Multiple sequence alignment - TraesCS4A01G239400

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 TraesCS4A01G239400 chr4A 100.000 3454 0 0 1 3454 548526431 548522978 0.000000e+00 6379
1 TraesCS4A01G239400 chr4B 99.083 3272 27 2 185 3454 439195477 439198747 0.000000e+00 5873
2 TraesCS4A01G239400 chr4B 95.676 185 4 2 1 185 71597772 71597952 9.370000e-76 294
3 TraesCS4A01G239400 chr6A 99.022 3272 30 1 185 3454 466092189 466095460 0.000000e+00 5864
4 TraesCS4A01G239400 chr5A 98.594 3272 19 4 185 3454 422075408 422072162 0.000000e+00 5762
5 TraesCS4A01G239400 chr6B 97.802 3275 64 5 185 3454 698114883 698118154 0.000000e+00 5642
6 TraesCS4A01G239400 chr6B 97.035 3272 84 2 184 3454 458495684 458498943 0.000000e+00 5493
7 TraesCS4A01G239400 chr6B 99.129 2526 21 1 929 3454 325035064 325037588 0.000000e+00 4542
8 TraesCS4A01G239400 chr1A 99.296 2558 18 0 897 3454 80308210 80305653 0.000000e+00 4625
9 TraesCS4A01G239400 chr7A 99.367 2526 16 0 929 3454 176257263 176259788 0.000000e+00 4577
10 TraesCS4A01G239400 chr7A 97.625 758 15 2 185 940 176256562 176257318 0.000000e+00 1297
11 TraesCS4A01G239400 chr2A 99.287 2526 18 0 929 3454 642923998 642921473 0.000000e+00 4566
12 TraesCS4A01G239400 chr2A 96.719 762 20 4 185 943 642924699 642923940 0.000000e+00 1264
13 TraesCS4A01G239400 chr5B 99.129 2526 22 0 929 3454 161075547 161078072 0.000000e+00 4543
14 TraesCS4A01G239400 chr5B 98.021 758 12 2 185 940 161074846 161075602 0.000000e+00 1314
15 TraesCS4A01G239400 chr7D 90.981 754 41 19 182 924 264763319 264764056 0.000000e+00 990
16 TraesCS4A01G239400 chr2D 90.642 748 43 20 185 924 33017492 33018220 0.000000e+00 968
17 TraesCS4A01G239400 chr4D 92.391 184 9 2 1 184 48716120 48716298 1.230000e-64 257


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 TraesCS4A01G239400 chr4A 548522978 548526431 3453 True 6379.0 6379 100.000 1 3454 1 chr4A.!!$R1 3453
1 TraesCS4A01G239400 chr4B 439195477 439198747 3270 False 5873.0 5873 99.083 185 3454 1 chr4B.!!$F2 3269
2 TraesCS4A01G239400 chr6A 466092189 466095460 3271 False 5864.0 5864 99.022 185 3454 1 chr6A.!!$F1 3269
3 TraesCS4A01G239400 chr5A 422072162 422075408 3246 True 5762.0 5762 98.594 185 3454 1 chr5A.!!$R1 3269
4 TraesCS4A01G239400 chr6B 698114883 698118154 3271 False 5642.0 5642 97.802 185 3454 1 chr6B.!!$F3 3269
