Multiple sequence alignment - TraesCS5A01G122800

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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 TraesCS5A01G122800 chr5A 100.000 2351 0 0 1 2351 268344189 268346539 0.000000e+00 4342
1 TraesCS5A01G122800 chr5A 97.272 2236 56 3 116 2351 109667608 109669838 0.000000e+00 3786
2 TraesCS5A01G122800 chr5A 99.167 120 1 0 1 120 326144903 326144784 1.410000e-52 217
3 TraesCS5A01G122800 chr6A 96.783 2238 64 6 119 2350 204306933 204304698 0.000000e+00 3727
4 TraesCS5A01G122800 chr6A 96.437 2245 77 3 109 2351 136164330 136162087 0.000000e+00 3699
5 TraesCS5A01G122800 chr6A 96.392 2245 77 4 109 2351 328875918 328878160 0.000000e+00 3694
6 TraesCS5A01G122800 chr6A 96.207 2241 82 3 112 2351 518075644 518073406 0.000000e+00 3664
7 TraesCS5A01G122800 chr6A 96.078 2244 78 5 109 2351 213994235 213992001 0.000000e+00 3648
8 TraesCS5A01G122800 chr6A 97.026 1984 57 2 369 2351 473515388 473517370 0.000000e+00 3336
9 TraesCS5A01G122800 chr2A 96.346 2244 80 2 109 2350 616456360 616454117 0.000000e+00 3688
10 TraesCS5A01G122800 chr2A 88.482 191 19 3 5 192 464761202 464761392 6.540000e-56 228
11 TraesCS5A01G122800 chr2A 84.475 219 22 8 1 209 531871469 531871685 3.060000e-49 206
12 TraesCS5A01G122800 chr3A 95.057 2266 83 10 109 2351 134617326 134619585 0.000000e+00 3537
13 TraesCS5A01G122800 chr3A 98.361 122 1 1 3 124 34390421 34390301 1.830000e-51 213
14 TraesCS5A01G122800 chr3A 98.361 122 1 1 3 124 568224121 568224001 1.830000e-51 213
15 TraesCS5A01G122800 chr1A 97.001 1834 52 3 519 2351 465251795 465253626 0.000000e+00 3079
16 TraesCS5A01G122800 chr1A 98.361 122 1 1 3 124 187974189 187974309 1.830000e-51 213
17 TraesCS5A01G122800 chr7A 98.361 122 1 1 3 124 342781491 342781371 1.830000e-51 213
18 TraesCS5A01G122800 chr4A 98.361 122 1 1 3 124 70849544 70849664 1.830000e-51 213
19 TraesCS5A01G122800 chr4A 98.361 122 1 1 3 124 489156173 489156293 1.830000e-51 213


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 TraesCS5A01G122800 chr5A 268344189 268346539 2350 False 4342 4342 100.000 1 2351 1 chr5A.!!$F2 2350
1 TraesCS5A01G122800 chr5A 109667608 109669838 2230 False 3786 3786 97.272 116 2351 1 chr5A.!!$F1 2235
2 TraesCS5A01G122800 chr6A 204304698 204306933 2235 True 3727 3727 96.783 119 2350 1 chr6A.!!$R2 2231
3 TraesCS5A01G122800 chr6A 136162087 136164330 2243 True 3699 3699 96.437 109 2351 1 chr6A.!!$R1 2242
