Multiple sequence alignment - TraesCS6B01G325600

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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 TraesCS6B01G325600 chr6B 100.000 2507 0 0 1 2507 574737323 574734817 0.000000e+00 4630.0
1 TraesCS6B01G325600 chr6B 79.032 186 28 5 473 657 641023251 641023426 1.580000e-22 117.0
2 TraesCS6B01G325600 chr6B 79.762 168 18 8 503 666 448666025 448665870 9.480000e-20 108.0
3 TraesCS6B01G325600 chr6D 94.025 1590 80 12 920 2505 384534478 384532900 0.000000e+00 2396.0
4 TraesCS6B01G325600 chr6D 86.422 626 31 23 303 889 384552293 384551683 9.780000e-179 636.0
5 TraesCS6B01G325600 chr6D 89.105 514 31 9 390 889 384534979 384534477 1.270000e-172 616.0
6 TraesCS6B01G325600 chr6D 85.217 115 5 5 141 255 384548208 384548106 9.480000e-20 108.0
7 TraesCS6B01G325600 chr6A 97.196 642 18 0 980 1621 529048500 529047859 0.000000e+00 1086.0
8 TraesCS6B01G325600 chr6A 85.516 863 56 26 138 946 529049344 529048497 0.000000e+00 837.0
9 TraesCS6B01G325600 chr6A 91.463 246 18 3 1605 1847 529046912 529046667 4.000000e-88 335.0
10 TraesCS6B01G325600 chr6A 79.204 226 34 9 441 663 535814809 535815024 7.230000e-31 145.0
11 TraesCS6B01G325600 chr2B 89.333 150 13 3 1 148 748070289 748070141 4.260000e-43 185.0
12 TraesCS6B01G325600 chr2B 85.714 77 9 2 585 660 81769693 81769618 2.070000e-11 80.5
13 TraesCS6B01G325600 chr3D 90.141 142 13 1 1 141 141334767 141334626 1.530000e-42 183.0
14 TraesCS6B01G325600 chr3A 82.667 225 21 11 439 659 501225853 501225643 1.530000e-42 183.0
15 TraesCS6B01G325600 chr3A 80.000 180 21 7 483 659 703203197 703203364 4.380000e-23 119.0
16 TraesCS6B01G325600 chr2D 91.538 130 9 2 1 129 639701434 639701306 7.130000e-41 178.0
17 TraesCS6B01G325600 chr1B 88.514 148 15 2 1 146 161207786 161207933 7.130000e-41 178.0
18 TraesCS6B01G325600 chr4B 90.769 130 10 2 1 129 449341140 449341268 3.320000e-39 172.0
19 TraesCS6B01G325600 chr1A 89.209 139 13 2 4 141 262295270 262295133 3.320000e-39 172.0
20 TraesCS6B01G325600 chr4D 88.571 140 14 2 4 141 419487786 419487647 4.290000e-38 169.0
21 TraesCS6B01G325600 chr7B 88.028 142 16 1 1 141 658416524 658416665 1.540000e-37 167.0
22 TraesCS6B01G325600 chr1D 88.028 142 16 1 1 141 13730091 13729950 1.540000e-37 167.0
23 TraesCS6B01G325600 chr1D 87.755 49 5 1 151 198 402839914 402839866 3.480000e-04 56.5
24 TraesCS6B01G325600 chr3B 79.724 217 28 8 443 657 739874241 739874443 2.600000e-30 143.0
25 TraesCS6B01G325600 chr3B 78.636 220 35 5 443 660 794395056 794395265 4.350000e-28 135.0
