Multiple sequence alignment - TraesCS5D01G250100

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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 TraesCS5D01G250100 chr5D 100.000 5417 0 0 1 5417 356618748 356624164 0.000000e+00 10004.0
1 TraesCS5D01G250100 chr5D 84.877 734 83 12 3295 4024 35483908 35483199 0.000000e+00 715.0
2 TraesCS5D01G250100 chr5D 84.877 734 83 12 3295 4024 539778930 539778221 0.000000e+00 715.0
3 TraesCS5D01G250100 chr5D 90.780 423 27 8 2313 2727 539779343 539778925 6.130000e-154 555.0
4 TraesCS5D01G250100 chr5D 90.544 423 28 8 2313 2727 35484321 35483903 2.850000e-152 549.0
5 TraesCS5D01G250100 chr5B 93.524 5343 213 49 1 5279 421446203 421451476 0.000000e+00 7827.0
6 TraesCS5D01G250100 chr5B 80.753 239 22 7 4780 5005 421761288 421761515 1.210000e-36 165.0
7 TraesCS5D01G250100 chr5B 88.889 117 8 1 5301 5417 421451721 421451832 7.320000e-29 139.0
8 TraesCS5D01G250100 chr5A 95.375 4519 135 26 377 4853 458102020 458106506 0.000000e+00 7119.0
9 TraesCS5D01G250100 chr5A 88.730 488 36 5 62 532 458003046 458003531 3.640000e-161 579.0
10 TraesCS5D01G250100 chr5A 88.172 279 14 7 1 262 458101647 458101923 1.130000e-81 315.0
11 TraesCS5D01G250100 chr5A 91.406 128 2 3 4850 4968 458109630 458109757 3.360000e-37 167.0
12 TraesCS5D01G250100 chr1B 85.422 734 81 13 3295 4024 252373683 252374394 0.000000e+00 739.0
13 TraesCS5D01G250100 chr1B 84.392 756 89 16 3279 4028 653970089 653970821 0.000000e+00 715.0
14 TraesCS5D01G250100 chr1B 91.781 292 22 2 5017 5306 398323208 398322917 6.530000e-109 405.0
15 TraesCS5D01G250100 chr1B 91.000 200 12 5 2534 2727 252373489 252373688 1.160000e-66 265.0
16 TraesCS5D01G250100 chr1B 83.395 271 22 4 2240 2498 252373237 252373496 4.220000e-56 230.0
17 TraesCS5D01G250100 chr6D 84.584 733 86 11 3295 4024 231080972 231080264 0.000000e+00 702.0
18 TraesCS5D01G250100 chr6D 90.164 427 27 8 2313 2727 231081390 231080967 4.770000e-150 542.0
19 TraesCS5D01G250100 chr7A 89.899 495 36 7 1664 2152 665439470 665439956 4.610000e-175 625.0
20 TraesCS5D01G250100 chr7D 86.538 572 65 8 3295 3863 598732116 598732678 2.140000e-173 619.0
21 TraesCS5D01G250100 chr7D 90.544 423 29 7 2313 2727 598731702 598732121 2.850000e-152 549.0
22 TraesCS5D01G250100 chr1A 89.516 496 37 7 1664 2152 466349109 466349596 9.970000e-172 614.0
23 TraesCS5D01G250100 chr7B 85.827 508 48 13 2240 2727 82146999 82147502 8.040000e-143 518.0
24 TraesCS5D01G250100 chr7B 91.724 290 23 1 5018 5306 54719826 54719537 8.450000e-108 401.0
25 TraesCS5D01G250100 chr1D 90.411 292 26 2 5017 5306 183710624 183710915 3.060000e-102 383.0
26 TraesCS5D01G250100 chr6B 90.592 287 26 1 5018 5303 50209952 50210238 3.960000e-101 379.0
27 TraesCS5D01G250100 chr6B 82.101 257 25 6 2240 2484 304153962 304154209 3.310000e-47 200.0
28 TraesCS5D01G250100 chr2D 90.345 290 27 1 5018 5306 143454549 143454260 3.960000e-101 379.0
29 TraesCS5D01G250100 chr2D 92.135 89 7 0 1037 1125 405062396 405062484 5.700000e-25 126.0
30 TraesCS5D01G250100 chrUn 90.068 292 28 1 5016 5306 250157147 250156856 1.420000e-100 377.0
31 TraesCS5D01G250100 chr3B 90.068 292 27 2 5017 5306 817456667 817456376 1.420000e-100 377.0
32 TraesCS5D01G250100 chr4B 90.034 291 28 1 5017 5306 625093920 625093630 5.120000e-100 375.0
33 TraesCS5D01G250100 chr4A 89.527 296 30 1 5009 5303 402469661 402469956 1.840000e-99 374.0
34 TraesCS5D01G250100 chr2A 92.135 89 7 0 1037 1125 543120696 543120784 5.700000e-25 126.0
35 TraesCS5D01G250100 chr2A 79.200 125 26 0 3785 3909 543123076 543123200 2.690000e-13 87.9


