Multiple sequence alignment - TraesCS2A01G414900

Loading Multiple Alignment...

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 TraesCS2A01G414900 chr2A 100.000 3454 0 0 1 3454 672096729 672093276 0.000000e+00 6379
1 TraesCS2A01G414900 chr2A 99.301 429 3 0 3026 3454 642919383 642918955 0.000000e+00 776
2 TraesCS2A01G414900 chr2A 93.382 136 8 1 1 135 64951445 64951580 2.100000e-47 200
3 TraesCS2A01G414900 chr2A 93.382 136 8 1 1 135 432460650 432460785 2.100000e-47 200
4 TraesCS2A01G414900 chr5B 98.826 3321 37 2 135 3454 325080846 325077527 0.000000e+00 5915
5 TraesCS2A01G414900 chr5B 95.759 3325 119 14 135 3454 146820940 146817633 0.000000e+00 5339
6 TraesCS2A01G414900 chr6B 98.796 3321 38 2 135 3454 415879344 415882663 0.000000e+00 5910
7 TraesCS2A01G414900 chr6B 91.391 151 10 3 135 284 458501057 458501205 1.630000e-48 204
8 TraesCS2A01G414900 chr6B 83.945 218 26 9 135 347 458495685 458495898 2.100000e-47 200
9 TraesCS2A01G414900 chr4B 98.735 3321 39 3 135 3454 165291386 165294704 0.000000e+00 5897
10 TraesCS2A01G414900 chr7A 98.585 3321 44 3 135 3454 1410243 1413561 0.000000e+00 5869
11 TraesCS2A01G414900 chr7A 98.930 2897 29 1 560 3454 217766973 217764077 0.000000e+00 5177
12 TraesCS2A01G414900 chr3D 95.836 3338 107 23 132 3454 152827199 152830519 0.000000e+00 5365
13 TraesCS2A01G414900 chr3D 95.823 3328 93 17 135 3454 247889326 247886037 0.000000e+00 5334
14 TraesCS2A01G414900 chr5A 95.527 3331 129 14 131 3454 489873414 489876731 0.000000e+00 5308
15 TraesCS2A01G414900 chr5A 94.853 136 6 1 1 135 280431231 280431366 9.710000e-51 211
16 TraesCS2A01G414900 chr5A 94.118 136 7 1 1 135 63681401 63681266 4.520000e-49 206
17 TraesCS2A01G414900 chr5A 94.118 136 7 1 1 135 487062688 487062553 4.520000e-49 206
18 TraesCS2A01G414900 chr4A 94.853 136 6 1 1 135 76087551 76087686 9.710000e-51 211
19 TraesCS2A01G414900 chr4A 94.118 136 7 1 1 135 116006383 116006518 4.520000e-49 206
20 TraesCS2A01G414900 chr4A 93.382 136 8 1 1 135 583609366 583609231 2.100000e-47 200
21 TraesCS2A01G414900 chr6A 94.118 136 7 1 1 135 590316233 590316368 4.520000e-49 206


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 TraesCS2A01G414900 chr2A 672093276 672096729 3453 True 6379 6379 100.000 1 3454 1 chr2A.!!$R2 3453
1 TraesCS2A01G414900 chr5B 325077527 325080846 3319 True 5915 5915 98.826 135 3454 1 chr5B.!!$R2 3319
2 TraesCS2A01G414900 chr5B 146817633 146820940 3307 True 5339 5339 95.759 135 3454 1 chr5B.!!$R1 3319
3 TraesCS2A01G414900 chr6B 415879344 415882663 3319 False 5910 5910 98.796 135 3454 1 chr6B.!!$F1 3319
4 TraesCS2A01G414900 chr4B 165291386 165294704 3318 False 5897 5897 98.735 135 3454 1 chr4B.!!$F1 3319
5 TraesCS2A01G414900 chr7A 1410243 1413561 3318 False 5869 5869 98.585 135 3454 1 chr7A.!!$F1 3319
