.667 0.00 0.00 32.19 4.41
863 902 0.883833 CTGACATGTGGGCCTGAAAC 59.116 55.000 1.15 0.00 0.00 2.78
864 903 0.478072 TGACATGTGGGCCTGAAACT 59.522 50.000 1.15 0.00 0.00 2.66
905 944 1.656818 GACATGTGGGCCCAATCGTG 61.657 60.000 30.64 27.62 0.00 4.35
923 975 2.418746 CGTGAGAAGGGGTAGATTGGTG 60.419 54.545 0.00 0.00 0.00 4.17
934 986 3.381590 GGTAGATTGGTGGATTTTGGCTC 59.618 47.826 0.00 0.00 0.00 4.70
935 987 3.173953 AGATTGGTGGATTTTGGCTCA 57.826 42.857 0.00 0.00 0.00 4.26
937 989 3.259123 AGATTGGTGGATTTTGGCTCAAC 59.741 43.478 0.00 0.00 0.00 3.18
945 997 3.068024 GGATTTTGGCTCAACAGTGTTGA 59.932 43.478 31.33 31.33 0.00 3.18
1050 1107 2.607750 TTCCTCCTGGCGCTCCTT 60.608 61.111 7.64 0.00 0.00 3.36
1140 1197 4.954118 TCGGAGCCACCCACCACT 62.954 66.667 0.00 0.00 34.64 4.00
1638 1698 1.117749 TGATCCTGCCCATCTCGAGG 61.118 60.000 13.56 0.00 0.00 4.63
1644 1704 1.531840 GCCCATCTCGAGGAGCCTA 60.532 63.158 13.56 0.00 0.00 3.93
1698 1758 4.794439 TCCGCCGATGTGCAGTCG 62.794 66.667 13.05 13.05 38.75 4.18
1700 1760 3.250323 CGCCGATGTGCAGTCGAG 61.250 66.667 19.72 12.16 41.40 4.04
1908 1968 0.738389 CTGTTTGGCCGTTCACTGTT 59.262 50.000 0.00 0.00 0.00 3.16
2001 2061 4.284490 ACCTATGACATTGATATCACGCCT 59.716 41.667 4.48 0.00 0.00 5.52
2022 2082 0.627451 TCTTGGGCAAGCTCATGGAT 59.373 50.000 7.81 0.00 38.28 3.41
2451 2517 3.796111 TCTTTTCTCTGGGACCTCAGAT 58.204 45.455 11.66 0.00 42.19 2.90
2513 2579 2.172082 TGAGCATCAATGAGAAGAGGGG 59.828 50.000 0.00 0.00 45.97 4.79
2613 2679 3.498661 GGAATTTGGTGACTTCTGGGTCT 60.499 47.826 0.00 0.00 37.16 3.85
2855 2924 3.737355 GCCTCGTGTGGTAGGTAGAAATC 60.737 52.174 0.00 0.00 35.16 2.17
2863 2938 6.713450 GTGTGGTAGGTAGAAATCTTGGAAAA 59.287 38.462 0.00 0.00 0.00 2.29
3037 3119 3.508402 TGCATGTTCACAAGCATCTGATT 59.492 39.130 5.76 0.00 44.32 2.57
3045 3127 3.247886 CACAAGCATCTGATTGGATCTCG 59.752 47.826 12.30 0.00 44.91 4.04
3053 3135 1.737236 TGATTGGATCTCGTTTTGGCG 59.263 47.619 0.00 0.00 0.00 5.69
3108 3190 2.299582 CTCATCGCTGGAGAATGGAGAT 59.700 50.000 0.00 0.00 34.24 2.75
3121 3203 6.461648 GGAGAATGGAGATCGATTTACTGTCA 60.462 42.308 0.00 0.00 0.00 3.58
3176 3262 0.679505 TGAGTGACACCGGGAAGAAG 59.320 55.000 6.32 0.00 0.00 2.85
3199 3289 1.915614 GCGTGCTCACAAGATGGGTG 61.916 60.000 0.69 0.00 37.60 4.61
3348 3445 3.452264 AGTGCTACTGCTCCATTGATGTA 59.548 43.478 0.00 0.00 40.48 2.29
3447 3544 3.190744 ACGTTCTTCGCTGATCTCACTTA 59.809 43.478 0.00 0.00 44.19 2.24
3510 3607 1.709147 CTTCCGCTGGAGATTTGGCG 61.709 60.000 0.00 0.00 45.97 5.69