5 TraesCS4A01G239400 chr6B 458495684 458498943 3259 False 5493.0 5493 97.035 184 3454 1 chr6B.!!$F2 3270
6 TraesCS4A01G239400 chr6B 325035064 325037588 2524 False 4542.0 4542 99.129 929 3454 1 chr6B.!!$F1 2525
7 TraesCS4A01G239400 chr1A 80305653 80308210 2557 True 4625.0 4625 99.296 897 3454 1 chr1A.!!$R1 2557
8 TraesCS4A01G239400 chr7A 176256562 176259788 3226 False 2937.0 4577 98.496 185 3454 2 chr7A.!!$F1 3269
9 TraesCS4A01G239400 chr2A 642921473 642924699 3226 True 2915.0 4566 98.003 185 3454 2 chr2A.!!$R1 3269
10 TraesCS4A01G239400 chr5B 161074846 161078072 3226 False 2928.5 4543 98.575 185 3454 2 chr5B.!!$F1 3269
11 TraesCS4A01G239400 chr7D 264763319 264764056 737 False 990.0 990 90.981 182 924 1 chr7D.!!$F1 742
12 TraesCS4A01G239400 chr2D 33017492 33018220 728 False 968.0 968 90.642 185 924 1 chr2D.!!$F1 739

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
109 110 0.177373 AGAATGATCAGCTCTGCGCA 59.823 50.000 10.98 10.98 42.61 6.09 F
110 111 0.582482 GAATGATCAGCTCTGCGCAG 59.418 55.000 31.53 31.53 42.61 5.18 F
986 1084 1.066002 TGAGTTTTGCTGTTGCTGCTC 59.934 47.619 0.00 0.00 40.48 4.26 F
2067 2165 1.818642 ATGGAGACTTTGCTCACTGC 58.181 50.000 0.00 0.00 43.25 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1850 1948 2.982488 CCTCTGTTATATCCCCTGCCTT 59.018 50.000 0.0 0.0 0.00 4.35 R
2067 2165 4.528674 CCTTCATCAGTGGAGGCG 57.471 61.111 0.0 0.0 44.15 5.52 R
2420 2518 2.525629 TCCCAACCGTCTGGCTCA 60.526 61.111 0.0 0.0 39.70 4.26 R
3387 3489 2.362397 GAGATCAGTCGGCTCACCATAA 59.638 50.000 0.0 0.0 34.57 1.90 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
20 21 2.797177 AGAATGAGAAAGGCCTCCAC 57.203 50.000 5.23 0.00 32.32 4.02
21 22 1.283321 AGAATGAGAAAGGCCTCCACC 59.717 52.381 5.23 0.00 32.32 4.61
22 23 0.332972 AATGAGAAAGGCCTCCACCC 59.667 55.000 5.23 0.00 32.32 4.61
23 24 0.551131 ATGAGAAAGGCCTCCACCCT 60.551 55.000 5.23 0.00 32.32 4.34
24 25 0.772124 TGAGAAAGGCCTCCACCCTT 60.772 55.000 5.23 0.00 44.35 3.95
25 26 0.322906 GAGAAAGGCCTCCACCCTTG 60.323 60.000 5.23 0.00 41.70 3.61
26 27 1.304464 GAAAGGCCTCCACCCTTGG 60.304 63.158 5.23 0.00 41.70 3.61
27 28 2.081585 GAAAGGCCTCCACCCTTGGT 62.082 60.000 5.23 0.00 44.35 3.67
36 37 4.599860 ACCCTTGGTGCCTATCCA 57.400 55.556 0.00 0.00 32.98 3.41
37 38 2.799576 ACCCTTGGTGCCTATCCAA 58.200 52.632 0.00 0.00 41.84 3.53