26 TraesCS6B01G325600 chr5D 78.947 209 29 9 451 657 389350827 389350632 7.280000e-26 128.0
27 TraesCS6B01G325600 chr5D 86.667 75 8 2 586 659 304202505 304202432 5.750000e-12 82.4
28 TraesCS6B01G325600 chr5D 81.395 86 14 2 1405 1489 246766758 246766842 4.470000e-08 69.4
29 TraesCS6B01G325600 chr5B 82.558 86 13 2 1405 1489 281644335 281644251 9.620000e-10 75.0
30 TraesCS6B01G325600 chr5A 81.395 86 14 2 1405 1489 330964443 330964527 4.470000e-08 69.4


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 TraesCS6B01G325600 chr6B 574734817 574737323 2506 True 4630.000000 4630 100.000000 1 2507 1 chr6B.!!$R2 2506
1 TraesCS6B01G325600 chr6D 384532900 384534979 2079 True 1506.000000 2396 91.565000 390 2505 2 chr6D.!!$R1 2115
2 TraesCS6B01G325600 chr6D 384548106 384552293 4187 True 372.000000 636 85.819500 141 889 2 chr6D.!!$R2 748
3 TraesCS6B01G325600 chr6A 529046667 529049344 2677 True 752.666667 1086 91.391667 138 1847 3 chr6A.!!$R1 1709

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
281 283 0.240145 GGACTAAACGGCAAGGCAAC 59.760 55.0 0.0 0.0 0.00 4.17 F
576 615 0.527565 ATCATGTTTGCCAACCTCGC 59.472 50.0 0.0 0.0 31.02 5.03 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1314 1507 0.111266 CGCCGTTCTCGTCAAACTTG 60.111 55.0 0.00 0.00 35.01 3.16 R
2154 4787 0.734889 GTTCACATGCATTAGCGGCT 59.265 50.0 7.98 7.98 46.23 5.52 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
67 68 9.995003 TCTACTACGGGTTTAATGTTAGAAAAA 57.005 29.630 0.00 0.00 0.00 1.94
70 71 9.287373 ACTACGGGTTTAATGTTAGAAAAATCA 57.713 29.630 0.00 0.00 0.00 2.57
71 72 9.769093 CTACGGGTTTAATGTTAGAAAAATCAG 57.231 33.333 0.00 0.00 0.00 2.90
72 73 7.599171 ACGGGTTTAATGTTAGAAAAATCAGG 58.401 34.615 0.00 0.00 0.00 3.86
73 74 7.449086 ACGGGTTTAATGTTAGAAAAATCAGGA 59.551 33.333 0.00 0.00 0.00 3.86
74 75 7.968405 CGGGTTTAATGTTAGAAAAATCAGGAG 59.032 37.037 0.00 0.00 0.00 3.69
75 76 9.020731 GGGTTTAATGTTAGAAAAATCAGGAGA 57.979 33.333 0.00 0.00 0.00 3.71
97 98 9.173939 GGAGATTTTTCATAAAATAGCATGACG 57.826 33.333 0.00 0.00 42.51 4.35
98 99 9.173939 GAGATTTTTCATAAAATAGCATGACGG 57.826 33.333 0.00 0.00 42.51 4.79
99 100 8.902806 AGATTTTTCATAAAATAGCATGACGGA 58.097 29.630 0.00 0.00 42.51 4.69
100 101 8.856490 ATTTTTCATAAAATAGCATGACGGAC 57.144 30.769 0.00 0.00 41.09 4.79
101 102 7.624360 TTTTCATAAAATAGCATGACGGACT 57.376 32.000 0.00 0.00 31.04 3.85
102 103 8.725405 TTTTCATAAAATAGCATGACGGACTA 57.275 30.769 0.00 0.00 31.04 2.59
103 104 8.725405 TTTCATAAAATAGCATGACGGACTAA 57.275 30.769 0.00 0.00 31.04 2.24