3512 3609 3.880846 CGCTGGAGATTTGGCGGC 61.881 66.667 0.00 0.00 43.25 6.53
3594 3691 1.988406 ACCAACTCGTAGCCCCCTC 60.988 63.158 0.00 0.00 0.00 4.30
3595 3692 1.686110 CCAACTCGTAGCCCCCTCT 60.686 63.158 0.00 0.00 0.00 3.69
3596 3693 1.677637 CCAACTCGTAGCCCCCTCTC 61.678 65.000 0.00 0.00 0.00 3.20
3597 3694 1.381463 AACTCGTAGCCCCCTCTCC 60.381 63.158 0.00 0.00 0.00 3.71
3598 3695 1.876546 AACTCGTAGCCCCCTCTCCT 61.877 60.000 0.00 0.00 0.00 3.69
3609 3706 2.785857 CCCCCTCTCCTTGGATTATGTT 59.214 50.000 0.00 0.00 0.00 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 5.460419 CGGAGCTAAATGAGTGAATCTACAC 59.540 44.000 0.00 0.00 40.60 2.90
11 12 5.127194 ACGGAGCTAAATGAGTGAATCTACA 59.873 40.000 0.00 0.00 0.00 2.74
12 13 5.593010 ACGGAGCTAAATGAGTGAATCTAC 58.407 41.667 0.00 0.00 0.00 2.59
13 14 5.854010 ACGGAGCTAAATGAGTGAATCTA 57.146 39.130 0.00 0.00 0.00 1.98
14 15 4.744795 ACGGAGCTAAATGAGTGAATCT 57.255 40.909 0.00 0.00 0.00 2.40
15 16 5.986135 ACATACGGAGCTAAATGAGTGAATC 59.014 40.000 0.00 0.00 0.00 2.52
16 17 5.918608 ACATACGGAGCTAAATGAGTGAAT 58.081 37.500 0.00 0.00 0.00 2.57
17 18 5.339008 ACATACGGAGCTAAATGAGTGAA 57.661 39.130 0.00 0.00 0.00 3.18
18 19 5.593095 ACTACATACGGAGCTAAATGAGTGA 59.407 40.000 0.00 0.00 0.00 3.41
19 20 5.833082 ACTACATACGGAGCTAAATGAGTG 58.167 41.667 0.00 0.00 0.00 3.51
20 21 5.593095 TGACTACATACGGAGCTAAATGAGT 59.407 40.000 0.00 0.00 0.00 3.41
21 22 5.915758 GTGACTACATACGGAGCTAAATGAG 59.084 44.000 0.00 0.00 0.00 2.90
22 23 5.593095 AGTGACTACATACGGAGCTAAATGA 59.407 40.000 0.00 0.00 0.00 2.57
23 24 5.833082 AGTGACTACATACGGAGCTAAATG 58.167 41.667 0.00 0.00 0.00 2.32
24 25 6.127423 ACAAGTGACTACATACGGAGCTAAAT 60.127 38.462 0.00 0.00 0.00 1.40
25 26 5.184479 ACAAGTGACTACATACGGAGCTAAA 59.816 40.000 0.00 0.00 0.00 1.85
26 27 4.703575 ACAAGTGACTACATACGGAGCTAA 59.296 41.667 0.00 0.00 0.00 3.09
27 28 4.267536 ACAAGTGACTACATACGGAGCTA 58.732 43.478 0.00 0.00 0.00 3.32
28 29 3.090037 ACAAGTGACTACATACGGAGCT 58.910 45.455 0.00 0.00 0.00 4.09
29 30 3.505464 ACAAGTGACTACATACGGAGC 57.495 47.619 0.00 0.00 0.00 4.70
30 31 5.055642 TCAACAAGTGACTACATACGGAG 57.944 43.478 0.00 0.00 0.00 4.63
31 32 5.456548 TTCAACAAGTGACTACATACGGA 57.543 39.130 0.00 0.00 35.39 4.69
32 33 6.590292 AGATTTCAACAAGTGACTACATACGG 59.410 38.462 0.00 0.00 35.39 4.02
33 34 7.542477 AGAGATTTCAACAAGTGACTACATACG 59.458 37.037 0.00 0.00 35.39 3.06
34 35 8.764524 AGAGATTTCAACAAGTGACTACATAC 57.235 34.615 0.00 0.00 35.39 2.39
36 37 8.807118 TCTAGAGATTTCAACAAGTGACTACAT 58.193 33.333 0.00 0.00 35.39 2.29