4 TraesCS5A01G122800 chr6A 328875918 328878160 2242 False 3694 3694 96.392 109 2351 1 chr6A.!!$F1 2242
5 TraesCS5A01G122800 chr6A 518073406 518075644 2238 True 3664 3664 96.207 112 2351 1 chr6A.!!$R4 2239
6 TraesCS5A01G122800 chr6A 213992001 213994235 2234 True 3648 3648 96.078 109 2351 1 chr6A.!!$R3 2242
7 TraesCS5A01G122800 chr6A 473515388 473517370 1982 False 3336 3336 97.026 369 2351 1 chr6A.!!$F2 1982
8 TraesCS5A01G122800 chr2A 616454117 616456360 2243 True 3688 3688 96.346 109 2350 1 chr2A.!!$R1 2241
9 TraesCS5A01G122800 chr3A 134617326 134619585 2259 False 3537 3537 95.057 109 2351 1 chr3A.!!$F1 2242
10 TraesCS5A01G122800 chr1A 465251795 465253626 1831 False 3079 3079 97.001 519 2351 1 chr1A.!!$F2 1832

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
37 38 0.105658 CATAGAGGGGAAGGGTCCGA 60.106 60.0 0.00 0.00 46.04 4.55 F
669 677 0.108851 CGTGATGTCACCGTCCATCA 60.109 55.0 7.51 6.38 43.77 3.07 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1181 1211 1.407258 AGAGCGAGATGTAGCACTTCC 59.593 52.381 0.0 0.0 30.43 3.46 R
2064 2104 2.163818 AACACAACGGACATCGACAT 57.836 45.000 0.0 0.0 42.43 3.06 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
25 26 5.808366 TTGGGTTGAGTATAGCATAGAGG 57.192 43.478 0.00 0.00 0.00 3.69
26 27 4.160329 TGGGTTGAGTATAGCATAGAGGG 58.840 47.826 0.00 0.00 0.00 4.30
27 28 3.515901 GGGTTGAGTATAGCATAGAGGGG 59.484 52.174 0.00 0.00 0.00 4.79
28 29 4.417437 GGTTGAGTATAGCATAGAGGGGA 58.583 47.826 0.00 0.00 0.00 4.81
29 30 4.838986 GGTTGAGTATAGCATAGAGGGGAA 59.161 45.833 0.00 0.00 0.00 3.97
30 31 5.046950 GGTTGAGTATAGCATAGAGGGGAAG 60.047 48.000 0.00 0.00 0.00 3.46
31 32 4.678256 TGAGTATAGCATAGAGGGGAAGG 58.322 47.826 0.00 0.00 0.00 3.46
32 33 4.027437 GAGTATAGCATAGAGGGGAAGGG 58.973 52.174 0.00 0.00 0.00 3.95
33 34 3.406498 AGTATAGCATAGAGGGGAAGGGT 59.594 47.826 0.00 0.00 0.00 4.34
34 35 2.400467 TAGCATAGAGGGGAAGGGTC 57.600 55.000 0.00 0.00 0.00 4.46
35 36 0.400670 AGCATAGAGGGGAAGGGTCC 60.401 60.000 0.00 0.00 44.10 4.46
36 37 1.759459 GCATAGAGGGGAAGGGTCCG 61.759 65.000 0.00 0.00 46.04 4.79
37 38 0.105658 CATAGAGGGGAAGGGTCCGA 60.106 60.000 0.00 0.00 46.04 4.55
38 39 0.868186 ATAGAGGGGAAGGGTCCGAT 59.132 55.000 0.00 0.00 46.04 4.18
39 40 0.187851 TAGAGGGGAAGGGTCCGATC 59.812 60.000 0.00 0.00 46.04 3.69
40 41 1.382695 GAGGGGAAGGGTCCGATCA 60.383 63.158 0.00 0.00 46.04 2.92
41 42 1.687297 GAGGGGAAGGGTCCGATCAC 61.687 65.000 0.00 0.00 46.04 3.06