104 105 7.946655 TCATAAAATAGCATGACGGACTAAG 57.053 36.000 0.00 0.00 0.00 2.18
105 106 7.722363 TCATAAAATAGCATGACGGACTAAGA 58.278 34.615 0.00 0.00 0.00 2.10
106 107 8.201464 TCATAAAATAGCATGACGGACTAAGAA 58.799 33.333 0.00 0.00 0.00 2.52
107 108 8.993121 CATAAAATAGCATGACGGACTAAGAAT 58.007 33.333 0.00 0.00 0.00 2.40
109 110 7.948278 AAATAGCATGACGGACTAAGAATAC 57.052 36.000 0.00 0.00 0.00 1.89
110 111 6.650427 ATAGCATGACGGACTAAGAATACA 57.350 37.500 0.00 0.00 0.00 2.29
111 112 5.537300 AGCATGACGGACTAAGAATACAT 57.463 39.130 0.00 0.00 0.00 2.29
112 113 6.650427 AGCATGACGGACTAAGAATACATA 57.350 37.500 0.00 0.00 0.00 2.29
113 114 7.233389 AGCATGACGGACTAAGAATACATAT 57.767 36.000 0.00 0.00 0.00 1.78
114 115 7.671302 AGCATGACGGACTAAGAATACATATT 58.329 34.615 0.00 0.00 0.00 1.28
115 116 8.150945 AGCATGACGGACTAAGAATACATATTT 58.849 33.333 0.00 0.00 0.00 1.40
116 117 8.436200 GCATGACGGACTAAGAATACATATTTC 58.564 37.037 0.00 0.00 0.00 2.17
117 118 9.698309 CATGACGGACTAAGAATACATATTTCT 57.302 33.333 0.00 0.00 0.00 2.52
178 179 8.908903 TGGTAATACCATGGATTGTATTTTCAC 58.091 33.333 21.47 7.13 44.79 3.18
213 215 7.415541 CCACTGAATTTCTATGGGTGTACAATG 60.416 40.741 0.00 0.00 0.00 2.82
220 222 5.412640 TCTATGGGTGTACAATGTAACACG 58.587 41.667 14.88 6.13 45.54 4.49
224 226 3.998522 GGTGTACAATGTAACACGCATC 58.001 45.455 14.88 0.00 45.54 3.91
281 283 0.240145 GGACTAAACGGCAAGGCAAC 59.760 55.000 0.00 0.00 0.00 4.17
283 285 1.442017 CTAAACGGCAAGGCAACGC 60.442 57.895 0.00 0.00 46.39 4.84
293 295 2.758770 AAGGCAACGCGCGTCTTCTA 62.759 55.000 37.77 0.00 43.84 2.10
294 296 2.165301 GGCAACGCGCGTCTTCTAT 61.165 57.895 37.77 17.37 43.84 1.98
353 355 4.553330 TTTTTGGTTTTTACAGGGCACA 57.447 36.364 0.00 0.00 0.00 4.57
400 427 3.973305 TGGAGGGAGTATGATGCATACAA 59.027 43.478 17.04 0.00 46.30 2.41
404 431 5.945310 AGGGAGTATGATGCATACAACATT 58.055 37.500 17.04 0.00 46.30 2.71
455 491 4.900635 AATCCGGATTTAAGCATGTCAC 57.099 40.909 24.27 0.00 0.00 3.67
462 498 2.799126 TTAAGCATGTCACCCCGAAT 57.201 45.000 0.00 0.00 0.00 3.34
490 526 5.499004 TTTATGGCTAGTTCAGTTGACCT 57.501 39.130 0.00 0.00 0.00 3.85
576 615 0.527565 ATCATGTTTGCCAACCTCGC 59.472 50.000 0.00 0.00 31.02 5.03
577 616 1.442520 CATGTTTGCCAACCTCGCG 60.443 57.895 0.00 0.00 31.02 5.87
578 617 1.896660 ATGTTTGCCAACCTCGCGT 60.897 52.632 5.77 0.00 31.02 6.01
579 618 2.051345 GTTTGCCAACCTCGCGTG 60.051 61.111 5.77 2.75 0.00 5.34
580 619 2.203084 TTTGCCAACCTCGCGTGA 60.203 55.556 10.21 0.00 0.00 4.35