37 38 8.178313 TCTAGAGATTTCAACAAGTGACTACA 57.822 34.615 0.00 0.00 35.39 2.74
38 39 9.477484 TTTCTAGAGATTTCAACAAGTGACTAC 57.523 33.333 0.00 0.00 35.39 2.73
39 40 9.698309 CTTTCTAGAGATTTCAACAAGTGACTA 57.302 33.333 0.00 0.00 35.39 2.59
40 41 8.424918 TCTTTCTAGAGATTTCAACAAGTGACT 58.575 33.333 0.00 0.00 35.39 3.41
41 42 8.491950 GTCTTTCTAGAGATTTCAACAAGTGAC 58.508 37.037 0.00 0.00 35.39 3.67
42 43 8.204160 TGTCTTTCTAGAGATTTCAACAAGTGA 58.796 33.333 0.00 0.00 0.00 3.41
43 44 8.370493 TGTCTTTCTAGAGATTTCAACAAGTG 57.630 34.615 0.00 0.00 0.00 3.16
44 45 8.964476 TTGTCTTTCTAGAGATTTCAACAAGT 57.036 30.769 0.00 0.00 0.00 3.16
57 58 9.595823 CCGTTCCTAAATATTTGTCTTTCTAGA 57.404 33.333 11.05 0.00 0.00 2.43
58 59 9.595823 TCCGTTCCTAAATATTTGTCTTTCTAG 57.404 33.333 11.05 0.00 0.00 2.43
59 60 9.595823 CTCCGTTCCTAAATATTTGTCTTTCTA 57.404 33.333 11.05 0.00 0.00 2.10
60 61 7.553044 CCTCCGTTCCTAAATATTTGTCTTTCT 59.447 37.037 11.05 0.00 0.00 2.52
61 62 7.551617 TCCTCCGTTCCTAAATATTTGTCTTTC 59.448 37.037 11.05 0.00 0.00 2.62
62 63 7.399634 TCCTCCGTTCCTAAATATTTGTCTTT 58.600 34.615 11.05 0.00 0.00 2.52
63 64 6.954232 TCCTCCGTTCCTAAATATTTGTCTT 58.046 36.000 11.05 0.00 0.00 3.01
64 65 6.555463 TCCTCCGTTCCTAAATATTTGTCT 57.445 37.500 11.05 0.00 0.00 3.41
65 66 6.822170 ACTTCCTCCGTTCCTAAATATTTGTC 59.178 38.462 11.05 0.00 0.00 3.18
66 67 6.718294 ACTTCCTCCGTTCCTAAATATTTGT 58.282 36.000 11.05 0.00 0.00 2.83
67 68 8.202137 TCTACTTCCTCCGTTCCTAAATATTTG 58.798 37.037 11.05 1.40 0.00 2.32
68 69 8.315220 TCTACTTCCTCCGTTCCTAAATATTT 57.685 34.615 5.89 5.89 0.00 1.40
69 70 7.909485 TCTACTTCCTCCGTTCCTAAATATT 57.091 36.000 0.00 0.00 0.00 1.28
70 71 8.368668 CAATCTACTTCCTCCGTTCCTAAATAT 58.631 37.037 0.00 0.00 0.00 1.28
71 72 7.562454 TCAATCTACTTCCTCCGTTCCTAAATA 59.438 37.037 0.00 0.00 0.00 1.40
72 73 6.383147 TCAATCTACTTCCTCCGTTCCTAAAT 59.617 38.462 0.00 0.00 0.00 1.40
73 74 5.718130 TCAATCTACTTCCTCCGTTCCTAAA 59.282 40.000 0.00 0.00 0.00 1.85
74 75 5.126707 GTCAATCTACTTCCTCCGTTCCTAA 59.873 44.000 0.00 0.00 0.00 2.69
75 76 4.643784 GTCAATCTACTTCCTCCGTTCCTA 59.356 45.833 0.00 0.00 0.00 2.94
76 77 3.447944 GTCAATCTACTTCCTCCGTTCCT 59.552 47.826 0.00 0.00 0.00 3.36
77 78 3.194968 TGTCAATCTACTTCCTCCGTTCC 59.805 47.826 0.00 0.00 0.00 3.62
78 79 4.425520 CTGTCAATCTACTTCCTCCGTTC 58.574 47.826 0.00 0.00 0.00 3.95
79 80 3.195825 CCTGTCAATCTACTTCCTCCGTT 59.804 47.826 0.00 0.00 0.00 4.44
80 81 2.761208 CCTGTCAATCTACTTCCTCCGT 59.239 50.000 0.00 0.00 0.00 4.69