38 39 1.080638 ACCCTTGGTGCCTATCCAAA 58.919 50.000 0.00 0.00 43.16 3.28
39 40 1.272480 ACCCTTGGTGCCTATCCAAAC 60.272 52.381 0.00 0.00 43.16 2.93
40 41 1.005924 CCCTTGGTGCCTATCCAAACT 59.994 52.381 0.00 0.00 43.16 2.66
41 42 2.557452 CCCTTGGTGCCTATCCAAACTT 60.557 50.000 0.00 0.00 43.16 2.66
42 43 2.755103 CCTTGGTGCCTATCCAAACTTC 59.245 50.000 0.00 0.00 43.16 3.01
43 44 2.107950 TGGTGCCTATCCAAACTTCG 57.892 50.000 0.00 0.00 31.50 3.79
44 45 1.626321 TGGTGCCTATCCAAACTTCGA 59.374 47.619 0.00 0.00 31.50 3.71
45 46 2.039216 TGGTGCCTATCCAAACTTCGAA 59.961 45.455 0.00 0.00 31.50 3.71
46 47 2.678336 GGTGCCTATCCAAACTTCGAAG 59.322 50.000 23.43 23.43 0.00 3.79
47 48 3.335579 GTGCCTATCCAAACTTCGAAGT 58.664 45.455 24.93 24.93 42.04 3.01
58 59 4.402056 AACTTCGAAGTTTCACTGAGGA 57.598 40.909 32.60 0.00 46.52 3.71
59 60 4.608948 ACTTCGAAGTTTCACTGAGGAT 57.391 40.909 24.93 0.00 35.21 3.24
60 61 4.962155 ACTTCGAAGTTTCACTGAGGATT 58.038 39.130 24.93 0.00 35.21 3.01
61 62 4.752101 ACTTCGAAGTTTCACTGAGGATTG 59.248 41.667 24.93 0.00 35.21 2.67
62 63 4.600692 TCGAAGTTTCACTGAGGATTGA 57.399 40.909 0.00 0.00 0.00 2.57
63 64 4.307432 TCGAAGTTTCACTGAGGATTGAC 58.693 43.478 0.00 0.00 0.00 3.18
64 65 3.121944 CGAAGTTTCACTGAGGATTGACG 59.878 47.826 0.00 0.00 0.00 4.35
65 66 2.417719 AGTTTCACTGAGGATTGACGC 58.582 47.619 0.00 0.00 0.00 5.19
66 67 2.037772 AGTTTCACTGAGGATTGACGCT 59.962 45.455 0.00 0.00 0.00 5.07
67 68 2.808543 GTTTCACTGAGGATTGACGCTT 59.191 45.455 0.00 0.00 0.00 4.68
68 69 2.839486 TCACTGAGGATTGACGCTTT 57.161 45.000 0.00 0.00 0.00 3.51
69 70 2.688507 TCACTGAGGATTGACGCTTTC 58.311 47.619 0.00 0.00 0.00 2.62
70 71 2.037121 TCACTGAGGATTGACGCTTTCA 59.963 45.455 0.00 0.00 0.00 2.69
71 72 2.414481 CACTGAGGATTGACGCTTTCAG 59.586 50.000 0.00 0.00 38.34 3.02
72 73 2.037772 ACTGAGGATTGACGCTTTCAGT 59.962 45.455 0.00 0.00 40.11 3.41
73 74 3.258372 ACTGAGGATTGACGCTTTCAGTA 59.742 43.478 3.34 0.00 42.31 2.74
74 75 3.849911 TGAGGATTGACGCTTTCAGTAG 58.150 45.455 0.00 0.00 34.94 2.57
75 76 2.605366 GAGGATTGACGCTTTCAGTAGC 59.395 50.000 0.00 0.00 34.94 3.58
81 82 2.698020 GCTTTCAGTAGCGCGCTC 59.302 61.111 40.23 27.53 0.00 5.03
82 83 2.803713 GCTTTCAGTAGCGCGCTCC 61.804 63.158 40.23 28.58 0.00 4.70
83 84 1.153745 CTTTCAGTAGCGCGCTCCT 60.154 57.895 40.23 30.72 0.00 3.69