581 620 1.820056 TTTGCCAACCTCGCGTGAA 60.820 52.632 10.21 0.00 0.00 3.18
582 621 1.781025 TTTGCCAACCTCGCGTGAAG 61.781 55.000 10.21 0.00 0.00 3.02
583 622 4.090057 GCCAACCTCGCGTGAAGC 62.090 66.667 10.21 3.06 43.95 3.86
613 652 8.751302 AACTAAAGTTGTCATGAAAAACGTTT 57.249 26.923 20.72 7.96 36.80 3.60
629 668 1.994779 CGTTTGGATTGCCATGCTTTC 59.005 47.619 0.00 0.00 45.46 2.62
647 686 8.717821 CATGCTTTCAAATTCAAACATTCAGAT 58.282 29.630 0.00 0.00 0.00 2.90
695 736 7.359595 TCAATACGCTGCATATATTCCAAAAC 58.640 34.615 0.00 0.00 0.00 2.43
879 936 2.636412 CCCACGCGGTTGAGAGAGA 61.636 63.158 12.47 0.00 0.00 3.10
880 937 1.153939 CCACGCGGTTGAGAGAGAG 60.154 63.158 12.47 0.00 0.00 3.20
882 939 2.202676 CGCGGTTGAGAGAGAGCC 60.203 66.667 0.00 0.00 0.00 4.70
883 940 2.185608 GCGGTTGAGAGAGAGCCC 59.814 66.667 0.00 0.00 0.00 5.19
884 941 2.355193 GCGGTTGAGAGAGAGCCCT 61.355 63.158 0.00 0.00 0.00 5.19
885 942 1.038130 GCGGTTGAGAGAGAGCCCTA 61.038 60.000 0.00 0.00 0.00 3.53
891 948 5.298276 CGGTTGAGAGAGAGCCCTATATATC 59.702 48.000 0.00 0.00 0.00 1.63
896 953 7.811282 TGAGAGAGAGCCCTATATATCTAAGG 58.189 42.308 0.00 0.00 0.00 2.69
916 973 4.957164 GGCTTAAACCCTCTCCCG 57.043 61.111 0.00 0.00 0.00 5.14
944 1001 1.152546 AGAGCCCAAAACCCCACAC 60.153 57.895 0.00 0.00 0.00 3.82
946 1003 2.444895 GCCCAAAACCCCACACCA 60.445 61.111 0.00 0.00 0.00 4.17
948 1005 1.381872 CCCAAAACCCCACACCACA 60.382 57.895 0.00 0.00 0.00 4.17
1480 1673 2.484651 CTCTCCTTCGACGAGTTCAAGA 59.515 50.000 0.00 0.00 0.00 3.02
1580 1773 3.812262 AGTTACCGGCAAGTGTAAAGTT 58.188 40.909 0.00 0.00 0.00 2.66
1837 3592 6.558771 TTCTTTCTGATTTTCTCGAATGCA 57.441 33.333 0.00 0.00 0.00 3.96
1865 3620 9.094578 AGCAGTGGTATGTTAGAATGTATATCT 57.905 33.333 0.00 0.00 0.00 1.98
1927 3684 3.449632 GAGTTTTAGGCTTCTAGCTCCG 58.550 50.000 0.00 0.00 41.99 4.63
1957 3714 6.083630 GCAATCACAACATATGTACGTGTTT 58.916 36.000 25.84 22.50 41.46 2.83
2016 4587 4.339872 TTTACGTGAACTTTGGGAGCTA 57.660 40.909 0.00 0.00 0.00 3.32
2017 4588 4.546829 TTACGTGAACTTTGGGAGCTAT 57.453 40.909 0.00 0.00 0.00 2.97
2021 4592 4.023193 ACGTGAACTTTGGGAGCTATTTTG 60.023 41.667 0.00 0.00 0.00 2.44
2023 4594 5.507315 CGTGAACTTTGGGAGCTATTTTGTT 60.507 40.000 0.00 0.00 0.00 2.83
2024 4595 5.920840 GTGAACTTTGGGAGCTATTTTGTTC 59.079 40.000 0.00 0.00 33.94 3.18
2032 4603 6.009589 TGGGAGCTATTTTGTTCTGAAATGA 58.990 36.000 0.00 0.00 0.00 2.57
2046 4617 4.215399 TCTGAAATGAAACACCCACGATTC 59.785 41.667 0.00 0.00 0.00 2.52
2059 4630 3.944650 CCCACGATTCCATAAATCACACA 59.055 43.478 0.00 0.00 43.44 3.72