81 82 2.761208 ACCTGTCAATCTACTTCCTCCG 59.239 50.000 0.00 0.00 0.00 4.63
82 83 4.828072 AACCTGTCAATCTACTTCCTCC 57.172 45.455 0.00 0.00 0.00 4.30
83 84 5.422650 AGGTAACCTGTCAATCTACTTCCTC 59.577 44.000 0.00 0.00 29.57 3.71
84 85 5.342866 AGGTAACCTGTCAATCTACTTCCT 58.657 41.667 0.00 0.00 29.57 3.36
85 86 5.678955 AGGTAACCTGTCAATCTACTTCC 57.321 43.478 0.00 0.00 29.57 3.46
86 87 7.166691 TGTAGGTAACCTGTCAATCTACTTC 57.833 40.000 0.00 0.00 34.61 3.01
87 88 7.735326 ATGTAGGTAACCTGTCAATCTACTT 57.265 36.000 0.00 0.00 34.61 2.24
88 89 7.735326 AATGTAGGTAACCTGTCAATCTACT 57.265 36.000 0.00 0.00 34.61 2.57
89 90 8.788325 AAAATGTAGGTAACCTGTCAATCTAC 57.212 34.615 0.00 0.00 34.61 2.59
199 200 7.877097 ACATTGCTGGCAGTTTATTTTAATTCA 59.123 29.630 17.16 0.00 0.00 2.57
205 206 6.054295 TCAAACATTGCTGGCAGTTTATTTT 58.946 32.000 17.16 7.89 33.30 1.82
254 255 7.281549 CCAATCTACATGTGACATGAAGATGAA 59.718 37.037 30.26 9.62 33.36 2.57
255 256 6.764560 CCAATCTACATGTGACATGAAGATGA 59.235 38.462 30.26 18.63 33.36 2.92
256 257 6.541278 ACCAATCTACATGTGACATGAAGATG 59.459 38.462 30.26 19.63 35.49 2.90
257 258 6.656902 ACCAATCTACATGTGACATGAAGAT 58.343 36.000 30.26 11.69 0.00 2.40
258 259 6.053632 ACCAATCTACATGTGACATGAAGA 57.946 37.500 30.26 14.36 0.00 2.87
259 260 7.848223 TTACCAATCTACATGTGACATGAAG 57.152 36.000 30.26 12.84 0.00 3.02
334 335 9.743057 CACACAACTACAGATTTGGAAAAATTA 57.257 29.630 0.00 0.00 0.00 1.40
347 348 2.097110 ACCTCCCACACAACTACAGA 57.903 50.000 0.00 0.00 0.00 3.41
362 363 2.841442 ACTGCCAGTGAGTTAACCTC 57.159 50.000 0.00 0.27 40.89 3.85
399 401 0.874390 GGCACGCATCAGAACTTCAA 59.126 50.000 0.00 0.00 0.00 2.69
405 407 1.266718 GAACAAAGGCACGCATCAGAA 59.733 47.619 0.00 0.00 0.00 3.02
639 641 3.737559 TGGTGAAAGCCTAATGGATGT 57.262 42.857 0.00 0.00 34.57 3.06
713 717 3.116096 AGACCCAACTAGGCTGACATA 57.884 47.619 0.00 0.00 35.39 2.29
717 721 3.011369 TCTCTAAGACCCAACTAGGCTGA 59.989 47.826 0.00 0.00 35.39 4.26
824 863 1.897560 GCCCTAGGCCATATTGACAC 58.102 55.000 5.01 0.00 44.06 3.67
863 902 1.338136 CCCCTAGGTGGTGCCACTAG 61.338 65.000 19.37 16.75 45.52 2.57
864 903 1.306654 CCCCTAGGTGGTGCCACTA 60.307 63.158 19.37 9.84 45.52 2.74
905 944 2.478292 TCCACCAATCTACCCCTTCTC 58.522 52.381 0.00 0.00 0.00 2.87
923 975 3.068024 TCAACACTGTTGAGCCAAAATCC 59.932 43.478 18.83 0.00 0.00 3.01
934 986 7.116948 TGGTTTAAACAATTGTCAACACTGTTG 59.883 33.333 19.57 14.79 0.00 3.33
935 987 7.155328 TGGTTTAAACAATTGTCAACACTGTT 58.845 30.769 19.57 2.35 0.00 3.16
937 989 6.237808 GCTGGTTTAAACAATTGTCAACACTG 60.238 38.462 19.57 12.54 0.00 3.66