84 85 1.142778 CTTTCAGTAGCGCGCTCCTC 61.143 60.000 40.23 27.20 0.00 3.71
85 86 1.873270 TTTCAGTAGCGCGCTCCTCA 61.873 55.000 40.23 17.44 0.00 3.86
86 87 1.873270 TTCAGTAGCGCGCTCCTCAA 61.873 55.000 40.23 23.53 0.00 3.02
87 88 1.227089 CAGTAGCGCGCTCCTCAAT 60.227 57.895 40.23 17.52 0.00 2.57
88 89 1.227089 AGTAGCGCGCTCCTCAATG 60.227 57.895 40.23 0.00 0.00 2.82
89 90 2.106938 TAGCGCGCTCCTCAATGG 59.893 61.111 40.23 0.00 37.10 3.16
90 91 2.423064 TAGCGCGCTCCTCAATGGA 61.423 57.895 40.23 14.56 43.86 3.41
101 102 4.082665 TCCTCAATGGAGAATGATCAGC 57.917 45.455 0.09 0.00 44.26 4.26
102 103 3.715315 TCCTCAATGGAGAATGATCAGCT 59.285 43.478 0.09 0.51 44.26 4.24
103 104 4.066490 CCTCAATGGAGAATGATCAGCTC 58.934 47.826 16.23 16.23 44.26 4.09
104 105 4.202377 CCTCAATGGAGAATGATCAGCTCT 60.202 45.833 21.08 15.92 44.26 4.09
105 106 4.704965 TCAATGGAGAATGATCAGCTCTG 58.295 43.478 21.08 14.62 0.00 3.35
106 107 2.616634 TGGAGAATGATCAGCTCTGC 57.383 50.000 21.08 19.26 0.00 4.26
107 108 1.202498 TGGAGAATGATCAGCTCTGCG 60.202 52.381 21.08 0.00 30.75 5.18
108 109 0.860533 GAGAATGATCAGCTCTGCGC 59.139 55.000 16.92 0.00 39.57 6.09
109 110 0.177373 AGAATGATCAGCTCTGCGCA 59.823 50.000 10.98 10.98 42.61 6.09
110 111 0.582482 GAATGATCAGCTCTGCGCAG 59.418 55.000 31.53 31.53 42.61 5.18
128 129 5.136250 CGCAGCAACAAACAAAATAAACA 57.864 34.783 0.00 0.00 0.00 2.83
129 130 5.189625 CGCAGCAACAAACAAAATAAACAG 58.810 37.500 0.00 0.00 0.00 3.16
130 131 5.005203 CGCAGCAACAAACAAAATAAACAGA 59.995 36.000 0.00 0.00 0.00 3.41
131 132 6.454848 CGCAGCAACAAACAAAATAAACAGAA 60.455 34.615 0.00 0.00 0.00 3.02
132 133 6.682441 GCAGCAACAAACAAAATAAACAGAAC 59.318 34.615 0.00 0.00 0.00 3.01
133 134 7.412891 GCAGCAACAAACAAAATAAACAGAACT 60.413 33.333 0.00 0.00 0.00 3.01
134 135 8.110002 CAGCAACAAACAAAATAAACAGAACTC 58.890 33.333 0.00 0.00 0.00 3.01
135 136 8.034804 AGCAACAAACAAAATAAACAGAACTCT 58.965 29.630 0.00 0.00 0.00 3.24
173 174 5.518848 AAAATGATGAACAGAACACAGCA 57.481 34.783 0.00 0.00 34.61 4.41
174 175 4.494350 AATGATGAACAGAACACAGCAC 57.506 40.909 0.00 0.00 33.01 4.40
175 176 2.916640 TGATGAACAGAACACAGCACA 58.083 42.857 0.00 0.00 0.00 4.57
176 177 3.277715 TGATGAACAGAACACAGCACAA 58.722 40.909 0.00 0.00 0.00 3.33
177 178 3.693578 TGATGAACAGAACACAGCACAAA 59.306 39.130 0.00 0.00 0.00 2.83