6 TraesCS2A01G414900 chr7A 217764077 217766973 2896 True 5177 5177 98.930 560 3454 1 chr7A.!!$R1 2894
7 TraesCS2A01G414900 chr3D 152827199 152830519 3320 False 5365 5365 95.836 132 3454 1 chr3D.!!$F1 3322
8 TraesCS2A01G414900 chr3D 247886037 247889326 3289 True 5334 5334 95.823 135 3454 1 chr3D.!!$R1 3319
9 TraesCS2A01G414900 chr5A 489873414 489876731 3317 False 5308 5308 95.527 131 3454 1 chr5A.!!$F2 3323

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
27 28 0.033504 CACACACCGCTGGTAAGTCT 59.966 55.0 0.00 0.0 32.11 3.24 F
28 29 0.317479 ACACACCGCTGGTAAGTCTC 59.683 55.0 0.00 0.0 32.11 3.36 F
34 35 0.386113 CGCTGGTAAGTCTCCTAGGC 59.614 60.0 2.96 0.0 0.00 3.93 F
2072 2091 0.538287 GACTTTGCTCACTGGGCCTT 60.538 55.0 4.53 0.0 0.00 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1874 1893 1.277557 CACTTCTACCTCTGCCTGCTT 59.722 52.381 0.0 0.0 0.00 3.91 R
2072 2091 3.371034 TCCGGATTACCTTCATCAGTGA 58.629 45.455 0.0 0.0 0.00 3.41 R
2370 2389 2.900716 TGTCAAGGATCACACGACAA 57.099 45.000 0.0 0.0 33.86 3.18 R
2898 2921 0.533491 CCGTTCCATTGTCCGTCCTA 59.467 55.000 0.0 0.0 0.00 2.94 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
17 18 4.539152 CAATTCTGCACACACCGC 57.461 55.556 0.00 0.00 0.00 5.68
18 19 1.951510 CAATTCTGCACACACCGCT 59.048 52.632 0.00 0.00 0.00 5.52
19 20 0.386352 CAATTCTGCACACACCGCTG 60.386 55.000 0.00 0.00 0.00 5.18
20 21 1.518056 AATTCTGCACACACCGCTGG 61.518 55.000 0.00 0.00 0.00 4.85
21 22 2.680974 ATTCTGCACACACCGCTGGT 62.681 55.000 0.00 0.00 35.62 4.00
22 23 2.030412 CTGCACACACCGCTGGTA 59.970 61.111 0.00 0.00 32.11 3.25
23 24 1.596752 CTGCACACACCGCTGGTAA 60.597 57.895 0.00 0.00 32.11 2.85
24 25 1.568612 CTGCACACACCGCTGGTAAG 61.569 60.000 0.00 0.00 32.11 2.34
25 26 1.597027 GCACACACCGCTGGTAAGT 60.597 57.895 0.00 0.32 32.11 2.24
26 27 1.566018 GCACACACCGCTGGTAAGTC 61.566 60.000 0.00 0.00 32.11 3.01
27 28 0.033504 CACACACCGCTGGTAAGTCT 59.966 55.000 0.00 0.00 32.11 3.24
28 29 0.317479 ACACACCGCTGGTAAGTCTC 59.683 55.000 0.00 0.00 32.11 3.36
29 30 0.389948 CACACCGCTGGTAAGTCTCC 60.390 60.000 0.00 0.00 32.11 3.71
30 31 0.542232 ACACCGCTGGTAAGTCTCCT 60.542 55.000 0.00 0.00 32.11 3.69
31 32 1.272313 ACACCGCTGGTAAGTCTCCTA 60.272 52.381 0.00 0.00 32.11 2.94
32 33 1.405821 CACCGCTGGTAAGTCTCCTAG 59.594 57.143 0.00 0.00 32.11 3.02
33 34 1.033574 CCGCTGGTAAGTCTCCTAGG 58.966 60.000 0.82 0.82 0.00 3.02
34 35 0.386113 CGCTGGTAAGTCTCCTAGGC 59.614 60.000 2.96 0.00 0.00 3.93
35 36 1.486211 GCTGGTAAGTCTCCTAGGCA 58.514 55.000 2.96 0.00 0.00 4.75
36 37 1.137282 GCTGGTAAGTCTCCTAGGCAC 59.863 57.143 2.96 3.02 0.00 5.01
37 38 2.741145 CTGGTAAGTCTCCTAGGCACT 58.259 52.381 2.96 5.60 46.37 4.40
38 39 2.691011 CTGGTAAGTCTCCTAGGCACTC 59.309 54.545 12.33 3.25 41.75 3.51
