Multiple sequence alignment - TraesCS6D01G154100

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 TraesCS6D01G154100 chr6D 100.000 3064 0 0 1 3064 129150102 129153165 0.000000e+00 5659
1 TraesCS6D01G154100 chr6A 92.018 3032 144 43 88 3064 166508937 166505949 0.000000e+00 4169
2 TraesCS6D01G154100 chr6B 91.597 1666 65 37 847 2477 227268496 227270121 0.000000e+00 2231
3 TraesCS6D01G154100 chr6B 93.766 401 9 2 440 825 227267771 227268170 3.400000e-164 588
4 TraesCS6D01G154100 chr6B 84.927 617 39 21 2473 3064 227270175 227270762 2.650000e-160 575
5 TraesCS6D01G154100 chr6B 87.135 342 29 2 1 327 227258227 227258568 1.040000e-99 374
6 TraesCS6D01G154100 chr7D 79.291 536 79 23 1537 2065 512281824 512281314 2.260000e-91 346
7 TraesCS6D01G154100 chr7B 77.798 563 94 22 1511 2065 544139592 544139053 4.930000e-83 318
8 TraesCS6D01G154100 chr7A 78.318 535 86 22 1537 2065 585066490 585065980 4.930000e-83 318


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 TraesCS6D01G154100 chr6D 129150102 129153165 3063 False 5659.000000 5659 100.000000 1 3064 1 chr6D.!!$F1 3063
1 TraesCS6D01G154100 chr6A 166505949 166508937 2988 True 4169.000000 4169 92.018000 88 3064 1 chr6A.!!$R1 2976
2 TraesCS6D01G154100 chr6B 227267771 227270762 2991 False 1131.333333 2231 90.096667 440 3064 3 chr6B.!!$F2 2624
3 TraesCS6D01G154100 chr7D 512281314 512281824 510 True 346.000000 346 79.291000 1537 2065 1 chr7D.!!$R1 528
4 TraesCS6D01G154100 chr7B 544139053 544139592 539 True 318.000000 318 77.798000 1511 2065 1 chr7B.!!$R1 554
5 TraesCS6D01G154100 chr7A 585065980 585066490 510 True 318.000000 318 78.318000 1537 2065 1 chr7A.!!$R1 528

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
85 86 0.178992 CCAACAAGGGTCCAGCTGAA 60.179 55.0 17.39 0.0 0.0 3.02 F
1003 1353 0.034896 GGGGTCGTGTTCTGTGATGT 59.965 55.0 0.00 0.0 0.0 3.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1269 1627 0.322098 CCAACCACCGCTACCAATCA 60.322 55.0 0.0 0.0 0.0 2.57 R
2228 2614 0.598562 ACACAACACGCAAACCACAA 59.401 45.0 0.0 0.0 0.0 3.33 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
21 22 4.593597 AACATGTGTATTCGCCTTAACG 57.406 40.909 0.00 0.00 0.00 3.18
22 23 2.933906 ACATGTGTATTCGCCTTAACGG 59.066 45.455 0.00 0.00 0.00 4.44
23 24 3.191669 CATGTGTATTCGCCTTAACGGA 58.808 45.455 0.00 0.00 33.16 4.69
24 25 3.316071 TGTGTATTCGCCTTAACGGAA 57.684 42.857 0.00 0.00 33.16 4.30
25 26 3.661944 TGTGTATTCGCCTTAACGGAAA 58.338 40.909 0.00 0.00 33.16 3.13
26 27 3.432933 TGTGTATTCGCCTTAACGGAAAC 59.567 43.478 0.00 0.00 33.16 2.78
27 28 3.432933 GTGTATTCGCCTTAACGGAAACA 59.567 43.478 0.00 0.00 33.16 2.83
28 29 4.063689 TGTATTCGCCTTAACGGAAACAA 58.936 39.130 0.00 0.00 33.16 2.83