178 179 3.763097 TGAACAGAACACAGCACAAAG 57.237 42.857 0.00 0.00 0.00 2.77
179 180 3.081061 TGAACAGAACACAGCACAAAGT 58.919 40.909 0.00 0.00 0.00 2.66
180 181 4.257731 TGAACAGAACACAGCACAAAGTA 58.742 39.130 0.00 0.00 0.00 2.24
692 700 3.426615 CACTAGTGGAGAGAAGGAGTGT 58.573 50.000 15.49 0.00 0.00 3.55
863 871 1.553651 GGGAGAAGGAAGAGGAGGTGT 60.554 57.143 0.00 0.00 0.00 4.16
986 1084 1.066002 TGAGTTTTGCTGTTGCTGCTC 59.934 47.619 0.00 0.00 40.48 4.26
2067 2165 1.818642 ATGGAGACTTTGCTCACTGC 58.181 50.000 0.00 0.00 43.25 4.40
2420 2518 2.625737 CTTGATTCAGGTGCGACAGAT 58.374 47.619 0.00 0.00 0.00 2.90
2845 2943 5.140454 AGGATGAGGTGTTTAGCTGTTTTT 58.860 37.500 0.00 0.00 34.13 1.94
3296 3398 5.071788 TGAAGTGTGTCTTTCTGGGATACTT 59.928 40.000 0.00 0.00 36.40 2.24
3387 3489 1.661463 TCAGGGAGTCTGAGCCATTT 58.339 50.000 0.00 0.00 46.71 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.291217 GGTGGAGGCCTTTCTCATTCTT 60.291 50.000 6.77 0.00 35.58 2.52
1 2 1.283321 GGTGGAGGCCTTTCTCATTCT 59.717 52.381 6.77 0.00 35.58 2.40
2 3 1.683319 GGGTGGAGGCCTTTCTCATTC 60.683 57.143 6.77 0.00 35.58 2.67
3 4 0.332972 GGGTGGAGGCCTTTCTCATT 59.667 55.000 6.77 0.00 35.58 2.57
4 5 0.551131 AGGGTGGAGGCCTTTCTCAT 60.551 55.000 6.77 0.00 35.58 2.90
5 6 0.772124 AAGGGTGGAGGCCTTTCTCA 60.772 55.000 6.77 0.20 35.58 3.27
6 7 0.322906 CAAGGGTGGAGGCCTTTCTC 60.323 60.000 6.77 3.53 0.00 2.87
7 8 1.770324 CAAGGGTGGAGGCCTTTCT 59.230 57.895 6.77 0.00 0.00 2.52
8 9 4.423231 CAAGGGTGGAGGCCTTTC 57.577 61.111 6.77 2.94 0.00 2.62
19 20 1.080638 TTTGGATAGGCACCAAGGGT 58.919 50.000 9.83 0.00 46.05 4.34
20 21 1.005924 AGTTTGGATAGGCACCAAGGG 59.994 52.381 9.83 0.00 46.05 3.95
21 22 2.514458 AGTTTGGATAGGCACCAAGG 57.486 50.000 9.83 0.00 46.05 3.61
22 23 2.420022 CGAAGTTTGGATAGGCACCAAG 59.580 50.000 9.83 0.00 46.05 3.61
23 24 2.039216 TCGAAGTTTGGATAGGCACCAA 59.961 45.455 6.70 6.70 44.27 3.67
24 25 1.626321 TCGAAGTTTGGATAGGCACCA 59.374 47.619 0.00 0.00 35.47 4.17
25 26 2.396590 TCGAAGTTTGGATAGGCACC 57.603 50.000 0.00 0.00 0.00 5.01
26 27 3.335579 ACTTCGAAGTTTGGATAGGCAC 58.664 45.455 24.93 0.00 35.21 5.01
27 28 3.695830 ACTTCGAAGTTTGGATAGGCA 57.304 42.857 24.93 0.00 35.21 4.75
46 47 2.417719 AGCGTCAATCCTCAGTGAAAC 58.582 47.619 0.00 0.00 0.00 2.78
47 48 2.839486 AGCGTCAATCCTCAGTGAAA 57.161 45.000 0.00 0.00 0.00 2.69
