Multiple sequence alignment - TraesCS7A01G002200

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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 TraesCS7A01G002200 chr7A 100.000 3454 0 0 1 3454 1410108 1413561 0.000000e+00 6379
1 TraesCS7A01G002200 chr7A 98.861 2897 31 2 560 3454 217766973 217764077 0.000000e+00 5166
2 TraesCS7A01G002200 chr5B 98.916 3321 35 1 135 3454 325080847 325077527 0.000000e+00 5932
3 TraesCS7A01G002200 chr5B 96.030 3325 111 12 135 3454 146820941 146817633 0.000000e+00 5389
4 TraesCS7A01G002200 chr6B 98.857 3326 36 2 130 3454 415879339 415882663 0.000000e+00 5930
5 TraesCS7A01G002200 chr4B 98.825 3320 37 2 136 3454 165291386 165294704 0.000000e+00 5914
6 TraesCS7A01G002200 chr2A 98.585 3321 44 3 136 3454 672096595 672093276 0.000000e+00 5869
7 TraesCS7A01G002200 chr2A 99.534 429 2 0 3026 3454 642919383 642918955 0.000000e+00 782
8 TraesCS7A01G002200 chr2A 98.333 120 2 0 131 250 351178746 351178627 9.710000e-51 211
9 TraesCS7A01G002200 chr2A 98.261 115 2 0 136 250 351419579 351419693 5.850000e-48 202
10 TraesCS7A01G002200 chr3D 96.188 3332 100 19 136 3454 152827202 152830519 0.000000e+00 5424
11 TraesCS7A01G002200 chr3D 96.179 3324 88 13 136 3454 247889326 247886037 0.000000e+00 5398
12 TraesCS7A01G002200 chr5A 95.823 3328 116 16 136 3454 489873418 489876731 0.000000e+00 5354
13 TraesCS7A01G002200 chrUn 89.051 137 7 5 7 136 89026618 89026483 2.760000e-36 163


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 TraesCS7A01G002200 chr7A 1410108 1413561 3453 False 6379 6379 100.000 1 3454 1 chr7A.!!$F1 3453
1 TraesCS7A01G002200 chr7A 217764077 217766973 2896 True 5166 5166 98.861 560 3454 1 chr7A.!!$R1 2894
2 TraesCS7A01G002200 chr5B 325077527 325080847 3320 True 5932 5932 98.916 135 3454 1 chr5B.!!$R2 3319
3 TraesCS7A01G002200 chr5B 146817633 146820941 3308 True 5389 5389 96.030 135 3454 1 chr5B.!!$R1 3319
4 TraesCS7A01G002200 chr6B 415879339 415882663 3324 False 5930 5930 98.857 130 3454 1 chr6B.!!$F1 3324
5 TraesCS7A01G002200 chr4B 165291386 165294704 3318 False 5914 5914 98.825 136 3454 1 chr4B.!!$F1 3318
6 TraesCS7A01G002200 chr2A 672093276 672096595 3319 True 5869 5869 98.585 136 3454 1 chr2A.!!$R3 3318
7 TraesCS7A01G002200 chr3D 152827202 152830519 3317 False 5424 5424 96.188 136 3454 1 chr3D.!!$F1 3318
8 TraesCS7A01G002200 chr3D 247886037 247889326 3289 True 5398 5398 96.179 136 3454 1 chr3D.!!$R1 3318