29 30 4.514441 TGTATTCGCCTTAACGGAAACAAA 59.486 37.500 0.00 0.00 33.16 2.83
30 31 4.571372 ATTCGCCTTAACGGAAACAAAA 57.429 36.364 0.00 0.00 33.16 2.44
31 32 3.612472 TCGCCTTAACGGAAACAAAAG 57.388 42.857 0.00 0.00 33.16 2.27
32 33 3.204526 TCGCCTTAACGGAAACAAAAGA 58.795 40.909 0.00 0.00 33.16 2.52
33 34 3.816523 TCGCCTTAACGGAAACAAAAGAT 59.183 39.130 0.00 0.00 33.16 2.40
34 35 3.911964 CGCCTTAACGGAAACAAAAGATG 59.088 43.478 0.00 0.00 33.16 2.90
35 36 4.319911 CGCCTTAACGGAAACAAAAGATGA 60.320 41.667 0.00 0.00 33.16 2.92
36 37 4.915667 GCCTTAACGGAAACAAAAGATGAC 59.084 41.667 0.00 0.00 33.16 3.06
37 38 5.506649 GCCTTAACGGAAACAAAAGATGACA 60.507 40.000 0.00 0.00 33.16 3.58
38 39 5.912955 CCTTAACGGAAACAAAAGATGACAC 59.087 40.000 0.00 0.00 33.16 3.67
39 40 4.974368 AACGGAAACAAAAGATGACACA 57.026 36.364 0.00 0.00 0.00 3.72
40 41 4.974368 ACGGAAACAAAAGATGACACAA 57.026 36.364 0.00 0.00 0.00 3.33
41 42 4.920376 ACGGAAACAAAAGATGACACAAG 58.080 39.130 0.00 0.00 0.00 3.16
42 43 4.202010 ACGGAAACAAAAGATGACACAAGG 60.202 41.667 0.00 0.00 0.00 3.61
43 44 4.620982 GGAAACAAAAGATGACACAAGGG 58.379 43.478 0.00 0.00 0.00 3.95
44 45 4.340950 GGAAACAAAAGATGACACAAGGGA 59.659 41.667 0.00 0.00 0.00 4.20
45 46 5.011023 GGAAACAAAAGATGACACAAGGGAT 59.989 40.000 0.00 0.00 0.00 3.85
46 47 6.208599 GGAAACAAAAGATGACACAAGGGATA 59.791 38.462 0.00 0.00 0.00 2.59
47 48 7.255801 GGAAACAAAAGATGACACAAGGGATAA 60.256 37.037 0.00 0.00 0.00 1.75
48 49 6.575162 ACAAAAGATGACACAAGGGATAAC 57.425 37.500 0.00 0.00 0.00 1.89
49 50 5.181245 ACAAAAGATGACACAAGGGATAACG 59.819 40.000 0.00 0.00 0.00 3.18
50 51 3.543680 AGATGACACAAGGGATAACGG 57.456 47.619 0.00 0.00 0.00 4.44
51 52 1.940613 GATGACACAAGGGATAACGGC 59.059 52.381 0.00 0.00 0.00 5.68
52 53 0.981183 TGACACAAGGGATAACGGCT 59.019 50.000 0.00 0.00 0.00 5.52
53 54 1.066430 TGACACAAGGGATAACGGCTC 60.066 52.381 0.00 0.00 0.00 4.70
54 55 0.252197 ACACAAGGGATAACGGCTCC 59.748 55.000 0.00 0.00 0.00 4.70
55 56 0.810031 CACAAGGGATAACGGCTCCG 60.810 60.000 6.79 6.79 46.03 4.63
72 73 3.053291 GTCGCCGGATGCCAACAA 61.053 61.111 5.05 0.00 36.24 2.83
73 74 2.745884 TCGCCGGATGCCAACAAG 60.746 61.111 5.05 0.00 36.24 3.16
74 75 3.814268 CGCCGGATGCCAACAAGG 61.814 66.667 5.05 0.00 41.84 3.61
75 76 3.451894 GCCGGATGCCAACAAGGG 61.452 66.667 5.05 0.00 38.09 3.95
76 77 2.035626 CCGGATGCCAACAAGGGT 59.964 61.111 0.00 0.00 38.09 4.34
77 78 2.046285 CCGGATGCCAACAAGGGTC 61.046 63.158 0.00 0.00 38.09 4.46
78 79 2.046285 CGGATGCCAACAAGGGTCC 61.046 63.158 0.00 0.00 38.09 4.46
79 80 1.076549 GGATGCCAACAAGGGTCCA 59.923 57.895 0.00 0.00 38.09 4.02
80 81 0.967380 GGATGCCAACAAGGGTCCAG 60.967 60.000 0.00 0.00 38.09 3.86
81 82 1.598701 GATGCCAACAAGGGTCCAGC 61.599 60.000 0.00 0.00 38.09 4.85