2070 4702 5.065218 CCATAAATCACACAGGCTCAGTAAC 59.935 44.000 0.00 0.00 0.00 2.50
2072 4704 2.820059 TCACACAGGCTCAGTAACAG 57.180 50.000 0.00 0.00 0.00 3.16
2085 4718 2.855963 CAGTAACAGTATTGGCCGTACG 59.144 50.000 8.69 8.69 0.00 3.67
2108 4741 7.110155 ACGAACCTTTACATCATCAGGTAAAT 58.890 34.615 0.00 0.00 38.80 1.40
2154 4787 2.399856 GTGACCACGAGCACCAAAA 58.600 52.632 0.00 0.00 0.00 2.44
2182 4815 2.363306 TGCATGTGAACTTTGGGAGT 57.637 45.000 0.00 0.00 41.47 3.85
2204 4837 8.897752 GGAGTTTTATTGATTGATAGCAAGTCT 58.102 33.333 0.00 0.00 37.45 3.24
2216 4849 7.953158 TGATAGCAAGTCTATTACAATCAGC 57.047 36.000 0.00 0.00 38.09 4.26
2249 4882 2.091885 TCACAAGGAAGTCCAGGCTTTT 60.092 45.455 0.00 0.00 38.89 2.27
2251 4884 3.888930 CACAAGGAAGTCCAGGCTTTTAA 59.111 43.478 0.00 0.00 38.89 1.52
2257 4890 4.767409 GGAAGTCCAGGCTTTTAATGAACT 59.233 41.667 0.00 0.00 35.64 3.01
2270 4903 2.455674 ATGAACTAGCAGTCGCACAA 57.544 45.000 0.00 0.00 42.27 3.33
2281 4914 1.069204 AGTCGCACAACATCAGAGTGT 59.931 47.619 0.00 0.00 35.75 3.55
2293 4926 5.368145 ACATCAGAGTGTAAACAAGCTTGA 58.632 37.500 32.50 7.93 0.00 3.02
2300 4933 1.332375 GTAAACAAGCTTGACGGCACA 59.668 47.619 32.50 7.40 34.17 4.57
2326 4959 8.671921 AGAAAGATATGCCGAATTATTAGCATG 58.328 33.333 19.10 0.00 45.18 4.06
2357 4990 0.809385 GCCTAACCGAAAAAGAGGCC 59.191 55.000 0.00 0.00 45.80 5.19
2425 5058 2.483876 CATCTGGAGTTGTGACGTGTT 58.516 47.619 0.00 0.00 0.00 3.32
2426 5059 1.934589 TCTGGAGTTGTGACGTGTTG 58.065 50.000 0.00 0.00 0.00 3.33
2429 5062 1.206132 TGGAGTTGTGACGTGTTGACT 59.794 47.619 0.00 0.00 0.00 3.41
2430 5063 2.427812 TGGAGTTGTGACGTGTTGACTA 59.572 45.455 0.00 0.00 0.00 2.59
2450 5083 5.205056 ACTAGAGGTTGATGGTCTCTAAGG 58.795 45.833 0.00 0.00 38.96 2.69
2470 5103 2.173356 GGAATCCATCTCCATCACCACA 59.827 50.000 0.00 0.00 32.77 4.17
2505 5139 1.748493 TGTGCAAAACCACTCCTTCAC 59.252 47.619 0.00 0.00 36.68 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
41 42 9.995003 TTTTTCTAACATTAAACCCGTAGTAGA 57.005 29.630 0.00 0.00 0.00 2.59
44 45 9.287373 TGATTTTTCTAACATTAAACCCGTAGT 57.713 29.630 0.00 0.00 0.00 2.73
45 46 9.769093 CTGATTTTTCTAACATTAAACCCGTAG 57.231 33.333 0.00 0.00 0.00 3.51
46 47 8.732531 CCTGATTTTTCTAACATTAAACCCGTA 58.267 33.333 0.00 0.00 0.00 4.02
47 48 7.449086 TCCTGATTTTTCTAACATTAAACCCGT 59.551 33.333 0.00 0.00 0.00 5.28
48 49 7.822658 TCCTGATTTTTCTAACATTAAACCCG 58.177 34.615 0.00 0.00 0.00 5.28
49 50 9.020731 TCTCCTGATTTTTCTAACATTAAACCC 57.979 33.333 0.00 0.00 0.00 4.11