9 TraesCS7A01G002200 chr5A 489873418 489876731 3313 False 5354 5354 95.823 136 3454 1 chr5A.!!$F1 3318

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
128 129 0.249398 ACCTACCAAGATGTGCGGTC 59.751 55.0 0.0 0.0 34.12 4.79 F
282 283 0.317269 CACTCACGCAAGCAACAAGG 60.317 55.0 0.0 0.0 45.62 3.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1710 1730 0.035725 TGTCTGCATGCTCAAGGGAG 60.036 55.000 20.33 5.9 44.33 4.30 R
2903 2923 2.569853 ACATACTCCGTTCCATTGTCCA 59.430 45.455 0.00 0.0 0.00 4.02 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 5.573337 AGCTGTATGAAAGAAAAGATGCC 57.427 39.130 0.00 0.00 0.00 4.40
36 37 5.012239 AGCTGTATGAAAGAAAAGATGCCA 58.988 37.500 0.00 0.00 0.00 4.92
37 38 5.477984 AGCTGTATGAAAGAAAAGATGCCAA 59.522 36.000 0.00 0.00 0.00 4.52
38 39 5.574443 GCTGTATGAAAGAAAAGATGCCAAC 59.426 40.000 0.00 0.00 0.00 3.77
39 40 5.698832 TGTATGAAAGAAAAGATGCCAACG 58.301 37.500 0.00 0.00 0.00 4.10
40 41 5.471797 TGTATGAAAGAAAAGATGCCAACGA 59.528 36.000 0.00 0.00 0.00 3.85
41 42 4.223320 TGAAAGAAAAGATGCCAACGAC 57.777 40.909 0.00 0.00 0.00 4.34
42 43 3.629855 TGAAAGAAAAGATGCCAACGACA 59.370 39.130 0.00 0.00 0.00 4.35
43 44 3.626028 AAGAAAAGATGCCAACGACAC 57.374 42.857 0.00 0.00 0.00 3.67
44 45 2.571212 AGAAAAGATGCCAACGACACA 58.429 42.857 0.00 0.00 0.00 3.72
45 46 2.948979 AGAAAAGATGCCAACGACACAA 59.051 40.909 0.00 0.00 0.00 3.33
46 47 3.569701 AGAAAAGATGCCAACGACACAAT 59.430 39.130 0.00 0.00 0.00 2.71
47 48 4.037923 AGAAAAGATGCCAACGACACAATT 59.962 37.500 0.00 0.00 0.00 2.32
48 49 5.240623 AGAAAAGATGCCAACGACACAATTA 59.759 36.000 0.00 0.00 0.00 1.40
49 50 5.643379 AAAGATGCCAACGACACAATTAT 57.357 34.783 0.00 0.00 0.00 1.28
50 51 5.643379 AAGATGCCAACGACACAATTATT 57.357 34.783 0.00 0.00 0.00 1.40
51 52 5.235305 AGATGCCAACGACACAATTATTC 57.765 39.130 0.00 0.00 0.00 1.75
52 53 4.699735 AGATGCCAACGACACAATTATTCA 59.300 37.500 0.00 0.00 0.00 2.57
53 54 4.153958 TGCCAACGACACAATTATTCAC 57.846 40.909 0.00 0.00 0.00 3.18
54 55 3.057876 TGCCAACGACACAATTATTCACC 60.058 43.478 0.00 0.00 0.00 4.02
55 56 3.190535 GCCAACGACACAATTATTCACCT 59.809 43.478 0.00 0.00 0.00 4.00
56 57 4.320935 GCCAACGACACAATTATTCACCTT 60.321 41.667 0.00 0.00 0.00 3.50
57 58 5.106475 GCCAACGACACAATTATTCACCTTA 60.106 40.000 0.00 0.00 0.00 2.69
58 59 6.311723 CCAACGACACAATTATTCACCTTAC 58.688 40.000 0.00 0.00 0.00 2.34
59 60 6.311723 CAACGACACAATTATTCACCTTACC 58.688 40.000 0.00 0.00 0.00 2.85
60 61 5.553123 ACGACACAATTATTCACCTTACCA 58.447 37.500 0.00 0.00 0.00 3.25