48 49 2.839486 AAGCGTCAATCCTCAGTGAA 57.161 45.000 0.00 0.00 0.00 3.18
49 50 2.037121 TGAAAGCGTCAATCCTCAGTGA 59.963 45.455 0.00 0.00 31.51 3.41
50 51 2.414481 CTGAAAGCGTCAATCCTCAGTG 59.586 50.000 0.00 0.00 35.22 3.66
51 52 2.037772 ACTGAAAGCGTCAATCCTCAGT 59.962 45.455 0.00 0.00 38.88 3.41
52 53 2.693069 ACTGAAAGCGTCAATCCTCAG 58.307 47.619 0.00 0.00 37.60 3.35
53 54 2.839486 ACTGAAAGCGTCAATCCTCA 57.161 45.000 0.00 0.00 37.60 3.86
54 55 2.605366 GCTACTGAAAGCGTCAATCCTC 59.395 50.000 0.00 0.00 37.60 3.71
55 56 2.622436 GCTACTGAAAGCGTCAATCCT 58.378 47.619 0.00 0.00 37.60 3.24
64 65 2.698020 GAGCGCGCTACTGAAAGC 59.302 61.111 36.69 15.60 37.60 3.51
65 66 1.153745 AGGAGCGCGCTACTGAAAG 60.154 57.895 43.43 0.00 35.56 2.62
66 67 2.970639 AGGAGCGCGCTACTGAAA 59.029 55.556 43.43 0.00 35.56 2.69
70 71 1.227089 CATTGAGGAGCGCGCTACT 60.227 57.895 44.53 44.53 40.55 2.57
71 72 2.240500 CCATTGAGGAGCGCGCTAC 61.241 63.158 36.01 36.01 41.22 3.58
72 73 2.106938 CCATTGAGGAGCGCGCTA 59.893 61.111 36.69 19.60 41.22 4.26
73 74 3.774528 TCCATTGAGGAGCGCGCT 61.775 61.111 37.28 37.28 43.07 5.92
80 81 3.715315 AGCTGATCATTCTCCATTGAGGA 59.285 43.478 0.00 0.00 46.75 3.71
81 82 4.066490 GAGCTGATCATTCTCCATTGAGG 58.934 47.826 11.91 0.00 39.23 3.86
82 83 4.752604 CAGAGCTGATCATTCTCCATTGAG 59.247 45.833 16.87 0.00 40.17 3.02
83 84 4.704965 CAGAGCTGATCATTCTCCATTGA 58.295 43.478 16.87 0.00 0.00 2.57
84 85 3.251245 GCAGAGCTGATCATTCTCCATTG 59.749 47.826 16.87 12.01 0.00 2.82
85 86 3.478509 GCAGAGCTGATCATTCTCCATT 58.521 45.455 16.87 2.15 0.00 3.16
86 87 2.548280 CGCAGAGCTGATCATTCTCCAT 60.548 50.000 16.87 2.70 0.00 3.41
87 88 1.202498 CGCAGAGCTGATCATTCTCCA 60.202 52.381 16.87 0.00 0.00 3.86
88 89 1.500108 CGCAGAGCTGATCATTCTCC 58.500 55.000 16.87 5.27 0.00 3.71
89 90 0.860533 GCGCAGAGCTGATCATTCTC 59.139 55.000 0.30 14.10 44.04 2.87
90 91 2.989196 GCGCAGAGCTGATCATTCT 58.011 52.632 0.30 0.00 44.04 2.40
101 102 0.248580 TTGTTTGTTGCTGCGCAGAG 60.249 50.000 40.21 17.53 40.61 3.35
102 103 0.172127 TTTGTTTGTTGCTGCGCAGA 59.828 45.000 40.21 22.16 40.61 4.26
103 104 0.997932 TTTTGTTTGTTGCTGCGCAG 59.002 45.000 32.83 32.83 40.61 5.18
104 105 1.649664 ATTTTGTTTGTTGCTGCGCA 58.350 40.000 10.98 10.98 36.47 6.09
105 106 3.850657 TTATTTTGTTTGTTGCTGCGC 57.149 38.095 0.00 0.00 0.00 6.09
106 107 5.005203 TCTGTTTATTTTGTTTGTTGCTGCG 59.995 36.000 0.00 0.00 0.00 5.18