71 72 9.173939 CGTCATGCTATTTTATGAAAAATCTCC 57.826 33.333 0.00 0.00 42.86 3.71
72 73 9.173939 CCGTCATGCTATTTTATGAAAAATCTC 57.826 33.333 0.00 0.00 42.86 2.75
73 74 8.902806 TCCGTCATGCTATTTTATGAAAAATCT 58.097 29.630 0.00 0.00 42.86 2.40
74 75 8.958043 GTCCGTCATGCTATTTTATGAAAAATC 58.042 33.333 0.00 0.00 42.86 2.17
75 76 8.686334 AGTCCGTCATGCTATTTTATGAAAAAT 58.314 29.630 2.09 2.09 45.21 1.82
76 77 8.050778 AGTCCGTCATGCTATTTTATGAAAAA 57.949 30.769 0.00 0.00 38.87 1.94
77 78 7.624360 AGTCCGTCATGCTATTTTATGAAAA 57.376 32.000 0.00 0.00 35.29 2.29
78 79 8.725405 TTAGTCCGTCATGCTATTTTATGAAA 57.275 30.769 0.00 0.00 35.29 2.69
79 80 8.201464 TCTTAGTCCGTCATGCTATTTTATGAA 58.799 33.333 0.00 0.00 35.29 2.57
80 81 7.722363 TCTTAGTCCGTCATGCTATTTTATGA 58.278 34.615 0.00 0.00 0.00 2.15
81 82 7.946655 TCTTAGTCCGTCATGCTATTTTATG 57.053 36.000 0.00 0.00 0.00 1.90
83 84 9.472361 GTATTCTTAGTCCGTCATGCTATTTTA 57.528 33.333 0.00 0.00 0.00 1.52
84 85 7.985184 TGTATTCTTAGTCCGTCATGCTATTTT 59.015 33.333 0.00 0.00 0.00 1.82
85 86 7.497595 TGTATTCTTAGTCCGTCATGCTATTT 58.502 34.615 0.00 0.00 0.00 1.40
86 87 7.050970 TGTATTCTTAGTCCGTCATGCTATT 57.949 36.000 0.00 0.00 0.00 1.73
87 88 6.650427 TGTATTCTTAGTCCGTCATGCTAT 57.350 37.500 0.00 0.00 0.00 2.97
88 89 6.650427 ATGTATTCTTAGTCCGTCATGCTA 57.350 37.500 0.00 0.00 0.00 3.49
89 90 5.537300 ATGTATTCTTAGTCCGTCATGCT 57.463 39.130 0.00 0.00 0.00 3.79
90 91 7.891183 AATATGTATTCTTAGTCCGTCATGC 57.109 36.000 0.00 0.00 0.00 4.06
91 92 9.698309 AGAAATATGTATTCTTAGTCCGTCATG 57.302 33.333 0.00 0.00 33.41 3.07
155 156 7.229707 CCCGTGAAAATACAATCCATGGTATTA 59.770 37.037 12.58 0.00 38.80 0.98
156 157 6.040391 CCCGTGAAAATACAATCCATGGTATT 59.960 38.462 12.58 5.58 40.82 1.89
200 201 2.745281 GCGTGTTACATTGTACACCCAT 59.255 45.455 16.74 0.00 41.16 4.00
201 202 2.144730 GCGTGTTACATTGTACACCCA 58.855 47.619 16.74 3.64 41.16 4.51
213 215 4.725556 TTTCTTCTGTGATGCGTGTTAC 57.274 40.909 0.00 0.00 0.00 2.50
220 222 4.683320 GCCTTTTCTTTTCTTCTGTGATGC 59.317 41.667 0.00 0.00 0.00 3.91
224 226 3.384467 TGGGCCTTTTCTTTTCTTCTGTG 59.616 43.478 4.53 0.00 0.00 3.66
281 283 1.448677 GCTAGAAATAGAAGACGCGCG 59.551 52.381 30.96 30.96 0.00 6.86
283 285 5.212934 TGTATGCTAGAAATAGAAGACGCG 58.787 41.667 3.53 3.53 0.00 6.01
293 295 7.625828 GGTAACAAGGTTGTATGCTAGAAAT 57.374 36.000 0.00 0.00 41.31 2.17
400 427 7.666623 CCCTTGATTTTACAAAGTACCAATGT 58.333 34.615 0.00 0.00 0.00 2.71
404 431 4.525100 GGCCCTTGATTTTACAAAGTACCA 59.475 41.667 0.00 0.00 0.00 3.25
490 526 6.716934 TTAACAACTAAATTTGCCACCTCA 57.283 33.333 0.00 0.00 0.00 3.86