61 62 5.642063 ACGACACAATTATTCACCTTACCAG 59.358 40.000 0.00 0.00 0.00 4.00
62 63 5.642063 CGACACAATTATTCACCTTACCAGT 59.358 40.000 0.00 0.00 0.00 4.00
63 64 6.148811 CGACACAATTATTCACCTTACCAGTT 59.851 38.462 0.00 0.00 0.00 3.16
64 65 7.332430 CGACACAATTATTCACCTTACCAGTTA 59.668 37.037 0.00 0.00 0.00 2.24
65 66 9.174166 GACACAATTATTCACCTTACCAGTTAT 57.826 33.333 0.00 0.00 0.00 1.89
66 67 8.956426 ACACAATTATTCACCTTACCAGTTATG 58.044 33.333 0.00 0.00 0.00 1.90
67 68 7.915397 CACAATTATTCACCTTACCAGTTATGC 59.085 37.037 0.00 0.00 0.00 3.14
68 69 7.068226 ACAATTATTCACCTTACCAGTTATGCC 59.932 37.037 0.00 0.00 0.00 4.40
69 70 4.862641 ATTCACCTTACCAGTTATGCCT 57.137 40.909 0.00 0.00 0.00 4.75
70 71 4.650972 TTCACCTTACCAGTTATGCCTT 57.349 40.909 0.00 0.00 0.00 4.35
71 72 4.216411 TCACCTTACCAGTTATGCCTTC 57.784 45.455 0.00 0.00 0.00 3.46
72 73 3.585289 TCACCTTACCAGTTATGCCTTCA 59.415 43.478 0.00 0.00 0.00 3.02
73 74 4.227300 TCACCTTACCAGTTATGCCTTCAT 59.773 41.667 0.00 0.00 36.73 2.57
74 75 4.336433 CACCTTACCAGTTATGCCTTCATG 59.664 45.833 0.00 0.00 34.22 3.07
75 76 4.018415 ACCTTACCAGTTATGCCTTCATGT 60.018 41.667 0.00 0.00 34.22 3.21
76 77 4.576463 CCTTACCAGTTATGCCTTCATGTC 59.424 45.833 0.00 0.00 34.22 3.06
77 78 5.431765 CTTACCAGTTATGCCTTCATGTCT 58.568 41.667 0.00 0.00 34.22 3.41
78 79 6.408092 CCTTACCAGTTATGCCTTCATGTCTA 60.408 42.308 0.00 0.00 34.22 2.59
79 80 5.435686 ACCAGTTATGCCTTCATGTCTAA 57.564 39.130 0.00 0.00 34.22 2.10
80 81 5.815581 ACCAGTTATGCCTTCATGTCTAAA 58.184 37.500 0.00 0.00 34.22 1.85
81 82 6.426587 ACCAGTTATGCCTTCATGTCTAAAT 58.573 36.000 0.00 0.00 34.22 1.40
82 83 7.573710 ACCAGTTATGCCTTCATGTCTAAATA 58.426 34.615 0.00 0.00 34.22 1.40
83 84 8.220559 ACCAGTTATGCCTTCATGTCTAAATAT 58.779 33.333 0.00 0.00 34.22 1.28
84 85 9.725019 CCAGTTATGCCTTCATGTCTAAATATA 57.275 33.333 0.00 0.00 34.22 0.86
87 88 9.994432 GTTATGCCTTCATGTCTAAATATATGC 57.006 33.333 0.00 0.00 34.22 3.14
88 89 9.964354 TTATGCCTTCATGTCTAAATATATGCT 57.036 29.630 0.00 0.00 34.22 3.79
89 90 8.874744 ATGCCTTCATGTCTAAATATATGCTT 57.125 30.769 0.00 0.00 0.00 3.91
90 91 8.696043 TGCCTTCATGTCTAAATATATGCTTT 57.304 30.769 0.00 0.00 0.00 3.51
91 92 8.786898 TGCCTTCATGTCTAAATATATGCTTTC 58.213 33.333 0.00 0.00 0.00 2.62
92 93 8.786898 GCCTTCATGTCTAAATATATGCTTTCA 58.213 33.333 0.00 0.00 0.00 2.69
122 123 8.661752 AAAACTACTACTACCTACCAAGATGT 57.338 34.615 0.00 0.00 0.00 3.06
123 124 7.642082 AACTACTACTACCTACCAAGATGTG 57.358 40.000 0.00 0.00 0.00 3.21