945 997 4.649218 AGTGGAGCTGGTTTAAACAATTGT 59.351 37.500 19.57 4.92 0.00 2.71
1140 1197 1.005394 GCGGTCCACCTCGAAGAAA 60.005 57.895 0.00 0.00 34.09 2.52
1200 1257 1.077357 GGAGTCGGAGAGGAGCAGA 60.077 63.158 0.00 0.00 36.95 4.26
1426 1483 2.105128 CGACCAGAGGATGCCGTC 59.895 66.667 0.00 0.00 0.00 4.79
1638 1698 0.099082 CGTCGTTCAGAGGTAGGCTC 59.901 60.000 0.00 0.00 0.00 4.70
1644 1704 2.915659 TGCCCGTCGTTCAGAGGT 60.916 61.111 0.00 0.00 33.15 3.85
1698 1758 1.884926 CGGAATGGCGAGCTTCCTC 60.885 63.158 12.32 0.00 39.04 3.71
1700 1760 2.125106 ACGGAATGGCGAGCTTCC 60.125 61.111 6.15 6.15 38.03 3.46
2001 2061 1.203038 TCCATGAGCTTGCCCAAGAAA 60.203 47.619 11.96 0.00 40.79 2.52
2022 2082 1.070445 CCAAAATTGTGCTCCTTGCCA 59.930 47.619 0.00 0.00 42.00 4.92
2451 2517 2.492088 CGAGTACTCATCACCCACTTCA 59.508 50.000 22.37 0.00 0.00 3.02
2485 2551 7.201830 CCTCTTCTCATTGATGCTCAATTTGAT 60.202 37.037 0.00 0.00 44.03 2.57
2494 2560 1.133853 GCCCCTCTTCTCATTGATGCT 60.134 52.381 0.00 0.00 0.00 3.79
3037 3119 0.871722 CAACGCCAAAACGAGATCCA 59.128 50.000 0.00 0.00 36.70 3.41
3045 3127 2.278531 ACGCAGCAACGCCAAAAC 60.279 55.556 0.00 0.00 36.19 2.43
3053 3135 0.593128 ATTGGAACAGACGCAGCAAC 59.407 50.000 0.00 0.00 42.39 4.17
3176 3262 1.135859 CCATCTTGTGAGCACGCTTTC 60.136 52.381 0.00 0.00 0.00 2.62
3348 3445 2.373502 AGAAGCTAGCTGGAAAACCACT 59.626 45.455 20.16 0.00 0.00 4.00
3362 3459 4.899352 AGGCTCAGAAAGAAAGAAGCTA 57.101 40.909 0.00 0.00 0.00 3.32
3504 3601 1.781025 CGACTGACAAAGCCGCCAAA 61.781 55.000 0.00 0.00 0.00 3.28
3510 3607 2.552315 TGGAATTTCGACTGACAAAGCC 59.448 45.455 0.00 0.00 0.00 4.35
3511 3608 3.365364 CCTGGAATTTCGACTGACAAAGC 60.365 47.826 0.00 0.00 0.00 3.51
3512 3609 3.365364 GCCTGGAATTTCGACTGACAAAG 60.365 47.826 0.00 0.00 0.00 2.77
3580 3677 1.876546 AAGGAGAGGGGGCTACGAGT 61.877 60.000 0.00 0.00 0.00 4.18
3594 3691 6.648192 AGTCAGAAGAACATAATCCAAGGAG 58.352 40.000 0.00 0.00 0.00 3.69
3595 3692 6.441924 AGAGTCAGAAGAACATAATCCAAGGA 59.558 38.462 0.00 0.00 0.00 3.36
3596 3693 6.648192 AGAGTCAGAAGAACATAATCCAAGG 58.352 40.000 0.00 0.00 0.00 3.61
3597 3694 7.821359 TCAAGAGTCAGAAGAACATAATCCAAG 59.179 37.037 0.00 0.00 0.00 3.61
3598 3695 7.604164 GTCAAGAGTCAGAAGAACATAATCCAA 59.396 37.037 0.00 0.00 0.00 3.53
3609 3706 3.761218 CCTAGCAGTCAAGAGTCAGAAGA 59.239 47.826 0.00 0.00 0.00 2.87
3706 4944 9.819267 AGATACTTCTTTCCTTTTTCCGTATAG 57.181 33.333 0.00 0.00 0.00 1.31


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

AutoCloner maintained by Alex Coulton.