82 83 2.085343 ATGCCAACAAGGGTCCAGCT 62.085 55.000 0.00 0.00 38.09 4.24
83 84 2.270986 GCCAACAAGGGTCCAGCTG 61.271 63.158 6.78 6.78 38.09 4.24
84 85 1.455849 CCAACAAGGGTCCAGCTGA 59.544 57.895 17.39 0.00 0.00 4.26
85 86 0.178992 CCAACAAGGGTCCAGCTGAA 60.179 55.000 17.39 0.00 0.00 3.02
86 87 0.954452 CAACAAGGGTCCAGCTGAAC 59.046 55.000 17.39 4.31 0.00 3.18
99 100 1.067071 AGCTGAACGCCACTAGTAACC 60.067 52.381 0.00 0.00 40.39 2.85
100 101 1.337447 GCTGAACGCCACTAGTAACCA 60.337 52.381 0.00 0.00 0.00 3.67
109 110 3.054878 CCACTAGTAACCAACACACGAC 58.945 50.000 0.00 0.00 0.00 4.34
116 117 1.129809 CCAACACACGACGCGATTC 59.870 57.895 15.93 0.00 0.00 2.52
133 134 4.260670 CGATTCCGTGTAGCAATAAAACG 58.739 43.478 0.00 0.00 0.00 3.60
134 135 4.201647 CGATTCCGTGTAGCAATAAAACGT 60.202 41.667 0.00 0.00 32.53 3.99
135 136 4.392619 TTCCGTGTAGCAATAAAACGTG 57.607 40.909 0.00 0.00 32.53 4.49
154 155 6.687081 ACGTGTGGTTTTCATTCTAAGAAA 57.313 33.333 0.00 0.00 33.48 2.52
155 156 6.492254 ACGTGTGGTTTTCATTCTAAGAAAC 58.508 36.000 0.00 0.00 34.94 2.78
258 269 7.554118 CCTTCCTGTTAGAATCAAATTCAGCTA 59.446 37.037 2.79 0.00 41.71 3.32
260 271 7.624549 TCCTGTTAGAATCAAATTCAGCTAGT 58.375 34.615 2.79 0.00 41.71 2.57
261 272 8.758829 TCCTGTTAGAATCAAATTCAGCTAGTA 58.241 33.333 2.79 0.00 41.71 1.82
262 273 9.553064 CCTGTTAGAATCAAATTCAGCTAGTAT 57.447 33.333 2.79 0.00 41.71 2.12
303 314 3.685139 TGACCTTCATTCCTCTCACAC 57.315 47.619 0.00 0.00 0.00 3.82
308 319 3.193691 CCTTCATTCCTCTCACACGTACT 59.806 47.826 0.00 0.00 0.00 2.73
309 320 4.398358 CCTTCATTCCTCTCACACGTACTA 59.602 45.833 0.00 0.00 0.00 1.82
311 322 5.752892 TCATTCCTCTCACACGTACTATC 57.247 43.478 0.00 0.00 0.00 2.08
312 323 5.190677 TCATTCCTCTCACACGTACTATCA 58.809 41.667 0.00 0.00 0.00 2.15
313 324 5.650703 TCATTCCTCTCACACGTACTATCAA 59.349 40.000 0.00 0.00 0.00 2.57
314 325 4.959596 TCCTCTCACACGTACTATCAAC 57.040 45.455 0.00 0.00 0.00 3.18
315 326 3.693085 TCCTCTCACACGTACTATCAACC 59.307 47.826 0.00 0.00 0.00 3.77
316 327 3.442625 CCTCTCACACGTACTATCAACCA 59.557 47.826 0.00 0.00 0.00 3.67
364 386 6.220201 TGGATTCCGAATTCAAAAAGGAAAC 58.780 36.000 13.57 11.39 43.22 2.78
370 392 4.266502 CGAATTCAAAAAGGAAACGCAACA 59.733 37.500 6.22 0.00 0.00 3.33
372 394 5.717038 ATTCAAAAAGGAAACGCAACAAG 57.283 34.783 0.00 0.00 0.00 3.16
641 663 0.251033 GAGGGGCAAACCGGTACTTT 60.251 55.000 8.00 0.00 41.60 2.66
836 882 4.862823 CCCCCTCCGTCCCTCTCC 62.863 77.778 0.00 0.00 0.00 3.71
837 883 4.862823 CCCCTCCGTCCCTCTCCC 62.863 77.778 0.00 0.00 0.00 4.30
838 884 4.862823 CCCTCCGTCCCTCTCCCC 62.863 77.778 0.00 0.00 0.00 4.81
839 885 4.862823 CCTCCGTCCCTCTCCCCC 62.863 77.778 0.00 0.00 0.00 5.40