124 125 5.593502 ACTACTACTACCTACCAAGATGTGC 59.406 44.000 0.00 0.00 0.00 4.57
125 126 2.961526 ACTACCTACCAAGATGTGCG 57.038 50.000 0.00 0.00 0.00 5.34
126 127 1.480954 ACTACCTACCAAGATGTGCGG 59.519 52.381 0.00 0.00 0.00 5.69
127 128 1.480954 CTACCTACCAAGATGTGCGGT 59.519 52.381 0.00 0.00 36.79 5.68
128 129 0.249398 ACCTACCAAGATGTGCGGTC 59.751 55.000 0.00 0.00 34.12 4.79
129 130 0.537188 CCTACCAAGATGTGCGGTCT 59.463 55.000 0.00 0.00 34.12 3.85
130 131 1.471676 CCTACCAAGATGTGCGGTCTC 60.472 57.143 0.00 0.00 34.12 3.36
131 132 1.478510 CTACCAAGATGTGCGGTCTCT 59.521 52.381 0.00 0.00 34.12 3.10
132 133 1.557099 ACCAAGATGTGCGGTCTCTA 58.443 50.000 0.00 0.00 0.00 2.43
133 134 1.478510 ACCAAGATGTGCGGTCTCTAG 59.521 52.381 0.00 0.00 0.00 2.43
235 236 4.767892 CCCTCTTCCCCCTGCCCT 62.768 72.222 0.00 0.00 0.00 5.19
273 274 2.100087 TCTAAGACACACACTCACGCAA 59.900 45.455 0.00 0.00 0.00 4.85
282 283 0.317269 CACTCACGCAAGCAACAAGG 60.317 55.000 0.00 0.00 45.62 3.61
283 284 0.748005 ACTCACGCAAGCAACAAGGT 60.748 50.000 0.00 0.00 45.62 3.50
284 285 0.317269 CTCACGCAAGCAACAAGGTG 60.317 55.000 0.00 0.00 45.62 4.00
285 286 1.029408 TCACGCAAGCAACAAGGTGT 61.029 50.000 0.00 0.00 45.62 4.16
868 873 0.840617 TGGCTGGACCACTTGTGTAA 59.159 50.000 0.00 0.00 46.36 2.41
1206 1219 0.394080 AGCAGAAGGAGCTTGATGGC 60.394 55.000 0.00 0.00 39.87 4.40
1284 1297 1.902508 TGGAAGGTCATCCACTCTGTC 59.097 52.381 0.00 0.00 44.52 3.51
1608 1628 2.028203 GCTGAAATTTTTGGCTGGCCTA 60.028 45.455 13.05 2.16 36.94 3.93
1632 1652 1.551883 GGTTGCTTTGATGGCAGGAAT 59.448 47.619 0.00 0.00 40.90 3.01
2903 2923 0.617413 CAGGTCAAGGTGCTCAGGAT 59.383 55.000 0.00 0.00 0.00 3.24
3136 3158 1.271163 TGATCAACCGAACACCTTCCC 60.271 52.381 0.00 0.00 0.00 3.97
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 8.840321 GGCATCTTTTCTTTCATACAGCTATAA 58.160 33.333 0.00 0.0 0.00 0.98
10 11 7.992608 TGGCATCTTTTCTTTCATACAGCTATA 59.007 33.333 0.00 0.0 0.00 1.31
11 12 6.830324 TGGCATCTTTTCTTTCATACAGCTAT 59.170 34.615 0.00 0.0 0.00 2.97
12 13 6.179756 TGGCATCTTTTCTTTCATACAGCTA 58.820 36.000 0.00 0.0 0.00 3.32
13 14 5.012239 TGGCATCTTTTCTTTCATACAGCT 58.988 37.500 0.00 0.0 0.00 4.24
14 15 5.314923 TGGCATCTTTTCTTTCATACAGC 57.685 39.130 0.00 0.0 0.00 4.40
15 16 5.796935 CGTTGGCATCTTTTCTTTCATACAG 59.203 40.000 0.00 0.0 0.00 2.74
16 17 5.471797 TCGTTGGCATCTTTTCTTTCATACA 59.528 36.000 0.00 0.0 0.00 2.29
17 18 5.795441 GTCGTTGGCATCTTTTCTTTCATAC 59.205 40.000 0.00 0.0 0.00 2.39
18 19 5.471797 TGTCGTTGGCATCTTTTCTTTCATA 59.528 36.000 0.00 0.0 0.00 2.15