39 40 2.312140 TGGTAAGTCTCCTAGGCACTCT 59.688 50.000 12.33 6.98 41.75 3.24
40 41 3.245658 TGGTAAGTCTCCTAGGCACTCTT 60.246 47.826 12.33 11.64 41.75 2.85
41 42 4.017775 TGGTAAGTCTCCTAGGCACTCTTA 60.018 45.833 12.33 10.86 41.75 2.10
42 43 4.954826 GGTAAGTCTCCTAGGCACTCTTAA 59.045 45.833 12.33 0.00 41.75 1.85
43 44 5.421374 GGTAAGTCTCCTAGGCACTCTTAAA 59.579 44.000 12.33 0.00 41.75 1.52
44 45 5.408880 AAGTCTCCTAGGCACTCTTAAAC 57.591 43.478 12.33 0.00 41.75 2.01
45 46 3.770388 AGTCTCCTAGGCACTCTTAAACC 59.230 47.826 2.96 0.00 41.75 3.27
46 47 3.105283 TCTCCTAGGCACTCTTAAACCC 58.895 50.000 2.96 0.00 41.75 4.11
47 48 2.838202 CTCCTAGGCACTCTTAAACCCA 59.162 50.000 2.96 0.00 41.75 4.51
48 49 3.253220 TCCTAGGCACTCTTAAACCCAA 58.747 45.455 2.96 0.00 41.75 4.12
49 50 3.653836 TCCTAGGCACTCTTAAACCCAAA 59.346 43.478 2.96 0.00 41.75 3.28
50 51 4.105057 TCCTAGGCACTCTTAAACCCAAAA 59.895 41.667 2.96 0.00 41.75 2.44
51 52 4.459337 CCTAGGCACTCTTAAACCCAAAAG 59.541 45.833 0.00 0.00 41.75 2.27
52 53 3.230976 AGGCACTCTTAAACCCAAAAGG 58.769 45.455 0.00 0.00 43.78 3.11
53 54 2.288825 GGCACTCTTAAACCCAAAAGGC 60.289 50.000 0.00 0.00 40.58 4.35
54 55 2.364002 GCACTCTTAAACCCAAAAGGCA 59.636 45.455 0.00 0.00 40.58 4.75
55 56 3.006859 GCACTCTTAAACCCAAAAGGCAT 59.993 43.478 0.00 0.00 40.58 4.40
56 57 4.219725 GCACTCTTAAACCCAAAAGGCATA 59.780 41.667 0.00 0.00 40.58 3.14
57 58 5.622233 GCACTCTTAAACCCAAAAGGCATAG 60.622 44.000 0.00 0.00 40.58 2.23
58 59 5.710099 CACTCTTAAACCCAAAAGGCATAGA 59.290 40.000 0.00 0.00 40.58 1.98
59 60 5.710567 ACTCTTAAACCCAAAAGGCATAGAC 59.289 40.000 0.00 0.00 40.58 2.59
60 61 5.636123 TCTTAAACCCAAAAGGCATAGACA 58.364 37.500 0.00 0.00 40.58 3.41
61 62 5.475564 TCTTAAACCCAAAAGGCATAGACAC 59.524 40.000 0.00 0.00 40.58 3.67
62 63 2.969821 ACCCAAAAGGCATAGACACA 57.030 45.000 0.00 0.00 40.58 3.72
63 64 3.456380 ACCCAAAAGGCATAGACACAT 57.544 42.857 0.00 0.00 40.58 3.21
64 65 4.584638 ACCCAAAAGGCATAGACACATA 57.415 40.909 0.00 0.00 40.58 2.29
65 66 4.526970 ACCCAAAAGGCATAGACACATAG 58.473 43.478 0.00 0.00 40.58 2.23
66 67 3.316308 CCCAAAAGGCATAGACACATAGC 59.684 47.826 0.00 0.00 0.00 2.97
67 68 3.947196 CCAAAAGGCATAGACACATAGCA 59.053 43.478 0.00 0.00 0.00 3.49
68 69 4.036027 CCAAAAGGCATAGACACATAGCAG 59.964 45.833 0.00 0.00 0.00 4.24
69 70 4.760530 AAAGGCATAGACACATAGCAGA 57.239 40.909 0.00 0.00 0.00 4.26
70 71 4.760530 AAGGCATAGACACATAGCAGAA 57.239 40.909 0.00 0.00 0.00 3.02
71 72 4.760530 AGGCATAGACACATAGCAGAAA 57.239 40.909 0.00 0.00 0.00 2.52
72 73 4.701765 AGGCATAGACACATAGCAGAAAG 58.298 43.478 0.00 0.00 0.00 2.62
73 74 3.249559 GGCATAGACACATAGCAGAAAGC 59.750 47.826 0.00 0.00 46.19 3.51
87 88 5.573337 GCAGAAAGCTCCAATTGAGTAAT 57.427 39.130 7.12 0.00 43.48 1.89
88 89 5.338365 GCAGAAAGCTCCAATTGAGTAATG 58.662 41.667 7.12 0.00 43.48 1.90