889 1238 2.781595 ATCTGTTCCGTTCGGCGCTT 62.782 55.000 7.64 0.00 39.71 4.68
950 1300 1.856920 TCCAGGAAGGAGTTTTTGGGT 59.143 47.619 0.00 0.00 43.07 4.51
951 1301 2.158519 TCCAGGAAGGAGTTTTTGGGTC 60.159 50.000 0.00 0.00 43.07 4.46
953 1303 0.596577 GGAAGGAGTTTTTGGGTCGC 59.403 55.000 0.00 0.00 0.00 5.19
954 1304 1.605753 GAAGGAGTTTTTGGGTCGCT 58.394 50.000 0.00 0.00 0.00 4.93
955 1305 1.266989 GAAGGAGTTTTTGGGTCGCTG 59.733 52.381 0.00 0.00 0.00 5.18
956 1306 1.172812 AGGAGTTTTTGGGTCGCTGC 61.173 55.000 0.00 0.00 0.00 5.25
988 1338 2.762875 GGATCGACGGAAGGGGGT 60.763 66.667 0.00 0.00 0.00 4.95
1003 1353 0.034896 GGGGTCGTGTTCTGTGATGT 59.965 55.000 0.00 0.00 0.00 3.06
1006 1356 2.479837 GGTCGTGTTCTGTGATGTTCA 58.520 47.619 0.00 0.00 0.00 3.18
1075 1425 4.775253 TGTTGTTTTCCCCTTTTCTGTTCT 59.225 37.500 0.00 0.00 0.00 3.01
1078 1428 6.367374 TGTTTTCCCCTTTTCTGTTCTTTT 57.633 33.333 0.00 0.00 0.00 2.27
1146 1504 1.875514 GATTAGCTGAATCATGCGGCA 59.124 47.619 4.58 4.58 43.16 5.69
1177 1535 3.537806 CACGTTGTGTTCGATTTACCAC 58.462 45.455 0.00 0.00 0.00 4.16
1179 1537 2.410517 CGTTGTGTTCGATTTACCACCG 60.411 50.000 0.00 0.00 0.00 4.94
1191 1549 1.186917 TACCACCGCTCGGGAGAAAA 61.187 55.000 13.31 0.00 39.18 2.29
1245 1603 3.054503 CTCGTCTGGACCGTCGGT 61.055 66.667 18.94 18.94 39.44 4.69
1269 1627 6.599638 GTGAAATGGAAGTAATAAGTGGCTCT 59.400 38.462 0.00 0.00 0.00 4.09
1270 1628 6.599244 TGAAATGGAAGTAATAAGTGGCTCTG 59.401 38.462 0.00 0.00 0.00 3.35
1271 1629 5.957771 ATGGAAGTAATAAGTGGCTCTGA 57.042 39.130 0.00 0.00 0.00 3.27
1427 1800 9.590451 TTATAGTACGTTTAGGATTCTTGTTGG 57.410 33.333 0.00 0.00 0.00 3.77
1512 1885 2.610374 TGTTTACCGTTGTCTGTTCTGC 59.390 45.455 0.00 0.00 0.00 4.26
1586 1963 1.418908 CGGAGGGCCCAATCCTATGT 61.419 60.000 27.56 0.00 34.21 2.29
1751 2128 2.332514 CCTGTTGTTGCGGCTGTG 59.667 61.111 0.00 0.00 0.00 3.66
2227 2613 4.825422 CTGCAAGAACTCAATCCTCAGTA 58.175 43.478 0.00 0.00 34.07 2.74
2228 2614 5.426504 CTGCAAGAACTCAATCCTCAGTAT 58.573 41.667 0.00 0.00 34.07 2.12
2230 2616 5.645067 TGCAAGAACTCAATCCTCAGTATTG 59.355 40.000 0.00 0.00 35.98 1.90
2410 2801 7.542130 GGTTCATTTTCCATGTTTGAGTATGTC 59.458 37.037 0.00 0.00 0.00 3.06
2414 2805 6.573664 TTTCCATGTTTGAGTATGTCCAAG 57.426 37.500 0.00 0.00 0.00 3.61
2513 2963 6.427853 CCGCTCTCAAATATACATCCAAATCA 59.572 38.462 0.00 0.00 0.00 2.57
2522 2972 9.807649 AAATATACATCCAAATCAAAGAGCAAC 57.192 29.630 0.00 0.00 0.00 4.17
2556 3006 8.528044 TGGTTATGGTTCTCAAGTTTTAGTTT 57.472 30.769 0.00 0.00 0.00 2.66
2557 3007 8.410141 TGGTTATGGTTCTCAAGTTTTAGTTTG 58.590 33.333 0.00 0.00 0.00 2.93
2564 3014 9.366216 GGTTCTCAAGTTTTAGTTTGAAAACAT 57.634 29.630 12.74 0.16 46.98 2.71