19 20 4.278170 TGTCGTTGGCATCTTTTCTTTCAT 59.722 37.500 0.00 0.0 0.00 2.57
20 21 3.629855 TGTCGTTGGCATCTTTTCTTTCA 59.370 39.130 0.00 0.0 0.00 2.69
21 22 3.975035 GTGTCGTTGGCATCTTTTCTTTC 59.025 43.478 0.00 0.0 0.00 2.62
22 23 3.380004 TGTGTCGTTGGCATCTTTTCTTT 59.620 39.130 0.00 0.0 0.00 2.52
23 24 2.948979 TGTGTCGTTGGCATCTTTTCTT 59.051 40.909 0.00 0.0 0.00 2.52
24 25 2.571212 TGTGTCGTTGGCATCTTTTCT 58.429 42.857 0.00 0.0 0.00 2.52
25 26 3.347958 TTGTGTCGTTGGCATCTTTTC 57.652 42.857 0.00 0.0 0.00 2.29
26 27 4.320608 AATTGTGTCGTTGGCATCTTTT 57.679 36.364 0.00 0.0 0.00 2.27
27 28 5.643379 ATAATTGTGTCGTTGGCATCTTT 57.357 34.783 0.00 0.0 0.00 2.52
28 29 5.182950 TGAATAATTGTGTCGTTGGCATCTT 59.817 36.000 0.00 0.0 0.00 2.40
29 30 4.699735 TGAATAATTGTGTCGTTGGCATCT 59.300 37.500 0.00 0.0 0.00 2.90
30 31 4.793216 GTGAATAATTGTGTCGTTGGCATC 59.207 41.667 0.00 0.0 0.00 3.91
31 32 4.380444 GGTGAATAATTGTGTCGTTGGCAT 60.380 41.667 0.00 0.0 0.00 4.40
32 33 3.057876 GGTGAATAATTGTGTCGTTGGCA 60.058 43.478 0.00 0.0 0.00 4.92
33 34 3.190535 AGGTGAATAATTGTGTCGTTGGC 59.809 43.478 0.00 0.0 0.00 4.52
34 35 5.371115 AAGGTGAATAATTGTGTCGTTGG 57.629 39.130 0.00 0.0 0.00 3.77
35 36 6.072948 TGGTAAGGTGAATAATTGTGTCGTTG 60.073 38.462 0.00 0.0 0.00 4.10
36 37 5.998981 TGGTAAGGTGAATAATTGTGTCGTT 59.001 36.000 0.00 0.0 0.00 3.85
37 38 5.553123 TGGTAAGGTGAATAATTGTGTCGT 58.447 37.500 0.00 0.0 0.00 4.34
38 39 5.642063 ACTGGTAAGGTGAATAATTGTGTCG 59.358 40.000 0.00 0.0 0.00 4.35
39 40 7.448748 AACTGGTAAGGTGAATAATTGTGTC 57.551 36.000 0.00 0.0 0.00 3.67
40 41 8.956426 CATAACTGGTAAGGTGAATAATTGTGT 58.044 33.333 0.00 0.0 0.00 3.72
41 42 7.915397 GCATAACTGGTAAGGTGAATAATTGTG 59.085 37.037 0.00 0.0 0.00 3.33
42 43 7.068226 GGCATAACTGGTAAGGTGAATAATTGT 59.932 37.037 0.00 0.0 0.00 2.71
43 44 7.285401 AGGCATAACTGGTAAGGTGAATAATTG 59.715 37.037 0.00 0.0 0.00 2.32
44 45 7.354312 AGGCATAACTGGTAAGGTGAATAATT 58.646 34.615 0.00 0.0 0.00 1.40
45 46 6.911308 AGGCATAACTGGTAAGGTGAATAAT 58.089 36.000 0.00 0.0 0.00 1.28
46 47 6.321821 AGGCATAACTGGTAAGGTGAATAA 57.678 37.500 0.00 0.0 0.00 1.40
47 48 5.968676 AGGCATAACTGGTAAGGTGAATA 57.031 39.130 0.00 0.0 0.00 1.75
48 49 4.862641 AGGCATAACTGGTAAGGTGAAT 57.137 40.909 0.00 0.0 0.00 2.57
49 50 4.042311 TGAAGGCATAACTGGTAAGGTGAA 59.958 41.667 0.00 0.0 0.00 3.18
50 51 3.585289 TGAAGGCATAACTGGTAAGGTGA 59.415 43.478 0.00 0.0 0.00 4.02
51 52 3.950397 TGAAGGCATAACTGGTAAGGTG 58.050 45.455 0.00 0.0 0.00 4.00