42 43 1.993391 GGGGAAGGGTCCGATCACA 60.993 63.158 0.00 0.00 46.04 3.58
43 44 1.345715 GGGGAAGGGTCCGATCACAT 61.346 60.000 0.00 0.00 46.04 3.21
44 45 0.546598 GGGAAGGGTCCGATCACATT 59.453 55.000 0.00 0.00 46.04 2.71
45 46 1.475213 GGGAAGGGTCCGATCACATTC 60.475 57.143 0.00 0.00 46.04 2.67
46 47 1.209504 GGAAGGGTCCGATCACATTCA 59.790 52.381 0.00 0.00 33.05 2.57
47 48 2.280628 GAAGGGTCCGATCACATTCAC 58.719 52.381 0.00 0.00 0.00 3.18
48 49 1.573108 AGGGTCCGATCACATTCACT 58.427 50.000 0.00 0.00 0.00 3.41
49 50 1.909302 AGGGTCCGATCACATTCACTT 59.091 47.619 0.00 0.00 0.00 3.16
50 51 3.104512 AGGGTCCGATCACATTCACTTA 58.895 45.455 0.00 0.00 0.00 2.24
51 52 3.133003 AGGGTCCGATCACATTCACTTAG 59.867 47.826 0.00 0.00 0.00 2.18
52 53 2.866762 GGTCCGATCACATTCACTTAGC 59.133 50.000 0.00 0.00 0.00 3.09
53 54 3.521560 GTCCGATCACATTCACTTAGCA 58.478 45.455 0.00 0.00 0.00 3.49
54 55 3.553511 GTCCGATCACATTCACTTAGCAG 59.446 47.826 0.00 0.00 0.00 4.24
55 56 3.447229 TCCGATCACATTCACTTAGCAGA 59.553 43.478 0.00 0.00 0.00 4.26
56 57 4.081697 TCCGATCACATTCACTTAGCAGAA 60.082 41.667 0.00 0.00 0.00 3.02
57 58 4.631377 CCGATCACATTCACTTAGCAGAAA 59.369 41.667 0.00 0.00 0.00 2.52
58 59 5.122239 CCGATCACATTCACTTAGCAGAAAA 59.878 40.000 0.00 0.00 0.00 2.29
59 60 6.017933 CGATCACATTCACTTAGCAGAAAAC 58.982 40.000 0.00 0.00 0.00 2.43
60 61 5.689383 TCACATTCACTTAGCAGAAAACC 57.311 39.130 0.00 0.00 0.00 3.27
61 62 5.129634 TCACATTCACTTAGCAGAAAACCA 58.870 37.500 0.00 0.00 0.00 3.67
62 63 5.592282 TCACATTCACTTAGCAGAAAACCAA 59.408 36.000 0.00 0.00 0.00 3.67
63 64 5.687285 CACATTCACTTAGCAGAAAACCAAC 59.313 40.000 0.00 0.00 0.00 3.77
64 65 5.594317 ACATTCACTTAGCAGAAAACCAACT 59.406 36.000 0.00 0.00 0.00 3.16
65 66 6.096846 ACATTCACTTAGCAGAAAACCAACTT 59.903 34.615 0.00 0.00 0.00 2.66
66 67 5.499139 TCACTTAGCAGAAAACCAACTTG 57.501 39.130 0.00 0.00 0.00 3.16
67 68 5.189928 TCACTTAGCAGAAAACCAACTTGA 58.810 37.500 0.00 0.00 0.00 3.02
68 69 5.650266 TCACTTAGCAGAAAACCAACTTGAA 59.350 36.000 0.00 0.00 0.00 2.69
69 70 5.973565 CACTTAGCAGAAAACCAACTTGAAG 59.026 40.000 0.00 0.00 0.00 3.02
70 71 5.885912 ACTTAGCAGAAAACCAACTTGAAGA 59.114 36.000 0.00 0.00 0.00 2.87
71 72 6.377146 ACTTAGCAGAAAACCAACTTGAAGAA 59.623 34.615 0.00 0.00 0.00 2.52
72 73 5.659440 AGCAGAAAACCAACTTGAAGAAA 57.341 34.783 0.00 0.00 0.00 2.52
73 74 6.225981 AGCAGAAAACCAACTTGAAGAAAT 57.774 33.333 0.00 0.00 0.00 2.17
74 75 7.346751 AGCAGAAAACCAACTTGAAGAAATA 57.653 32.000 0.00 0.00 0.00 1.40