2566 3016 8.406172 TCTCAAGTTTTAGTTTGAAAACATGC 57.594 30.769 12.74 0.00 46.98 4.06
2643 3098 9.668497 CTGATGATATGTGGATTATGATGAAGT 57.332 33.333 0.00 0.00 0.00 3.01
2667 3122 2.716424 TCCAGGGTGAAAAGAATGGAGT 59.284 45.455 0.00 0.00 33.11 3.85
2696 3152 5.262588 GGTTGATCACCAGTTGAAAAACT 57.737 39.130 0.00 0.00 46.42 2.66
2697 3153 6.385649 GGTTGATCACCAGTTGAAAAACTA 57.614 37.500 0.00 0.00 46.42 2.24
2733 3189 6.944862 AGCTGAAGTTTAAATCAGGATTCAGT 59.055 34.615 16.74 7.56 42.49 3.41
2743 3199 6.630444 AATCAGGATTCAGTGTATGATTGC 57.370 37.500 0.00 0.00 37.89 3.56
2786 3260 1.066605 GCTTGCGCATTCTGATCCAAT 59.933 47.619 12.75 0.00 35.78 3.16
2928 3405 0.623723 GATTTGTGGTCAGGCCCCTA 59.376 55.000 0.00 0.00 36.04 3.53
2929 3406 0.625849 ATTTGTGGTCAGGCCCCTAG 59.374 55.000 0.00 0.00 36.04 3.02
2931 3408 1.198759 TTGTGGTCAGGCCCCTAGAC 61.199 60.000 0.00 2.55 36.04 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.372822 CCGTTAAGGCGAATACACATGTT 59.627 43.478 0.00 0.00 0.00 2.71
1 2 2.933906 CCGTTAAGGCGAATACACATGT 59.066 45.455 0.00 0.00 0.00 3.21
3 4 3.530265 TCCGTTAAGGCGAATACACAT 57.470 42.857 0.00 0.00 40.77 3.21
5 6 3.432933 TGTTTCCGTTAAGGCGAATACAC 59.567 43.478 0.00 0.00 40.77 2.90
8 9 5.469421 TCTTTTGTTTCCGTTAAGGCGAATA 59.531 36.000 0.00 0.00 40.77 1.75
9 10 4.276431 TCTTTTGTTTCCGTTAAGGCGAAT 59.724 37.500 0.00 0.00 40.77 3.34
10 11 3.626670 TCTTTTGTTTCCGTTAAGGCGAA 59.373 39.130 0.00 0.00 40.77 4.70
11 12 3.204526 TCTTTTGTTTCCGTTAAGGCGA 58.795 40.909 0.00 0.00 40.77 5.54
12 13 3.612472 TCTTTTGTTTCCGTTAAGGCG 57.388 42.857 0.00 0.00 40.77 5.52
13 14 4.915667 GTCATCTTTTGTTTCCGTTAAGGC 59.084 41.667 0.00 0.00 40.77 4.35
14 15 5.912955 GTGTCATCTTTTGTTTCCGTTAAGG 59.087 40.000 0.00 0.00 42.97 2.69
15 16 6.491394 TGTGTCATCTTTTGTTTCCGTTAAG 58.509 36.000 0.00 0.00 0.00 1.85
16 17 6.438259 TGTGTCATCTTTTGTTTCCGTTAA 57.562 33.333 0.00 0.00 0.00 2.01
17 18 6.438259 TTGTGTCATCTTTTGTTTCCGTTA 57.562 33.333 0.00 0.00 0.00 3.18
18 19 4.974368 TGTGTCATCTTTTGTTTCCGTT 57.026 36.364 0.00 0.00 0.00 4.44
19 20 4.202010 CCTTGTGTCATCTTTTGTTTCCGT 60.202 41.667 0.00 0.00 0.00 4.69
20 21 4.290155 CCTTGTGTCATCTTTTGTTTCCG 58.710 43.478 0.00 0.00 0.00 4.30
21 22 4.340950 TCCCTTGTGTCATCTTTTGTTTCC 59.659 41.667 0.00 0.00 0.00 3.13
22 23 5.514274 TCCCTTGTGTCATCTTTTGTTTC 57.486 39.130 0.00 0.00 0.00 2.78
23 24 7.433680 GTTATCCCTTGTGTCATCTTTTGTTT 58.566 34.615 0.00 0.00 0.00 2.83
24 25 6.293955 CGTTATCCCTTGTGTCATCTTTTGTT 60.294 38.462 0.00 0.00 0.00 2.83
25 26 5.181245 CGTTATCCCTTGTGTCATCTTTTGT 59.819 40.000 0.00 0.00 0.00 2.83
26 27 5.391950 CCGTTATCCCTTGTGTCATCTTTTG 60.392 44.000 0.00 0.00 0.00 2.44
27 28 4.700213 CCGTTATCCCTTGTGTCATCTTTT 59.300 41.667 0.00 0.00 0.00 2.27