52 53 4.018415 ACATGAAGGCATAACTGGTAAGGT 60.018 41.667 0.00 0.0 32.27 3.50
53 54 4.526970 ACATGAAGGCATAACTGGTAAGG 58.473 43.478 0.00 0.0 32.27 2.69
54 55 5.431765 AGACATGAAGGCATAACTGGTAAG 58.568 41.667 0.00 0.0 32.27 2.34
55 56 5.435686 AGACATGAAGGCATAACTGGTAA 57.564 39.130 0.00 0.0 32.27 2.85
56 57 6.553953 TTAGACATGAAGGCATAACTGGTA 57.446 37.500 0.00 0.0 32.27 3.25
57 58 5.435686 TTAGACATGAAGGCATAACTGGT 57.564 39.130 0.00 0.0 32.27 4.00
58 59 6.949352 ATTTAGACATGAAGGCATAACTGG 57.051 37.500 0.00 0.0 32.27 4.00
61 62 9.994432 GCATATATTTAGACATGAAGGCATAAC 57.006 33.333 0.00 0.0 32.27 1.89
62 63 9.964354 AGCATATATTTAGACATGAAGGCATAA 57.036 29.630 0.00 0.0 32.27 1.90
63 64 9.964354 AAGCATATATTTAGACATGAAGGCATA 57.036 29.630 0.00 0.0 32.27 3.14
64 65 8.874744 AAGCATATATTTAGACATGAAGGCAT 57.125 30.769 0.00 0.0 34.29 4.40
65 66 8.696043 AAAGCATATATTTAGACATGAAGGCA 57.304 30.769 0.00 0.0 0.00 4.75
66 67 8.786898 TGAAAGCATATATTTAGACATGAAGGC 58.213 33.333 0.00 0.0 0.00 4.35
96 97 9.097946 ACATCTTGGTAGGTAGTAGTAGTTTTT 57.902 33.333 0.00 0.0 0.00 1.94
97 98 8.529476 CACATCTTGGTAGGTAGTAGTAGTTTT 58.471 37.037 0.00 0.0 0.00 2.43
98 99 7.363617 GCACATCTTGGTAGGTAGTAGTAGTTT 60.364 40.741 0.00 0.0 0.00 2.66
99 100 6.096564 GCACATCTTGGTAGGTAGTAGTAGTT 59.903 42.308 0.00 0.0 0.00 2.24
100 101 5.593502 GCACATCTTGGTAGGTAGTAGTAGT 59.406 44.000 0.00 0.0 0.00 2.73
101 102 5.277876 CGCACATCTTGGTAGGTAGTAGTAG 60.278 48.000 0.00 0.0 0.00 2.57
102 103 4.577693 CGCACATCTTGGTAGGTAGTAGTA 59.422 45.833 0.00 0.0 0.00 1.82
103 104 3.380637 CGCACATCTTGGTAGGTAGTAGT 59.619 47.826 0.00 0.0 0.00 2.73
104 105 3.243434 CCGCACATCTTGGTAGGTAGTAG 60.243 52.174 0.00 0.0 0.00 2.57
105 106 2.691526 CCGCACATCTTGGTAGGTAGTA 59.308 50.000 0.00 0.0 0.00 1.82
106 107 1.480954 CCGCACATCTTGGTAGGTAGT 59.519 52.381 0.00 0.0 0.00 2.73
107 108 1.480954 ACCGCACATCTTGGTAGGTAG 59.519 52.381 0.00 0.0 33.25 3.18
108 109 1.479323 GACCGCACATCTTGGTAGGTA 59.521 52.381 0.00 0.0 35.75 3.08
109 110 0.249398 GACCGCACATCTTGGTAGGT 59.751 55.000 0.00 0.0 35.75 3.08
110 111 0.537188 AGACCGCACATCTTGGTAGG 59.463 55.000 0.00 0.0 35.75 3.18
111 112 1.478510 AGAGACCGCACATCTTGGTAG 59.521 52.381 0.00 0.0 35.75 3.18
112 113 1.557099 AGAGACCGCACATCTTGGTA 58.443 50.000 0.00 0.0 35.75 3.25
113 114 1.478510 CTAGAGACCGCACATCTTGGT 59.521 52.381 0.00 0.0 39.12 3.67
114 115 1.202463 CCTAGAGACCGCACATCTTGG 60.202 57.143 0.00 0.0 31.33 3.61
115 116 1.478510 ACCTAGAGACCGCACATCTTG 59.521 52.381 0.00 0.0 0.00 3.02