107 108 6.343226 TCTGTTTATTTTGTTTGTTGCTGC 57.657 33.333 0.00 0.00 0.00 5.25
108 109 7.962917 AGTTCTGTTTATTTTGTTTGTTGCTG 58.037 30.769 0.00 0.00 0.00 4.41
109 110 8.034804 AGAGTTCTGTTTATTTTGTTTGTTGCT 58.965 29.630 0.00 0.00 0.00 3.91
110 111 8.110002 CAGAGTTCTGTTTATTTTGTTTGTTGC 58.890 33.333 0.91 0.00 39.09 4.17
111 112 8.110002 GCAGAGTTCTGTTTATTTTGTTTGTTG 58.890 33.333 10.57 0.00 45.45 3.33
112 113 7.816995 TGCAGAGTTCTGTTTATTTTGTTTGTT 59.183 29.630 10.57 0.00 45.45 2.83
113 114 7.275560 GTGCAGAGTTCTGTTTATTTTGTTTGT 59.724 33.333 10.57 0.00 45.45 2.83
114 115 7.513505 CGTGCAGAGTTCTGTTTATTTTGTTTG 60.514 37.037 10.57 0.00 45.45 2.93
115 116 6.472163 CGTGCAGAGTTCTGTTTATTTTGTTT 59.528 34.615 10.57 0.00 45.45 2.83
116 117 5.971202 CGTGCAGAGTTCTGTTTATTTTGTT 59.029 36.000 10.57 0.00 45.45 2.83
117 118 5.295787 TCGTGCAGAGTTCTGTTTATTTTGT 59.704 36.000 10.57 0.00 45.45 2.83
118 119 5.621228 GTCGTGCAGAGTTCTGTTTATTTTG 59.379 40.000 10.57 0.00 45.45 2.44
119 120 5.295787 TGTCGTGCAGAGTTCTGTTTATTTT 59.704 36.000 10.57 0.00 45.45 1.82
120 121 4.814234 TGTCGTGCAGAGTTCTGTTTATTT 59.186 37.500 10.57 0.00 45.45 1.40
121 122 4.377021 TGTCGTGCAGAGTTCTGTTTATT 58.623 39.130 10.57 0.00 45.45 1.40
122 123 3.990092 TGTCGTGCAGAGTTCTGTTTAT 58.010 40.909 10.57 0.00 45.45 1.40
123 124 3.446310 TGTCGTGCAGAGTTCTGTTTA 57.554 42.857 10.57 0.00 45.45 2.01
124 125 2.309528 TGTCGTGCAGAGTTCTGTTT 57.690 45.000 10.57 0.00 45.45 2.83
150 151 5.750067 GTGCTGTGTTCTGTTCATCATTTTT 59.250 36.000 0.00 0.00 0.00 1.94
151 152 5.163530 TGTGCTGTGTTCTGTTCATCATTTT 60.164 36.000 0.00 0.00 0.00 1.82
152 153 4.338964 TGTGCTGTGTTCTGTTCATCATTT 59.661 37.500 0.00 0.00 0.00 2.32
153 154 3.884693 TGTGCTGTGTTCTGTTCATCATT 59.115 39.130 0.00 0.00 0.00 2.57
154 155 3.479489 TGTGCTGTGTTCTGTTCATCAT 58.521 40.909 0.00 0.00 0.00 2.45
155 156 2.916640 TGTGCTGTGTTCTGTTCATCA 58.083 42.857 0.00 0.00 0.00 3.07
156 157 3.969117 TTGTGCTGTGTTCTGTTCATC 57.031 42.857 0.00 0.00 0.00 2.92
157 158 3.696051 ACTTTGTGCTGTGTTCTGTTCAT 59.304 39.130 0.00 0.00 0.00 2.57
158 159 3.081061 ACTTTGTGCTGTGTTCTGTTCA 58.919 40.909 0.00 0.00 0.00 3.18
159 160 3.764885 ACTTTGTGCTGTGTTCTGTTC 57.235 42.857 0.00 0.00 0.00 3.18
160 161 5.183140 ACTTTACTTTGTGCTGTGTTCTGTT 59.817 36.000 0.00 0.00 0.00 3.16