28 29 4.261801 CCGTTATCCCTTGTGTCATCTTT 58.738 43.478 0.00 0.00 0.00 2.52
29 30 3.873910 CCGTTATCCCTTGTGTCATCTT 58.126 45.455 0.00 0.00 0.00 2.40
30 31 2.420129 GCCGTTATCCCTTGTGTCATCT 60.420 50.000 0.00 0.00 0.00 2.90
31 32 1.940613 GCCGTTATCCCTTGTGTCATC 59.059 52.381 0.00 0.00 0.00 2.92
32 33 1.559682 AGCCGTTATCCCTTGTGTCAT 59.440 47.619 0.00 0.00 0.00 3.06
33 34 0.981183 AGCCGTTATCCCTTGTGTCA 59.019 50.000 0.00 0.00 0.00 3.58
34 35 1.653151 GAGCCGTTATCCCTTGTGTC 58.347 55.000 0.00 0.00 0.00 3.67
35 36 0.252197 GGAGCCGTTATCCCTTGTGT 59.748 55.000 0.00 0.00 0.00 3.72
36 37 0.810031 CGGAGCCGTTATCCCTTGTG 60.810 60.000 0.00 0.00 32.86 3.33
37 38 1.520666 CGGAGCCGTTATCCCTTGT 59.479 57.895 0.00 0.00 32.86 3.16
38 39 4.438346 CGGAGCCGTTATCCCTTG 57.562 61.111 0.00 0.00 32.86 3.61
56 57 2.745884 CTTGTTGGCATCCGGCGA 60.746 61.111 9.30 0.00 46.16 5.54
57 58 3.814268 CCTTGTTGGCATCCGGCG 61.814 66.667 0.00 0.00 46.16 6.46
58 59 3.451894 CCCTTGTTGGCATCCGGC 61.452 66.667 0.00 0.00 43.74 6.13
59 60 2.035626 ACCCTTGTTGGCATCCGG 59.964 61.111 0.00 0.00 0.00 5.14
60 61 2.046285 GGACCCTTGTTGGCATCCG 61.046 63.158 0.00 0.00 32.25 4.18
61 62 0.967380 CTGGACCCTTGTTGGCATCC 60.967 60.000 0.00 0.00 39.03 3.51
62 63 1.598701 GCTGGACCCTTGTTGGCATC 61.599 60.000 0.00 0.00 0.00 3.91
63 64 1.607467 GCTGGACCCTTGTTGGCAT 60.607 57.895 0.00 0.00 0.00 4.40
64 65 2.203480 GCTGGACCCTTGTTGGCA 60.203 61.111 0.00 0.00 0.00 4.92
65 66 2.116125 AGCTGGACCCTTGTTGGC 59.884 61.111 0.00 0.00 0.00 4.52
66 67 0.178992 TTCAGCTGGACCCTTGTTGG 60.179 55.000 15.13 0.00 0.00 3.77
67 68 0.954452 GTTCAGCTGGACCCTTGTTG 59.046 55.000 14.82 0.00 0.00 3.33
68 69 0.535102 CGTTCAGCTGGACCCTTGTT 60.535 55.000 19.74 0.00 0.00 2.83
69 70 1.071471 CGTTCAGCTGGACCCTTGT 59.929 57.895 19.74 0.00 0.00 3.16
70 71 2.328099 GCGTTCAGCTGGACCCTTG 61.328 63.158 19.74 6.48 44.04 3.61
71 72 2.032681 GCGTTCAGCTGGACCCTT 59.967 61.111 19.74 0.00 44.04 3.95
81 82 2.735134 GTTGGTTACTAGTGGCGTTCAG 59.265 50.000 5.39 0.00 0.00 3.02
82 83 2.102757 TGTTGGTTACTAGTGGCGTTCA 59.897 45.455 5.39 0.00 0.00 3.18
83 84 2.477754 GTGTTGGTTACTAGTGGCGTTC 59.522 50.000 5.39 0.00 0.00 3.95
84 85 2.158928 TGTGTTGGTTACTAGTGGCGTT 60.159 45.455 5.39 0.00 0.00 4.84
85 86 1.413445 TGTGTTGGTTACTAGTGGCGT 59.587 47.619 5.39 0.00 0.00 5.68
86 87 1.796459 GTGTGTTGGTTACTAGTGGCG 59.204 52.381 5.39 0.00 0.00 5.69
99 100 1.129809 GGAATCGCGTCGTGTGTTG 59.870 57.895 5.77 0.00 0.00 3.33
100 101 2.369629 CGGAATCGCGTCGTGTGTT 61.370 57.895 5.77 2.51 0.00 3.32
109 110 1.483316 TATTGCTACACGGAATCGCG 58.517 50.000 0.00 0.00 40.63 5.87
116 117 3.475242 CACACGTTTTATTGCTACACGG 58.525 45.455 0.00 0.00 35.14 4.94
133 134 7.039313 AGGTTTCTTAGAATGAAAACCACAC 57.961 36.000 15.84 0.00 40.77 3.82