89 90 5.124457 GCAGAAAGCTCCAATTGAGTAATGA 59.876 40.000 7.12 0.00 43.48 2.57
90 91 6.349611 GCAGAAAGCTCCAATTGAGTAATGAA 60.350 38.462 7.12 0.00 43.48 2.57
91 92 7.596494 CAGAAAGCTCCAATTGAGTAATGAAA 58.404 34.615 7.12 0.00 43.48 2.69
92 93 7.754027 CAGAAAGCTCCAATTGAGTAATGAAAG 59.246 37.037 7.12 0.00 43.48 2.62
93 94 5.573337 AGCTCCAATTGAGTAATGAAAGC 57.427 39.130 7.12 0.97 43.48 3.51
94 95 5.259632 AGCTCCAATTGAGTAATGAAAGCT 58.740 37.500 7.12 3.15 43.48 3.74
95 96 5.125097 AGCTCCAATTGAGTAATGAAAGCTG 59.875 40.000 7.12 0.00 43.48 4.24
96 97 5.105997 GCTCCAATTGAGTAATGAAAGCTGT 60.106 40.000 7.12 0.00 43.48 4.40
97 98 6.500684 TCCAATTGAGTAATGAAAGCTGTC 57.499 37.500 7.12 0.00 0.00 3.51
98 99 6.240894 TCCAATTGAGTAATGAAAGCTGTCT 58.759 36.000 7.12 0.00 0.00 3.41
99 100 6.716628 TCCAATTGAGTAATGAAAGCTGTCTT 59.283 34.615 7.12 0.00 0.00 3.01
100 101 7.025963 CCAATTGAGTAATGAAAGCTGTCTTC 58.974 38.462 7.12 0.00 0.00 2.87
101 102 7.094463 CCAATTGAGTAATGAAAGCTGTCTTCT 60.094 37.037 7.12 0.00 0.00 2.85
102 103 7.608308 ATTGAGTAATGAAAGCTGTCTTCTC 57.392 36.000 5.28 8.04 0.00 2.87
103 104 5.482908 TGAGTAATGAAAGCTGTCTTCTCC 58.517 41.667 5.28 0.00 0.00 3.71
104 105 5.247110 TGAGTAATGAAAGCTGTCTTCTCCT 59.753 40.000 5.28 0.00 0.00 3.69
105 106 5.486526 AGTAATGAAAGCTGTCTTCTCCTG 58.513 41.667 5.28 0.00 0.00 3.86
106 107 4.630644 AATGAAAGCTGTCTTCTCCTGA 57.369 40.909 5.28 0.00 0.00 3.86
107 108 4.840716 ATGAAAGCTGTCTTCTCCTGAT 57.159 40.909 5.28 0.00 0.00 2.90
108 109 4.199432 TGAAAGCTGTCTTCTCCTGATC 57.801 45.455 5.28 0.00 0.00 2.92
109 110 3.055530 TGAAAGCTGTCTTCTCCTGATCC 60.056 47.826 5.28 0.00 0.00 3.36
110 111 2.548464 AGCTGTCTTCTCCTGATCCT 57.452 50.000 0.00 0.00 0.00 3.24
111 112 2.831565 AGCTGTCTTCTCCTGATCCTT 58.168 47.619 0.00 0.00 0.00 3.36
112 113 2.500910 AGCTGTCTTCTCCTGATCCTTG 59.499 50.000 0.00 0.00 0.00 3.61
113 114 2.499289 GCTGTCTTCTCCTGATCCTTGA 59.501 50.000 0.00 0.00 0.00 3.02
114 115 3.134442 GCTGTCTTCTCCTGATCCTTGAT 59.866 47.826 0.00 0.00 0.00 2.57
115 116 4.740334 GCTGTCTTCTCCTGATCCTTGATC 60.740 50.000 0.00 0.00 39.31 2.92
116 117 3.382865 TGTCTTCTCCTGATCCTTGATCG 59.617 47.826 0.00 0.00 41.51 3.69
117 118 2.363680 TCTTCTCCTGATCCTTGATCGC 59.636 50.000 0.00 0.00 41.51 4.58
118 119 1.043816 TCTCCTGATCCTTGATCGCC 58.956 55.000 0.00 0.00 41.51 5.54
119 120 0.755079 CTCCTGATCCTTGATCGCCA 59.245 55.000 0.00 0.00 41.51 5.69
120 121 1.347050 CTCCTGATCCTTGATCGCCAT 59.653 52.381 0.00 0.00 41.51 4.40
121 122 1.345741 TCCTGATCCTTGATCGCCATC 59.654 52.381 0.00 0.00 41.51 3.51
122 123 1.347050 CCTGATCCTTGATCGCCATCT 59.653 52.381 0.00 0.00 41.51 2.90
123 124 2.224475 CCTGATCCTTGATCGCCATCTT 60.224 50.000 0.00 0.00 41.51 2.40
124 125 3.007290 CCTGATCCTTGATCGCCATCTTA 59.993 47.826 0.00 0.00 41.51 2.10