75 76 7.428826 AGCAGAAAACCAACTTGAAGAAATAG 58.571 34.615 0.00 0.00 0.00 1.73
76 77 6.144563 GCAGAAAACCAACTTGAAGAAATAGC 59.855 38.462 0.00 0.00 0.00 2.97
77 78 7.202526 CAGAAAACCAACTTGAAGAAATAGCA 58.797 34.615 0.00 0.00 0.00 3.49
78 79 7.706179 CAGAAAACCAACTTGAAGAAATAGCAA 59.294 33.333 0.00 0.00 0.00 3.91
79 80 8.424133 AGAAAACCAACTTGAAGAAATAGCAAT 58.576 29.630 0.00 0.00 0.00 3.56
80 81 9.691362 GAAAACCAACTTGAAGAAATAGCAATA 57.309 29.630 0.00 0.00 0.00 1.90
82 83 9.696917 AAACCAACTTGAAGAAATAGCAATAAG 57.303 29.630 0.00 0.00 0.00 1.73
83 84 8.635765 ACCAACTTGAAGAAATAGCAATAAGA 57.364 30.769 0.00 0.00 0.00 2.10
84 85 8.734386 ACCAACTTGAAGAAATAGCAATAAGAG 58.266 33.333 0.00 0.00 0.00 2.85
85 86 8.950210 CCAACTTGAAGAAATAGCAATAAGAGA 58.050 33.333 0.00 0.00 0.00 3.10
89 90 9.448294 CTTGAAGAAATAGCAATAAGAGAATGC 57.552 33.333 0.00 0.00 40.34 3.56
97 98 5.921004 GCAATAAGAGAATGCTGTAGAGG 57.079 43.478 0.00 0.00 37.12 3.69
98 99 5.605534 GCAATAAGAGAATGCTGTAGAGGA 58.394 41.667 0.00 0.00 37.12 3.71
99 100 5.465056 GCAATAAGAGAATGCTGTAGAGGAC 59.535 44.000 0.00 0.00 37.12 3.85
100 101 6.577103 CAATAAGAGAATGCTGTAGAGGACA 58.423 40.000 0.00 0.00 36.35 4.02
101 102 6.992664 ATAAGAGAATGCTGTAGAGGACAT 57.007 37.500 0.00 0.00 37.45 3.06
102 103 8.363390 CAATAAGAGAATGCTGTAGAGGACATA 58.637 37.037 0.00 0.00 37.45 2.29
103 104 6.798427 AAGAGAATGCTGTAGAGGACATAA 57.202 37.500 0.00 0.00 37.45 1.90
104 105 6.798427 AGAGAATGCTGTAGAGGACATAAA 57.202 37.500 0.00 0.00 37.45 1.40
105 106 6.578023 AGAGAATGCTGTAGAGGACATAAAC 58.422 40.000 0.00 0.00 37.45 2.01
106 107 6.382570 AGAGAATGCTGTAGAGGACATAAACT 59.617 38.462 0.00 0.00 37.45 2.66
107 108 6.578023 AGAATGCTGTAGAGGACATAAACTC 58.422 40.000 0.00 0.00 37.45 3.01
551 558 1.522092 CCGGATCCAGCTGCAACTA 59.478 57.895 13.41 0.00 0.00 2.24
669 677 0.108851 CGTGATGTCACCGTCCATCA 60.109 55.000 7.51 6.38 43.77 3.07
769 799 3.402681 GGTGCAGCCTGCCCTCTA 61.403 66.667 15.29 0.00 44.23 2.43
969 999 1.808891 CGTCTTTGAGTTTGGTCCGGT 60.809 52.381 0.00 0.00 0.00 5.28
1087 1117 1.602323 CAAGGCCAGCAACCCGTTA 60.602 57.895 5.01 0.00 0.00 3.18
1181 1211 4.147322 GGAATGCGACACCGTGCG 62.147 66.667 0.00 4.79 38.24 5.34
1223 1253 0.676151 CAGCAGGTCAAGGAGAAGCC 60.676 60.000 0.00 0.00 0.00 4.35
1445 1484 2.695359 TCAGTTCGTAGGTTCAATGCC 58.305 47.619 0.00 0.00 0.00 4.40
1497 1536 5.760743 TGTGTACTACAAAACATTAGCTGCA 59.239 36.000 1.02 0.00 36.06 4.41