545 584 8.437742 GTTGGCAAACATGATAATTTTCTGAAG 58.562 33.333 0.00 0.00 36.24 3.02
557 596 0.527565 GCGAGGTTGGCAAACATGAT 59.472 50.000 18.93 0.00 38.10 2.45
576 615 2.132762 ACTTTAGTTCACGGCTTCACG 58.867 47.619 0.00 0.00 40.31 4.35
577 616 3.311596 ACAACTTTAGTTCACGGCTTCAC 59.688 43.478 0.00 0.00 35.83 3.18
578 617 3.537580 ACAACTTTAGTTCACGGCTTCA 58.462 40.909 0.00 0.00 35.83 3.02
579 618 3.558418 TGACAACTTTAGTTCACGGCTTC 59.442 43.478 0.00 0.00 35.83 3.86
580 619 3.537580 TGACAACTTTAGTTCACGGCTT 58.462 40.909 0.00 0.00 35.83 4.35
581 620 3.188159 TGACAACTTTAGTTCACGGCT 57.812 42.857 0.00 0.00 35.83 5.52
582 621 3.496884 TCATGACAACTTTAGTTCACGGC 59.503 43.478 0.00 0.00 35.83 5.68
583 622 5.666969 TTCATGACAACTTTAGTTCACGG 57.333 39.130 0.00 0.00 35.83 4.94
651 690 9.518906 CGTATTGATGATTGATTTTGGAAATGA 57.481 29.630 0.00 0.00 0.00 2.57
652 691 8.270799 GCGTATTGATGATTGATTTTGGAAATG 58.729 33.333 0.00 0.00 0.00 2.32
653 692 8.199449 AGCGTATTGATGATTGATTTTGGAAAT 58.801 29.630 0.00 0.00 0.00 2.17
658 699 5.744819 TGCAGCGTATTGATGATTGATTTTG 59.255 36.000 0.00 0.00 35.47 2.44
695 736 1.722011 AGACGCGTAGTGGATTTTGG 58.278 50.000 13.97 0.00 45.78 3.28
860 917 3.649277 CTCTCTCAACCGCGTGGGG 62.649 68.421 21.14 11.35 41.60 4.96
879 936 3.577919 CCCGCCTTAGATATATAGGGCT 58.422 50.000 23.34 0.00 43.79 5.19
882 939 6.726490 TTAAGCCCGCCTTAGATATATAGG 57.274 41.667 0.00 0.00 37.34 2.57
883 940 6.985059 GGTTTAAGCCCGCCTTAGATATATAG 59.015 42.308 0.00 0.00 37.34 1.31
884 941 6.126968 GGGTTTAAGCCCGCCTTAGATATATA 60.127 42.308 12.10 0.00 39.17 0.86
885 942 5.338953 GGGTTTAAGCCCGCCTTAGATATAT 60.339 44.000 12.10 0.00 39.17 0.86
891 948 2.789842 GGGTTTAAGCCCGCCTTAG 58.210 57.895 12.10 0.00 39.17 2.18
916 973 0.899717 TTTGGGCTCTGGTGGATTGC 60.900 55.000 0.00 0.00 0.00 3.56
944 1001 0.863957 GCGTTTCCGTGTGTTTGTGG 60.864 55.000 0.00 0.00 36.15 4.17
946 1003 0.179184 GTGCGTTTCCGTGTGTTTGT 60.179 50.000 0.00 0.00 36.15 2.83
948 1005 1.061253 CGTGCGTTTCCGTGTGTTT 59.939 52.632 0.00 0.00 36.15 2.83
1314 1507 0.111266 CGCCGTTCTCGTCAAACTTG 60.111 55.000 0.00 0.00 35.01 3.16
1407 1600 1.222936 CATCCTGGTGCACTCCTCC 59.777 63.158 17.98 0.00 0.00 4.30
1426 1619 3.573489 CTTGGTCAAACGCGGCGAC 62.573 63.158 30.94 16.31 0.00 5.19
1431 1624 2.549282 CCGTCTTGGTCAAACGCG 59.451 61.111 3.53 3.53 35.17 6.01
1480 1673 2.440796 CTTGGGCGCCATCATGGT 60.441 61.111 30.85 0.00 40.46 3.55
1614 1807 8.088981 TCAAGTTCTAGCCAGAAACTAACTAAG 58.911 37.037 0.00 0.00 42.41 2.18