125 126 4.503817 CCTGATCCTTGATCGCCATCTTAA 60.504 45.833 0.00 0.00 41.51 1.85
126 127 5.233083 TGATCCTTGATCGCCATCTTAAT 57.767 39.130 0.00 0.00 41.51 1.40
127 128 5.240891 TGATCCTTGATCGCCATCTTAATC 58.759 41.667 0.00 0.00 41.51 1.75
128 129 4.963318 TCCTTGATCGCCATCTTAATCT 57.037 40.909 0.00 0.00 0.00 2.40
129 130 4.635223 TCCTTGATCGCCATCTTAATCTG 58.365 43.478 0.00 0.00 0.00 2.90
132 133 5.121925 CCTTGATCGCCATCTTAATCTGATG 59.878 44.000 0.00 0.00 40.51 3.07
291 292 1.456287 GCAACAAGACAGGAGGGGT 59.544 57.895 0.00 0.00 0.00 4.95
347 349 2.782222 GGTATCGAGCCAGGCGACA 61.782 63.158 5.55 0.00 40.94 4.35
453 456 4.626081 GCGGGTCTGCTGTGGTGT 62.626 66.667 0.00 0.00 0.00 4.16
457 460 2.588877 GTCTGCTGTGGTGTGCGT 60.589 61.111 0.00 0.00 0.00 5.24
492 495 1.301716 GGCTCGAGGAGTTGCAACA 60.302 57.895 30.11 8.55 31.39 3.33
538 541 1.533033 TCCTGCTTCGTGTCCCTGA 60.533 57.895 0.00 0.00 0.00 3.86
643 649 3.113386 GAAGGCGGCAGCGGATTTC 62.113 63.158 13.08 0.00 46.35 2.17
816 823 2.979678 AGGAAGAAAGAGTGGTTGCCTA 59.020 45.455 0.00 0.00 0.00 3.93
1874 1893 2.763515 GCAGGGGATATAACAGAGGGGA 60.764 54.545 0.00 0.00 0.00 4.81
2072 2091 0.538287 GACTTTGCTCACTGGGCCTT 60.538 55.000 4.53 0.00 0.00 4.35
2370 2389 4.954202 AGTGCACTCATTGATCAAATGGAT 59.046 37.500 15.25 0.00 45.00 3.41
2462 2481 2.123425 CAGGCGTAGGGGGCTCTA 60.123 66.667 0.00 0.00 41.42 2.43
2845 2868 5.140454 AGGATGAGGTGTTTAGCTGTTTTT 58.860 37.500 0.00 0.00 34.13 1.94
2898 2921 1.072331 CAGGTACAGGTCAAGGTGCTT 59.928 52.381 0.00 0.00 0.00 3.91
3031 3055 2.797087 GCCGAACGGAAGAATCGTCATA 60.797 50.000 17.63 0.00 40.18 2.15
3266 3290 1.202915 TGTTGGCAAGCTTGATCCTCA 60.203 47.619 30.39 19.57 0.00 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.386352 CAGCGGTGTGTGCAGAATTG 60.386 55.000 6.41 0.00 33.85 2.32
1 2 1.518056 CCAGCGGTGTGTGCAGAATT 61.518 55.000 14.40 0.00 33.85 2.17
2 3 1.968017 CCAGCGGTGTGTGCAGAAT 60.968 57.895 14.40 0.00 33.85 2.40
3 4 2.034048 TACCAGCGGTGTGTGCAGAA 62.034 55.000 14.40 0.00 36.19 3.02
4 5 2.034048 TTACCAGCGGTGTGTGCAGA 62.034 55.000 14.40 0.00 36.19 4.26
5 6 1.568612 CTTACCAGCGGTGTGTGCAG 61.569 60.000 14.40 8.01 36.19 4.41
6 7 1.596752 CTTACCAGCGGTGTGTGCA 60.597 57.895 14.40 2.57 36.19 4.57
7 8 1.566018 GACTTACCAGCGGTGTGTGC 61.566 60.000 14.40 0.00 36.19 4.57
8 9 0.033504 AGACTTACCAGCGGTGTGTG 59.966 55.000 14.40 0.46 36.19 3.82
9 10 0.317479 GAGACTTACCAGCGGTGTGT 59.683 55.000 14.40 13.15 36.19 3.72
10 11 0.389948 GGAGACTTACCAGCGGTGTG 60.390 60.000 14.40 7.66 36.19 3.82
11 12 0.542232 AGGAGACTTACCAGCGGTGT 60.542 55.000 14.40 4.46 37.44 4.16
12 13 1.405821 CTAGGAGACTTACCAGCGGTG 59.594 57.143 7.86 7.86 43.67 4.94
13 14 1.685491 CCTAGGAGACTTACCAGCGGT 60.685 57.143 1.05 5.58 43.67 5.68
14 15 1.033574 CCTAGGAGACTTACCAGCGG 58.966 60.000 1.05 0.00 43.67 5.52