1795 1834 1.943046 GCAGCAGCAGAGTTCTTAGCA 60.943 52.381 0.00 0.00 41.58 3.49
1971 2011 2.224281 TGCAGACCAAGTCGAACTTCAT 60.224 45.455 0.00 0.00 36.03 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.227156 CCTCTATGCTATACTCAACCCAATTT 58.773 38.462 0.00 0.0 0.00 1.82
1 2 6.240002 CCCTCTATGCTATACTCAACCCAATT 60.240 42.308 0.00 0.0 0.00 2.32
2 3 5.249393 CCCTCTATGCTATACTCAACCCAAT 59.751 44.000 0.00 0.0 0.00 3.16
3 4 4.593206 CCCTCTATGCTATACTCAACCCAA 59.407 45.833 0.00 0.0 0.00 4.12
4 5 4.160329 CCCTCTATGCTATACTCAACCCA 58.840 47.826 0.00 0.0 0.00 4.51
5 6 3.515901 CCCCTCTATGCTATACTCAACCC 59.484 52.174 0.00 0.0 0.00 4.11
6 7 4.417437 TCCCCTCTATGCTATACTCAACC 58.583 47.826 0.00 0.0 0.00 3.77
7 8 5.046950 CCTTCCCCTCTATGCTATACTCAAC 60.047 48.000 0.00 0.0 0.00 3.18
8 9 5.087323 CCTTCCCCTCTATGCTATACTCAA 58.913 45.833 0.00 0.0 0.00 3.02
9 10 4.511112 CCCTTCCCCTCTATGCTATACTCA 60.511 50.000 0.00 0.0 0.00 3.41
10 11 4.027437 CCCTTCCCCTCTATGCTATACTC 58.973 52.174 0.00 0.0 0.00 2.59
11 12 3.406498 ACCCTTCCCCTCTATGCTATACT 59.594 47.826 0.00 0.0 0.00 2.12
12 13 3.770388 GACCCTTCCCCTCTATGCTATAC 59.230 52.174 0.00 0.0 0.00 1.47
13 14 3.246021 GGACCCTTCCCCTCTATGCTATA 60.246 52.174 0.00 0.0 35.57 1.31
14 15 2.495572 GGACCCTTCCCCTCTATGCTAT 60.496 54.545 0.00 0.0 35.57 2.97
15 16 1.132817 GGACCCTTCCCCTCTATGCTA 60.133 57.143 0.00 0.0 35.57 3.49
16 17 0.400670 GGACCCTTCCCCTCTATGCT 60.401 60.000 0.00 0.0 35.57 3.79
17 18 1.759459 CGGACCCTTCCCCTCTATGC 61.759 65.000 0.00 0.0 38.99 3.14
18 19 0.105658 TCGGACCCTTCCCCTCTATG 60.106 60.000 0.00 0.0 38.99 2.23
19 20 0.868186 ATCGGACCCTTCCCCTCTAT 59.132 55.000 0.00 0.0 38.99 1.98
20 21 0.187851 GATCGGACCCTTCCCCTCTA 59.812 60.000 0.00 0.0 38.99 2.43
21 22 1.075151 GATCGGACCCTTCCCCTCT 60.075 63.158 0.00 0.0 38.99 3.69
22 23 1.382695 TGATCGGACCCTTCCCCTC 60.383 63.158 0.00 0.0 38.99 4.30
23 24 1.689582 GTGATCGGACCCTTCCCCT 60.690 63.158 0.00 0.0 38.99 4.79
24 25 1.345715 ATGTGATCGGACCCTTCCCC 61.346 60.000 0.00 0.0 38.99 4.81
25 26 0.546598 AATGTGATCGGACCCTTCCC 59.453 55.000 0.00 0.0 38.99 3.97
26 27 1.209504 TGAATGTGATCGGACCCTTCC 59.790 52.381 0.00 0.0 38.77 3.46
27 28 2.093447 AGTGAATGTGATCGGACCCTTC 60.093 50.000 0.00 0.0 0.00 3.46
28 29 1.909302 AGTGAATGTGATCGGACCCTT 59.091 47.619 0.00 0.0 0.00 3.95
29 30 1.573108 AGTGAATGTGATCGGACCCT 58.427 50.000 0.00 0.0 0.00 4.34
30 31 2.403252 AAGTGAATGTGATCGGACCC 57.597 50.000 0.00 0.0 0.00 4.46