116 117 1.478510 CACCTAGAGACCGCACATCTT 59.521 52.381 0.00 0.0 0.00 2.40
117 118 1.107114 CACCTAGAGACCGCACATCT 58.893 55.000 0.00 0.0 0.00 2.90
118 119 0.818296 ACACCTAGAGACCGCACATC 59.182 55.000 0.00 0.0 0.00 3.06
119 120 1.066858 CAACACCTAGAGACCGCACAT 60.067 52.381 0.00 0.0 0.00 3.21
120 121 0.317160 CAACACCTAGAGACCGCACA 59.683 55.000 0.00 0.0 0.00 4.57
121 122 0.601558 TCAACACCTAGAGACCGCAC 59.398 55.000 0.00 0.0 0.00 5.34
122 123 1.000506 GTTCAACACCTAGAGACCGCA 59.999 52.381 0.00 0.0 0.00 5.69
123 124 1.672145 GGTTCAACACCTAGAGACCGC 60.672 57.143 0.00 0.0 43.29 5.68
124 125 1.402456 CGGTTCAACACCTAGAGACCG 60.402 57.143 0.00 0.0 44.69 4.79
125 126 1.067071 CCGGTTCAACACCTAGAGACC 60.067 57.143 0.00 0.0 44.69 3.85
126 127 1.617357 ACCGGTTCAACACCTAGAGAC 59.383 52.381 0.00 0.0 44.69 3.36
127 128 2.005370 ACCGGTTCAACACCTAGAGA 57.995 50.000 0.00 0.0 44.69 3.10
128 129 3.430374 CCATACCGGTTCAACACCTAGAG 60.430 52.174 15.04 0.0 44.69 2.43
129 130 2.498481 CCATACCGGTTCAACACCTAGA 59.502 50.000 15.04 0.0 44.69 2.43
130 131 2.419574 CCCATACCGGTTCAACACCTAG 60.420 54.545 15.04 0.0 44.69 3.02
131 132 1.555992 CCCATACCGGTTCAACACCTA 59.444 52.381 15.04 0.0 44.69 3.08
132 133 0.326927 CCCATACCGGTTCAACACCT 59.673 55.000 15.04 0.0 44.69 4.00
133 134 1.310216 GCCCATACCGGTTCAACACC 61.310 60.000 15.04 0.0 43.16 4.16
273 274 0.693049 CTCCCCTACACCTTGTTGCT 59.307 55.000 0.00 0.0 0.00 3.91
282 283 3.391382 ACAGCGCCTCCCCTACAC 61.391 66.667 2.29 0.0 0.00 2.90
283 284 3.390521 CACAGCGCCTCCCCTACA 61.391 66.667 2.29 0.0 0.00 2.74
284 285 3.391382 ACACAGCGCCTCCCCTAC 61.391 66.667 2.29 0.0 0.00 3.18
285 286 3.390521 CACACAGCGCCTCCCCTA 61.391 66.667 2.29 0.0 0.00 3.53
1206 1219 1.611491 ACAACGGTGCCCAACAAATAG 59.389 47.619 0.00 0.0 0.00 1.73
1254 1267 1.059584 TGACCTTCCACCTCTTGCCA 61.060 55.000 0.00 0.0 0.00 4.92
1284 1297 3.888930 AGTTCAACAACCACACCATAAGG 59.111 43.478 0.00 0.0 35.33 2.69
1608 1628 2.224354 CCTGCCATCAAAGCAACCTTTT 60.224 45.455 0.00 0.0 39.20 2.27
1632 1652 1.076412 TTGGTGCAACAGGGAAGCA 60.076 52.632 3.79 0.0 39.98 3.91
1706 1726 1.203441 TGCATGCTCAAGGGAGAGGT 61.203 55.000 20.33 0.0 44.26 3.85
1710 1730 0.035725 TGTCTGCATGCTCAAGGGAG 60.036 55.000 20.33 5.9 44.33 4.30
2903 2923 2.569853 ACATACTCCGTTCCATTGTCCA 59.430 45.455 0.00 0.0 0.00 4.02
3136 3158 3.499918 GGAGATTTCATGCCAAGTATCCG 59.500 47.826 0.00 0.0 0.00 4.18


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

AutoCloner maintained by Alex Coulton.