15 16 0.386113 GCCTAGGAGACTTACCAGCG 59.614 60.000 14.75 0.00 43.67 5.18
16 17 1.137282 GTGCCTAGGAGACTTACCAGC 59.863 57.143 14.75 0.00 43.67 4.85
17 18 2.691011 GAGTGCCTAGGAGACTTACCAG 59.309 54.545 14.75 0.00 43.67 4.00
18 19 2.312140 AGAGTGCCTAGGAGACTTACCA 59.688 50.000 14.75 0.00 43.67 3.25
19 20 3.021177 AGAGTGCCTAGGAGACTTACC 57.979 52.381 14.75 1.99 43.67 2.85
20 21 6.331845 GTTTAAGAGTGCCTAGGAGACTTAC 58.668 44.000 14.75 2.69 43.67 2.34
21 22 5.421374 GGTTTAAGAGTGCCTAGGAGACTTA 59.579 44.000 14.75 12.51 43.67 2.24
22 23 4.223255 GGTTTAAGAGTGCCTAGGAGACTT 59.777 45.833 14.75 13.47 43.67 3.01
24 25 3.118702 GGGTTTAAGAGTGCCTAGGAGAC 60.119 52.174 14.75 8.18 0.00 3.36
25 26 3.105283 GGGTTTAAGAGTGCCTAGGAGA 58.895 50.000 14.75 0.00 0.00 3.71
26 27 2.838202 TGGGTTTAAGAGTGCCTAGGAG 59.162 50.000 14.75 0.00 0.00 3.69
27 28 2.910544 TGGGTTTAAGAGTGCCTAGGA 58.089 47.619 14.75 0.00 0.00 2.94
28 29 3.713826 TTGGGTTTAAGAGTGCCTAGG 57.286 47.619 3.67 3.67 0.00 3.02
29 30 4.459337 CCTTTTGGGTTTAAGAGTGCCTAG 59.541 45.833 0.00 0.00 35.46 3.02
30 31 4.403734 CCTTTTGGGTTTAAGAGTGCCTA 58.596 43.478 0.00 0.00 35.46 3.93
31 32 3.230976 CCTTTTGGGTTTAAGAGTGCCT 58.769 45.455 0.00 0.00 35.46 4.75
32 33 2.288825 GCCTTTTGGGTTTAAGAGTGCC 60.289 50.000 0.00 0.00 40.82 5.01
33 34 2.364002 TGCCTTTTGGGTTTAAGAGTGC 59.636 45.455 0.00 0.00 40.82 4.40
34 35 4.871933 ATGCCTTTTGGGTTTAAGAGTG 57.128 40.909 0.00 0.00 40.82 3.51
35 36 5.710567 GTCTATGCCTTTTGGGTTTAAGAGT 59.289 40.000 0.00 0.00 40.82 3.24
36 37 5.710099 TGTCTATGCCTTTTGGGTTTAAGAG 59.290 40.000 0.00 0.00 40.82 2.85
37 38 5.475564 GTGTCTATGCCTTTTGGGTTTAAGA 59.524 40.000 0.00 0.00 40.82 2.10
38 39 5.242838 TGTGTCTATGCCTTTTGGGTTTAAG 59.757 40.000 0.00 0.00 40.82 1.85
39 40 5.141182 TGTGTCTATGCCTTTTGGGTTTAA 58.859 37.500 0.00 0.00 40.82 1.52
40 41 4.730966 TGTGTCTATGCCTTTTGGGTTTA 58.269 39.130 0.00 0.00 40.82 2.01
41 42 3.571590 TGTGTCTATGCCTTTTGGGTTT 58.428 40.909 0.00 0.00 40.82 3.27
42 43 3.237268 TGTGTCTATGCCTTTTGGGTT 57.763 42.857 0.00 0.00 40.82 4.11
43 44 2.969821 TGTGTCTATGCCTTTTGGGT 57.030 45.000 0.00 0.00 40.82 4.51
44 45 3.316308 GCTATGTGTCTATGCCTTTTGGG 59.684 47.826 0.00 0.00 40.82 4.12
45 46 3.947196 TGCTATGTGTCTATGCCTTTTGG 59.053 43.478 0.00 0.00 44.18 3.28
46 47 4.877823 TCTGCTATGTGTCTATGCCTTTTG 59.122 41.667 0.00 0.00 0.00 2.44
47 48 5.102953 TCTGCTATGTGTCTATGCCTTTT 57.897 39.130 0.00 0.00 0.00 2.27
48 49 4.760530 TCTGCTATGTGTCTATGCCTTT 57.239 40.909 0.00 0.00 0.00 3.11
49 50 4.760530 TTCTGCTATGTGTCTATGCCTT 57.239 40.909 0.00 0.00 0.00 4.35
50 51 4.701765 CTTTCTGCTATGTGTCTATGCCT 58.298 43.478 0.00 0.00 0.00 4.75
51 52 3.249559 GCTTTCTGCTATGTGTCTATGCC 59.750 47.826 0.00 0.00 38.95 4.40
52 53 4.465040 GCTTTCTGCTATGTGTCTATGC 57.535 45.455 0.00 0.00 38.95 3.14