134 135 7.996644 ACTAGGTTTCTTAGAATGAAAACCACA 59.003 33.333 15.84 4.90 40.77 4.17
135 136 8.392372 ACTAGGTTTCTTAGAATGAAAACCAC 57.608 34.615 15.84 0.00 40.77 4.16
147 148 8.246180 TGTGTCGGTTAATACTAGGTTTCTTAG 58.754 37.037 0.00 0.00 0.00 2.18
148 149 8.028938 GTGTGTCGGTTAATACTAGGTTTCTTA 58.971 37.037 0.00 0.00 0.00 2.10
151 152 5.287035 CGTGTGTCGGTTAATACTAGGTTTC 59.713 44.000 0.00 0.00 35.71 2.78
154 155 4.009675 TCGTGTGTCGGTTAATACTAGGT 58.990 43.478 0.00 0.00 40.32 3.08
155 156 4.497006 CCTCGTGTGTCGGTTAATACTAGG 60.497 50.000 0.00 0.00 40.32 3.02
198 199 9.342308 CTGCTCCTGGTATTTTGAGAATAAATA 57.658 33.333 0.00 0.00 0.00 1.40
201 212 6.957631 TCTGCTCCTGGTATTTTGAGAATAA 58.042 36.000 0.00 0.00 0.00 1.40
206 217 7.814264 ATTAATCTGCTCCTGGTATTTTGAG 57.186 36.000 0.00 0.00 0.00 3.02
258 269 7.228314 TGTTGTGAGTAGAGCAACTAATACT 57.772 36.000 7.91 0.00 41.93 2.12
260 271 7.759886 GTCATGTTGTGAGTAGAGCAACTAATA 59.240 37.037 7.91 0.00 41.93 0.98
261 272 6.591834 GTCATGTTGTGAGTAGAGCAACTAAT 59.408 38.462 7.91 0.00 41.93 1.73
262 273 5.926542 GTCATGTTGTGAGTAGAGCAACTAA 59.073 40.000 7.91 0.00 41.93 2.24
309 320 9.635520 GTTGCTTACTATATATACGTGGTTGAT 57.364 33.333 0.00 0.00 0.00 2.57
311 322 8.806177 TGTTGCTTACTATATATACGTGGTTG 57.194 34.615 0.00 0.00 0.00 3.77
312 323 9.820725 TTTGTTGCTTACTATATATACGTGGTT 57.179 29.630 0.00 0.00 0.00 3.67
313 324 9.820725 TTTTGTTGCTTACTATATATACGTGGT 57.179 29.630 0.00 0.00 0.00 4.16
347 368 4.266502 TGTTGCGTTTCCTTTTTGAATTCG 59.733 37.500 0.04 0.00 0.00 3.34
413 435 7.901283 TTATGGTGTGAATGGATGAATGAAT 57.099 32.000 0.00 0.00 0.00 2.57
414 436 7.614974 TCTTTATGGTGTGAATGGATGAATGAA 59.385 33.333 0.00 0.00 0.00 2.57
415 437 7.118060 TCTTTATGGTGTGAATGGATGAATGA 58.882 34.615 0.00 0.00 0.00 2.57
416 438 7.337480 TCTTTATGGTGTGAATGGATGAATG 57.663 36.000 0.00 0.00 0.00 2.67
668 690 0.029059 TGGGGGAGGGGGAGATAAAG 60.029 60.000 0.00 0.00 0.00 1.85
836 882 4.862823 GGAGAGGGACGGAGGGGG 62.863 77.778 0.00 0.00 0.00 5.40
837 883 4.862823 GGGAGAGGGACGGAGGGG 62.863 77.778 0.00 0.00 0.00 4.79
838 884 4.862823 GGGGAGAGGGACGGAGGG 62.863 77.778 0.00 0.00 0.00 4.30
839 885 4.862823 GGGGGAGAGGGACGGAGG 62.863 77.778 0.00 0.00 0.00 4.30
861 1210 0.953960 ACGGAACAGATCAAACCGGC 60.954 55.000 19.01 0.00 46.45 6.13
907 1257 1.078708 AAAACCCACGCGGATCGAT 60.079 52.632 12.47 0.00 41.67 3.59
1075 1425 9.134734 GTAAATCTAATCATTTCCGCACAAAAA 57.865 29.630 0.00 0.00 0.00 1.94
1078 1428 6.601613 AGGTAAATCTAATCATTTCCGCACAA 59.398 34.615 0.00 0.00 0.00 3.33
1119 1477 4.625028 CATGATTCAGCTAATCCAGACGA 58.375 43.478 11.15 0.00 42.97 4.20
1124 1482 2.497138 CCGCATGATTCAGCTAATCCA 58.503 47.619 0.00 0.00 42.97 3.41