31 32 2.866762 GCTAAGTGAATGTGATCGGACC 59.133 50.000 0.00 0.0 0.00 4.46
32 33 3.521560 TGCTAAGTGAATGTGATCGGAC 58.478 45.455 0.00 0.0 0.00 4.79
33 34 3.447229 TCTGCTAAGTGAATGTGATCGGA 59.553 43.478 0.00 0.0 0.00 4.55
34 35 3.785486 TCTGCTAAGTGAATGTGATCGG 58.215 45.455 0.00 0.0 0.00 4.18
35 36 5.784750 TTTCTGCTAAGTGAATGTGATCG 57.215 39.130 0.00 0.0 0.00 3.69
36 37 6.072508 TGGTTTTCTGCTAAGTGAATGTGATC 60.073 38.462 0.00 0.0 0.00 2.92
37 38 5.769662 TGGTTTTCTGCTAAGTGAATGTGAT 59.230 36.000 0.00 0.0 0.00 3.06
38 39 5.129634 TGGTTTTCTGCTAAGTGAATGTGA 58.870 37.500 0.00 0.0 0.00 3.58
39 40 5.437289 TGGTTTTCTGCTAAGTGAATGTG 57.563 39.130 0.00 0.0 0.00 3.21
40 41 5.594317 AGTTGGTTTTCTGCTAAGTGAATGT 59.406 36.000 0.00 0.0 0.00 2.71
41 42 6.076981 AGTTGGTTTTCTGCTAAGTGAATG 57.923 37.500 0.00 0.0 0.00 2.67
42 43 6.321181 TCAAGTTGGTTTTCTGCTAAGTGAAT 59.679 34.615 2.34 0.0 0.00 2.57
43 44 5.650266 TCAAGTTGGTTTTCTGCTAAGTGAA 59.350 36.000 2.34 0.0 0.00 3.18
44 45 5.189928 TCAAGTTGGTTTTCTGCTAAGTGA 58.810 37.500 2.34 0.0 0.00 3.41
45 46 5.499139 TCAAGTTGGTTTTCTGCTAAGTG 57.501 39.130 2.34 0.0 0.00 3.16
46 47 5.885912 TCTTCAAGTTGGTTTTCTGCTAAGT 59.114 36.000 2.34 0.0 0.00 2.24
47 48 6.377327 TCTTCAAGTTGGTTTTCTGCTAAG 57.623 37.500 2.34 0.0 0.00 2.18
48 49 6.767524 TTCTTCAAGTTGGTTTTCTGCTAA 57.232 33.333 2.34 0.0 0.00 3.09
49 50 6.767524 TTTCTTCAAGTTGGTTTTCTGCTA 57.232 33.333 2.34 0.0 0.00 3.49
50 51 5.659440 TTTCTTCAAGTTGGTTTTCTGCT 57.341 34.783 2.34 0.0 0.00 4.24
51 52 6.144563 GCTATTTCTTCAAGTTGGTTTTCTGC 59.855 38.462 2.34 0.0 0.00 4.26
52 53 7.202526 TGCTATTTCTTCAAGTTGGTTTTCTG 58.797 34.615 2.34 0.0 0.00 3.02
53 54 7.346751 TGCTATTTCTTCAAGTTGGTTTTCT 57.653 32.000 2.34 0.0 0.00 2.52
54 55 8.593492 ATTGCTATTTCTTCAAGTTGGTTTTC 57.407 30.769 2.34 0.0 0.00 2.29
56 57 9.696917 CTTATTGCTATTTCTTCAAGTTGGTTT 57.303 29.630 2.34 0.0 0.00 3.27
57 58 9.077885 TCTTATTGCTATTTCTTCAAGTTGGTT 57.922 29.630 2.34 0.0 0.00 3.67
58 59 8.635765 TCTTATTGCTATTTCTTCAAGTTGGT 57.364 30.769 2.34 0.0 0.00 3.67
59 60 8.950210 TCTCTTATTGCTATTTCTTCAAGTTGG 58.050 33.333 2.34 0.0 0.00 3.77
63 64 9.448294 GCATTCTCTTATTGCTATTTCTTCAAG 57.552 33.333 0.00 0.0 32.78 3.02
64 65 9.182214 AGCATTCTCTTATTGCTATTTCTTCAA 57.818 29.630 0.00 0.0 41.76 2.69
65 66 8.618677 CAGCATTCTCTTATTGCTATTTCTTCA 58.381 33.333 0.00 0.0 41.68 3.02
66 67 8.619546 ACAGCATTCTCTTATTGCTATTTCTTC 58.380 33.333 0.00 0.0 41.68 2.87
67 68 8.517062 ACAGCATTCTCTTATTGCTATTTCTT 57.483 30.769 0.00 0.0 41.68 2.52