74 75 6.240894 AGACAGCTTTCATTACTCAATTGGA 58.759 36.000 5.42 0.00 0.00 3.53
75 76 6.506500 AGACAGCTTTCATTACTCAATTGG 57.493 37.500 5.42 0.00 0.00 3.16
76 77 7.814642 AGAAGACAGCTTTCATTACTCAATTG 58.185 34.615 2.12 0.00 33.61 2.32
77 78 7.120432 GGAGAAGACAGCTTTCATTACTCAATT 59.880 37.037 2.12 0.00 33.61 2.32
78 79 6.597280 GGAGAAGACAGCTTTCATTACTCAAT 59.403 38.462 2.12 0.00 33.61 2.57
79 80 5.934625 GGAGAAGACAGCTTTCATTACTCAA 59.065 40.000 2.12 0.00 33.61 3.02
80 81 5.247110 AGGAGAAGACAGCTTTCATTACTCA 59.753 40.000 2.12 0.00 33.61 3.41
81 82 5.580297 CAGGAGAAGACAGCTTTCATTACTC 59.420 44.000 2.12 5.18 33.61 2.59
82 83 5.247110 TCAGGAGAAGACAGCTTTCATTACT 59.753 40.000 2.12 0.00 33.61 2.24
83 84 5.482908 TCAGGAGAAGACAGCTTTCATTAC 58.517 41.667 2.12 0.00 33.61 1.89
84 85 5.745312 TCAGGAGAAGACAGCTTTCATTA 57.255 39.130 2.12 0.00 33.61 1.90
85 86 4.630644 TCAGGAGAAGACAGCTTTCATT 57.369 40.909 2.12 0.00 33.61 2.57
86 87 4.383989 GGATCAGGAGAAGACAGCTTTCAT 60.384 45.833 2.12 0.00 33.61 2.57
87 88 3.055530 GGATCAGGAGAAGACAGCTTTCA 60.056 47.826 2.12 0.00 33.61 2.69
88 89 3.197549 AGGATCAGGAGAAGACAGCTTTC 59.802 47.826 0.00 0.00 33.61 2.62
89 90 3.180507 AGGATCAGGAGAAGACAGCTTT 58.819 45.455 0.00 0.00 33.61 3.51
90 91 2.831565 AGGATCAGGAGAAGACAGCTT 58.168 47.619 0.00 0.00 36.96 3.74
91 92 2.500910 CAAGGATCAGGAGAAGACAGCT 59.499 50.000 0.00 0.00 0.00 4.24
92 93 2.499289 TCAAGGATCAGGAGAAGACAGC 59.501 50.000 0.00 0.00 0.00 4.40
93 94 4.499526 CGATCAAGGATCAGGAGAAGACAG 60.500 50.000 6.98 0.00 38.84 3.51
94 95 3.382865 CGATCAAGGATCAGGAGAAGACA 59.617 47.826 6.98 0.00 38.84 3.41
95 96 3.798548 GCGATCAAGGATCAGGAGAAGAC 60.799 52.174 6.98 0.00 38.84 3.01
96 97 2.363680 GCGATCAAGGATCAGGAGAAGA 59.636 50.000 6.98 0.00 38.84 2.87
97 98 2.547642 GGCGATCAAGGATCAGGAGAAG 60.548 54.545 6.98 0.00 38.84 2.85
98 99 1.414181 GGCGATCAAGGATCAGGAGAA 59.586 52.381 6.98 0.00 38.84 2.87
99 100 1.043816 GGCGATCAAGGATCAGGAGA 58.956 55.000 6.98 0.00 38.84 3.71
100 101 0.755079 TGGCGATCAAGGATCAGGAG 59.245 55.000 6.98 0.00 38.84 3.69
101 102 1.345741 GATGGCGATCAAGGATCAGGA 59.654 52.381 3.53 0.00 38.84 3.86
102 103 1.347050 AGATGGCGATCAAGGATCAGG 59.653 52.381 11.55 0.00 38.84 3.86
103 104 2.835580 AGATGGCGATCAAGGATCAG 57.164 50.000 11.55 1.57 38.84 2.90
104 105 4.687901 TTAAGATGGCGATCAAGGATCA 57.312 40.909 11.55 0.00 38.84 2.92
105 106 5.350914 CAGATTAAGATGGCGATCAAGGATC 59.649 44.000 11.55 8.41 35.88 3.36
106 107 5.012458 TCAGATTAAGATGGCGATCAAGGAT 59.988 40.000 11.55 0.00 0.00 3.24
107 108 4.344968 TCAGATTAAGATGGCGATCAAGGA 59.655 41.667 11.55 0.00 0.00 3.36
108 109 4.635223 TCAGATTAAGATGGCGATCAAGG 58.365 43.478 11.55 0.00 0.00 3.61
109 110 5.930569 TCATCAGATTAAGATGGCGATCAAG 59.069 40.000 11.55 0.00 42.38 3.02