1146 1504 2.904866 ACAACGTGCGCCAACCAT 60.905 55.556 4.18 0.00 0.00 3.55
1177 1535 1.398390 CTGAAATTTTCTCCCGAGCGG 59.602 52.381 10.33 1.06 0.00 5.52
1179 1537 4.505313 AAACTGAAATTTTCTCCCGAGC 57.495 40.909 10.33 0.00 0.00 5.03
1191 1549 7.538678 CCGAATTCAAATCTCGAAAACTGAAAT 59.461 33.333 6.22 0.00 34.52 2.17
1245 1603 6.599244 CAGAGCCACTTATTACTTCCATTTCA 59.401 38.462 0.00 0.00 0.00 2.69
1269 1627 0.322098 CCAACCACCGCTACCAATCA 60.322 55.000 0.00 0.00 0.00 2.57
1270 1628 1.029947 CCCAACCACCGCTACCAATC 61.030 60.000 0.00 0.00 0.00 2.67
1271 1629 1.001393 CCCAACCACCGCTACCAAT 60.001 57.895 0.00 0.00 0.00 3.16
1512 1885 4.661993 TGAATAACTGTAAAGCTGCACG 57.338 40.909 1.02 0.00 0.00 5.34
1523 1896 6.207417 CCTTGTGTTCCATCTTGAATAACTGT 59.793 38.462 0.00 0.00 0.00 3.55
1586 1963 5.278758 GCCAAAGAAGCCACAGTTATTAACA 60.279 40.000 9.15 0.00 0.00 2.41
2203 2587 1.742268 GAGGATTGAGTTCTTGCAGCC 59.258 52.381 0.00 0.00 0.00 4.85
2227 2613 1.203523 ACACAACACGCAAACCACAAT 59.796 42.857 0.00 0.00 0.00 2.71
2228 2614 0.598562 ACACAACACGCAAACCACAA 59.401 45.000 0.00 0.00 0.00 3.33
2230 2616 2.159490 AGTTACACAACACGCAAACCAC 60.159 45.455 0.00 0.00 37.10 4.16
2441 2832 6.375736 TCCAAACTAACAACAATGAGAACACA 59.624 34.615 0.00 0.00 0.00 3.72
2513 2963 3.214328 ACCATGTTTCTCGTTGCTCTTT 58.786 40.909 0.00 0.00 0.00 2.52
2522 2972 5.470845 GAGAACCATAACCATGTTTCTCG 57.529 43.478 8.53 0.00 45.20 4.04
2565 3015 0.740868 TGTACGCCATTGCTCTCAGC 60.741 55.000 0.00 0.00 42.82 4.26
2566 3016 1.596260 CATGTACGCCATTGCTCTCAG 59.404 52.381 0.00 0.00 34.43 3.35
2580 3032 9.811995 TGACATATAAGAACTGTAACCATGTAC 57.188 33.333 0.00 0.00 0.00 2.90
2643 3098 5.015178 ACTCCATTCTTTTCACCCTGGATTA 59.985 40.000 0.00 0.00 32.66 1.75
2652 3107 4.022849 CCACAAGGACTCCATTCTTTTCAC 60.023 45.833 0.00 0.00 36.89 3.18
2695 3151 6.809630 AAACTTCAGCTTTTCTAAGGCTAG 57.190 37.500 0.00 0.00 31.76 3.42
2696 3152 8.685838 TTTAAACTTCAGCTTTTCTAAGGCTA 57.314 30.769 0.00 0.00 31.76 3.93
2697 3153 7.582667 TTTAAACTTCAGCTTTTCTAAGGCT 57.417 32.000 0.00 0.00 31.76 4.58
2733 3189 1.946745 TCCGCATTCGCAATCATACA 58.053 45.000 0.00 0.00 38.40 2.29
2743 3199 5.386323 GCGAAATGAATAAAATCCGCATTCG 60.386 40.000 0.00 0.00 40.88 3.34
2786 3260 3.576118 CCCATGTGTTGTAATTGTTCCCA 59.424 43.478 0.00 0.00 0.00 4.37
2895 3371 6.091986 TGACCACAAATCAAGCAAAAGAAAAC 59.908 34.615 0.00 0.00 0.00 2.43
2928 3405 4.266714 TGATCAATGTGCACATCATGTCT 58.733 39.130 31.45 17.78 35.10 3.41
2929 3406 4.625972 TGATCAATGTGCACATCATGTC 57.374 40.909 31.45 24.07 35.10 3.06
2931 3408 4.993905 AGTTGATCAATGTGCACATCATG 58.006 39.130 31.45 25.52 35.10 3.07


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

AutoCloner maintained by Alex Coulton.