1865 3620 8.545472 AGTGCCATACAAGTAGACCTATAAAAA 58.455 33.333 0.00 0.00 0.00 1.94
1927 3684 1.846007 TATGTTGTGATTGCACCCCC 58.154 50.000 0.00 0.00 44.51 5.40
1957 3714 5.709631 TGCCACAAATATTTAGAAGCACTCA 59.290 36.000 0.00 0.00 0.00 3.41
2016 4587 6.538381 GTGGGTGTTTCATTTCAGAACAAAAT 59.462 34.615 0.00 0.00 0.00 1.82
2017 4588 5.872070 GTGGGTGTTTCATTTCAGAACAAAA 59.128 36.000 0.00 0.00 0.00 2.44
2021 4592 3.314080 TCGTGGGTGTTTCATTTCAGAAC 59.686 43.478 0.00 0.00 0.00 3.01
2023 4594 3.201353 TCGTGGGTGTTTCATTTCAGA 57.799 42.857 0.00 0.00 0.00 3.27
2024 4595 4.475944 GAATCGTGGGTGTTTCATTTCAG 58.524 43.478 0.00 0.00 0.00 3.02
2032 4603 5.013547 TGATTTATGGAATCGTGGGTGTTT 58.986 37.500 0.00 0.00 45.85 2.83
2046 4617 3.614092 ACTGAGCCTGTGTGATTTATGG 58.386 45.455 0.00 0.00 0.00 2.74
2059 4630 2.092914 GGCCAATACTGTTACTGAGCCT 60.093 50.000 0.00 0.00 35.00 4.58
2070 4702 1.134907 AGGTTCGTACGGCCAATACTG 60.135 52.381 24.23 1.98 0.00 2.74
2072 4704 2.014335 AAGGTTCGTACGGCCAATAC 57.986 50.000 24.23 3.55 0.00 1.89
2154 4787 0.734889 GTTCACATGCATTAGCGGCT 59.265 50.000 7.98 7.98 46.23 5.52
2216 4849 7.287927 TGGACTTCCTTGTGAATAGTATCCTAG 59.712 40.741 0.00 0.00 36.82 3.02
2249 4882 3.586100 TGTGCGACTGCTAGTTCATTA 57.414 42.857 0.00 0.00 43.34 1.90
2251 4884 2.069273 GTTGTGCGACTGCTAGTTCAT 58.931 47.619 0.00 0.00 43.34 2.57
2257 4890 1.272212 TCTGATGTTGTGCGACTGCTA 59.728 47.619 0.00 0.00 43.34 3.49
2270 4903 5.237344 GTCAAGCTTGTTTACACTCTGATGT 59.763 40.000 25.19 0.00 36.56 3.06
2281 4914 1.601903 CTGTGCCGTCAAGCTTGTTTA 59.398 47.619 25.19 4.16 0.00 2.01
2293 4926 1.668419 GGCATATCTTTCTGTGCCGT 58.332 50.000 0.00 0.00 46.50 5.68
2300 4933 8.671921 CATGCTAATAATTCGGCATATCTTTCT 58.328 33.333 0.00 0.00 42.49 2.52
2326 4959 1.269831 CGGTTAGGCATGCTAGGAGAC 60.270 57.143 18.92 7.96 0.00 3.36
2381 5014 6.183361 TGGATTGTGACACCTATCTTAGATGG 60.183 42.308 4.78 1.36 0.00 3.51
2384 5017 6.841229 AGATGGATTGTGACACCTATCTTAGA 59.159 38.462 2.45 0.00 0.00 2.10
2425 5058 4.323569 AGAGACCATCAACCTCTAGTCA 57.676 45.455 0.00 0.00 35.68 3.41
2426 5059 5.300792 CCTTAGAGACCATCAACCTCTAGTC 59.699 48.000 0.00 0.00 39.71 2.59
2429 5062 5.467668 TCCTTAGAGACCATCAACCTCTA 57.532 43.478 0.00 0.00 38.20 2.43
2430 5063 4.338795 TCCTTAGAGACCATCAACCTCT 57.661 45.455 0.00 0.00 40.14 3.69
2450 5083 3.565764 TGTGGTGATGGAGATGGATTC 57.434 47.619 0.00 0.00 0.00 2.52
2470 5103 1.026718 GCACAACTTAGAGGGCGCAT 61.027 55.000 10.83 0.00 0.00 4.73


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

AutoCloner maintained by Alex Coulton.