110 111 5.857268 TCATCAGATTAAGATGGCGATCAA 58.143 37.500 11.55 0.00 42.38 2.57
111 112 5.473066 TCATCAGATTAAGATGGCGATCA 57.527 39.130 11.55 0.00 42.38 2.92
112 113 5.873712 ACATCATCAGATTAAGATGGCGATC 59.126 40.000 11.89 0.00 42.38 3.69
113 114 5.802465 ACATCATCAGATTAAGATGGCGAT 58.198 37.500 11.89 0.00 42.38 4.58
114 115 5.219343 ACATCATCAGATTAAGATGGCGA 57.781 39.130 11.89 0.00 42.38 5.54
115 116 5.467735 TCAACATCATCAGATTAAGATGGCG 59.532 40.000 11.89 4.83 42.38 5.69
116 117 6.872628 TCAACATCATCAGATTAAGATGGC 57.127 37.500 11.89 0.00 42.38 4.40
117 118 7.519488 CGGTTCAACATCATCAGATTAAGATGG 60.519 40.741 11.89 0.00 42.38 3.51
118 119 7.350467 CGGTTCAACATCATCAGATTAAGATG 58.650 38.462 7.40 7.40 43.25 2.90
119 120 6.484643 CCGGTTCAACATCATCAGATTAAGAT 59.515 38.462 0.00 0.00 30.20 2.40
120 121 5.817296 CCGGTTCAACATCATCAGATTAAGA 59.183 40.000 0.00 0.00 30.20 2.10
121 122 5.586243 ACCGGTTCAACATCATCAGATTAAG 59.414 40.000 0.00 0.00 30.20 1.85
122 123 5.496556 ACCGGTTCAACATCATCAGATTAA 58.503 37.500 0.00 0.00 30.20 1.40
123 124 5.097742 ACCGGTTCAACATCATCAGATTA 57.902 39.130 0.00 0.00 30.20 1.75
124 125 3.955471 ACCGGTTCAACATCATCAGATT 58.045 40.909 0.00 0.00 30.20 2.40
125 126 3.634397 ACCGGTTCAACATCATCAGAT 57.366 42.857 0.00 0.00 33.87 2.90
126 127 4.441792 CATACCGGTTCAACATCATCAGA 58.558 43.478 15.04 0.00 0.00 3.27
127 128 3.561310 CCATACCGGTTCAACATCATCAG 59.439 47.826 15.04 0.00 0.00 2.90
128 129 3.540617 CCATACCGGTTCAACATCATCA 58.459 45.455 15.04 0.00 0.00 3.07
129 130 2.878406 CCCATACCGGTTCAACATCATC 59.122 50.000 15.04 0.00 0.00 2.92
132 133 1.021968 GCCCATACCGGTTCAACATC 58.978 55.000 15.04 0.00 0.00 3.06
291 292 1.301401 GTACCTTCACACAGCGCCA 60.301 57.895 2.29 0.00 0.00 5.69
347 349 2.047560 GACTACGCCGCCACCTTT 60.048 61.111 0.00 0.00 0.00 3.11
538 541 2.581354 CTTCGCAGCTAGCCACCT 59.419 61.111 12.13 0.00 41.38 4.00
598 601 1.990060 CCTCCTCTTCTTCCCGCCA 60.990 63.158 0.00 0.00 0.00 5.69
816 823 0.827925 TCCAGAACGAGCAGTCCAGT 60.828 55.000 0.00 0.00 0.00 4.00
1874 1893 1.277557 CACTTCTACCTCTGCCTGCTT 59.722 52.381 0.00 0.00 0.00 3.91
2072 2091 3.371034 TCCGGATTACCTTCATCAGTGA 58.629 45.455 0.00 0.00 0.00 3.41
2370 2389 2.900716 TGTCAAGGATCACACGACAA 57.099 45.000 0.00 0.00 33.86 3.18
2462 2481 1.573108 CACCTCCTGGTCCATGTACT 58.427 55.000 0.00 0.00 46.60 2.73
2697 2720 6.633500 TCCGAATGAATAAGCATAAAAGGG 57.367 37.500 0.00 0.00 0.00 3.95
2845 2868 7.004555 TCTTTACAAGAGCATGGAAGTTCTA 57.995 36.000 2.25 0.00 32.71 2.10
2898 2921 0.533491 CCGTTCCATTGTCCGTCCTA 59.467 55.000 0.00 0.00 0.00 2.94
3031 3055 1.673033 CGACCGAGCAACCTCAAGAAT 60.673 52.381 0.00 0.00 38.00 2.40
3266 3290 2.171448 AGAAAGACACACTTCACTGCCT 59.829 45.455 0.00 0.00 37.93 4.75


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

AutoCloner maintained by Alex Coulton.