68 69 9.270640 CTACAGCATTCTCTTATTGCTATTTCT 57.729 33.333 0.00 0.0 41.68 2.52
69 70 9.265901 TCTACAGCATTCTCTTATTGCTATTTC 57.734 33.333 0.00 0.0 41.68 2.17
70 71 9.270640 CTCTACAGCATTCTCTTATTGCTATTT 57.729 33.333 0.00 0.0 41.68 1.40
71 72 7.877097 CCTCTACAGCATTCTCTTATTGCTATT 59.123 37.037 0.00 0.0 41.68 1.73
72 73 7.234371 TCCTCTACAGCATTCTCTTATTGCTAT 59.766 37.037 0.00 0.0 41.68 2.97
73 74 6.551227 TCCTCTACAGCATTCTCTTATTGCTA 59.449 38.462 0.00 0.0 41.68 3.49
74 75 5.365025 TCCTCTACAGCATTCTCTTATTGCT 59.635 40.000 0.00 0.0 43.80 3.91
75 76 5.465056 GTCCTCTACAGCATTCTCTTATTGC 59.535 44.000 0.00 0.0 35.19 3.56
76 77 6.577103 TGTCCTCTACAGCATTCTCTTATTG 58.423 40.000 0.00 0.0 33.01 1.90
77 78 6.798427 TGTCCTCTACAGCATTCTCTTATT 57.202 37.500 0.00 0.0 33.01 1.40
78 79 6.992664 ATGTCCTCTACAGCATTCTCTTAT 57.007 37.500 0.00 0.0 42.70 1.73
79 80 7.898014 TTATGTCCTCTACAGCATTCTCTTA 57.102 36.000 0.00 0.0 42.70 2.10
80 81 6.798427 TTATGTCCTCTACAGCATTCTCTT 57.202 37.500 0.00 0.0 42.70 2.85
81 82 6.382570 AGTTTATGTCCTCTACAGCATTCTCT 59.617 38.462 0.00 0.0 42.70 3.10
82 83 6.578023 AGTTTATGTCCTCTACAGCATTCTC 58.422 40.000 0.00 0.0 42.70 2.87
83 84 6.155221 TGAGTTTATGTCCTCTACAGCATTCT 59.845 38.462 0.00 0.0 42.70 2.40
84 85 6.341316 TGAGTTTATGTCCTCTACAGCATTC 58.659 40.000 0.00 0.0 42.70 2.67
85 86 6.299805 TGAGTTTATGTCCTCTACAGCATT 57.700 37.500 0.00 0.0 42.70 3.56
86 87 5.939764 TGAGTTTATGTCCTCTACAGCAT 57.060 39.130 0.00 0.0 42.70 3.79
87 88 5.939764 ATGAGTTTATGTCCTCTACAGCA 57.060 39.130 0.00 0.0 42.70 4.41
193 194 4.563786 GGGTTTTCTCAGGAGTTCGAGAAT 60.564 45.833 2.93 0.0 45.21 2.40
238 239 2.306715 GAAGTGGGTGGGGTGGGTTT 62.307 60.000 0.00 0.0 0.00 3.27
1087 1117 3.325135 CCTTGTACTCCTTCAGGTTCACT 59.675 47.826 0.00 0.0 36.34 3.41
1181 1211 1.407258 AGAGCGAGATGTAGCACTTCC 59.593 52.381 0.00 0.0 30.43 3.46
1223 1253 2.131709 TAGGGGTCGATCTTGCCGG 61.132 63.158 0.00 0.0 0.00 6.13
1445 1484 3.875727 CTGAACCTGAATACCTGATGCAG 59.124 47.826 0.00 0.0 40.64 4.41
1497 1536 5.012239 ACAGCATGGTTTTCTCACATACAT 58.988 37.500 0.00 0.0 43.62 2.29
1795 1834 6.068853 TCACATGGGGAAATTAGGAAGAAGAT 60.069 38.462 0.00 0.0 0.00 2.40
2064 2104 2.163818 AACACAACGGACATCGACAT 57.836 45.000 0.00 0.0 42.43 3.06
2303 2347 8.177119 ACATAGTTTCAATTGTTTCCTGCTTA 57.823 30.769 5.13 0.0 0.00 3.09


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

AutoCloner maintained by Alex Coulton.