161 162 4.700213 ACTTTACTTTGTGCTGTGTTCTGT 59.300 37.500 0.00 0.00 0.00 3.41
162 163 5.030295 CACTTTACTTTGTGCTGTGTTCTG 58.970 41.667 0.00 0.00 0.00 3.02
163 164 4.700213 ACACTTTACTTTGTGCTGTGTTCT 59.300 37.500 0.00 0.00 37.68 3.01
164 165 4.981794 ACACTTTACTTTGTGCTGTGTTC 58.018 39.130 0.00 0.00 37.68 3.18
165 166 5.048364 TCAACACTTTACTTTGTGCTGTGTT 60.048 36.000 0.00 0.00 44.53 3.32
166 167 4.457603 TCAACACTTTACTTTGTGCTGTGT 59.542 37.500 0.00 0.00 38.57 3.72
167 168 4.980590 TCAACACTTTACTTTGTGCTGTG 58.019 39.130 0.00 0.00 37.68 3.66
168 169 5.399013 GTTCAACACTTTACTTTGTGCTGT 58.601 37.500 0.00 0.00 37.68 4.40
169 170 4.798387 GGTTCAACACTTTACTTTGTGCTG 59.202 41.667 0.00 0.00 37.68 4.41
170 171 4.438200 CGGTTCAACACTTTACTTTGTGCT 60.438 41.667 0.00 0.00 37.68 4.40
171 172 3.789224 CGGTTCAACACTTTACTTTGTGC 59.211 43.478 0.00 0.00 37.68 4.57
172 173 4.142556 ACCGGTTCAACACTTTACTTTGTG 60.143 41.667 0.00 0.00 39.80 3.33
173 174 4.011698 ACCGGTTCAACACTTTACTTTGT 58.988 39.130 0.00 0.00 0.00 2.83
174 175 4.625972 ACCGGTTCAACACTTTACTTTG 57.374 40.909 0.00 0.00 0.00 2.77
175 176 5.239963 CCATACCGGTTCAACACTTTACTTT 59.760 40.000 15.04 0.00 0.00 2.66
176 177 4.758165 CCATACCGGTTCAACACTTTACTT 59.242 41.667 15.04 0.00 0.00 2.24
177 178 4.320870 CCATACCGGTTCAACACTTTACT 58.679 43.478 15.04 0.00 0.00 2.24
178 179 3.437741 CCCATACCGGTTCAACACTTTAC 59.562 47.826 15.04 0.00 0.00 2.01
179 180 3.677190 CCCATACCGGTTCAACACTTTA 58.323 45.455 15.04 0.00 0.00 1.85
180 181 2.510613 CCCATACCGGTTCAACACTTT 58.489 47.619 15.04 0.00 0.00 2.66
294 297 1.079750 GTTCCTCTCGTGTCTGGCC 60.080 63.158 0.00 0.00 0.00 5.36
863 871 1.134401 CCTCGCAGGAATAAGCTCCAA 60.134 52.381 0.00 0.00 37.67 3.53
1352 1450 6.436738 ACAGAATCTTCCATATCTCAGCAT 57.563 37.500 0.00 0.00 0.00 3.79
1850 1948 2.982488 CCTCTGTTATATCCCCTGCCTT 59.018 50.000 0.00 0.00 0.00 4.35
2067 2165 4.528674 CCTTCATCAGTGGAGGCG 57.471 61.111 0.00 0.00 44.15 5.52
2420 2518 2.525629 TCCCAACCGTCTGGCTCA 60.526 61.111 0.00 0.00 39.70 4.26
2845 2943 7.004555 TCTTTACAAGAGCATGGAAGTTCTA 57.995 36.000 2.25 0.00 32.71 2.10
3296 3398 2.848678 ATACCCCTGCTGACTAGACA 57.151 50.000 0.00 0.00 0.00 3.41
3387 3489 2.362397 GAGATCAGTCGGCTCACCATAA 59.638 50.000 0.00 0.00 34.57 1.90


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

AutoCloner maintained by Alex Coulton.