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 TraesCS5D01G250100 chr5D 356618748 356624164 5416 False 10004.000000 10004 100.000000 1 5417 1 chr5D.!!$F1 5416
1 TraesCS5D01G250100 chr5D 539778221 539779343 1122 True 635.000000 715 87.828500 2313 4024 2 chr5D.!!$R2 1711
2 TraesCS5D01G250100 chr5D 35483199 35484321 1122 True 632.000000 715 87.710500 2313 4024 2 chr5D.!!$R1 1711
3 TraesCS5D01G250100 chr5B 421446203 421451832 5629 False 3983.000000 7827 91.206500 1 5417 2 chr5B.!!$F2 5416
4 TraesCS5D01G250100 chr5A 458101647 458109757 8110 False 2533.666667 7119 91.651000 1 4968 3 chr5A.!!$F2 4967
5 TraesCS5D01G250100 chr1B 653970089 653970821 732 False 715.000000 715 84.392000 3279 4028 1 chr1B.!!$F1 749
6 TraesCS5D01G250100 chr1B 252373237 252374394 1157 False 411.333333 739 86.605667 2240 4024 3 chr1B.!!$F2 1784
7 TraesCS5D01G250100 chr6D 231080264 231081390 1126 True 622.000000 702 87.374000 2313 4024 2 chr6D.!!$R1 1711
8 TraesCS5D01G250100 chr7D 598731702 598732678 976 False 584.000000 619 88.541000 2313 3863 2 chr7D.!!$F1 1550
9 TraesCS5D01G250100 chr7B 82146999 82147502 503 False 518.000000 518 85.827000 2240 2727 1 chr7B.!!$F1 487

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
638 684 0.031616 CTACTGCTCCCTCCTCCCTT 60.032 60.0 0.00 0.00 0.00 3.95 F
1245 1311 0.035820 TTTCGCATACCCCACTGACC 60.036 55.0 0.00 0.00 0.00 4.02 F
1813 1894 0.103937 AGCCGATCTACTGCTGCTTC 59.896 55.0 0.00 0.00 37.65 3.86 F
2108 2195 1.161843 TTGTAGCAGCTAAAACGGGC 58.838 50.0 2.87 0.00 0.00 6.13 F
3015 3135 1.315690 CATATGAGCCTGGCTGTTGG 58.684 55.0 28.82 7.74 39.88 3.77 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1743 1820 0.041090 ACATCCCAATCCCCAACACC 59.959 55.0 0.00 0.00 0.00 4.16 R
2476 2590 0.671472 GCCCAGCAAAACCATCAAGC 60.671 55.0 0.00 0.00 0.00 4.01 R
2880 3000 0.890683 CTCCATTCAGTTGGGCCAAC 59.109 55.0 36.51 36.51 43.83 3.77 R
3982 4118 0.110056 GTGACAGAGCCAATGCAACG 60.110 55.0 0.00 0.00 41.13 4.10 R
4697 4843 1.021390 ATCAGAAACCGCGCAGAAGG 61.021 55.0 8.75 2.12 0.00 3.46 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 1.647702 GCGTGCGTACTCAAGTTAGTC 59.352 52.381 1.24 0.00 0.00 2.59
25 26 3.003585 TGCGTACTCAAGTTAGTCGTCAA 59.996 43.478 0.00 0.00 0.00 3.18
35 36 4.905269 AGTTAGTCGTCAAAGCACAAAAC 58.095 39.130 0.00 0.00 0.00 2.43
43 44 4.260294 CGTCAAAGCACAAAACGTAGGTTA 60.260 41.667 0.43 0.00 34.62 2.85
68 69 0.249657 GATCACCGGAGCAGGCTAAG 60.250 60.000 9.46 0.00 33.69 2.18
72 73 1.066430 CACCGGAGCAGGCTAAGTTAA 60.066 52.381 9.46 0.00 33.69 2.01
141 154 1.757699 CAGAGTTAGACCAGCCTACCC 59.242 57.143 0.00 0.00 0.00 3.69
234 252 7.208064 TCCCAGTCAAAAGCTATATTTAGGT 57.792 36.000 0.00 0.00 37.77 3.08
265 284 0.846427 TTTGACCAGCCAGGATCCCT 60.846 55.000 8.55 0.00 41.22 4.20
274 293 0.466922 CCAGGATCCCTCACATTGGC 60.467 60.000 8.55 0.00 0.00 4.52
297 316 6.446318 GCTCTGGTTCACTAGAATATCAGAG 58.554 44.000 19.49 19.49 45.73 3.35
308 327 9.237187 CACTAGAATATCAGAGCAGGATTACTA 57.763 37.037 0.00 0.00 0.00 1.82
313 332 3.833732 TCAGAGCAGGATTACTACGGAT 58.166 45.455 0.00 0.00 0.00 4.18
638 684 0.031616 CTACTGCTCCCTCCTCCCTT 60.032 60.000 0.00 0.00 0.00 3.95
658 714 0.338120 CTCCTCCACCTCTTCCCTCT 59.662 60.000 0.00 0.00 0.00 3.69
686 745 3.381949 CTCCAAATTATCTCCGTCGGAC 58.618 50.000 10.71 0.00 0.00 4.79
689 748 0.742505 AATTATCTCCGTCGGACGCA 59.257 50.000 24.26 9.79 40.91 5.24
810 873 2.255554 CAGCAGCAGCAGCAACAG 59.744 61.111 12.92 0.00 45.49 3.16
811 874 2.984155 AGCAGCAGCAGCAACAGG 60.984 61.111 12.92 0.00 45.49 4.00
812 875 3.292936 GCAGCAGCAGCAACAGGT 61.293 61.111 4.63 0.00 45.49 4.00
1245 1311 0.035820 TTTCGCATACCCCACTGACC 60.036 55.000 0.00 0.00 0.00 4.02
1589 1666 1.207791 CAGTCCCCTAGATTGGCTGT 58.792 55.000 0.00 0.00 0.00 4.40
1611 1688 1.477014 GCAAGGCAAGATACCCCCTAC 60.477 57.143 0.00 0.00 0.00 3.18
1743 1820 0.665068 GGCCCGTTTTTAGTTTGGCG 60.665 55.000 0.00 0.00 39.78 5.69
1801 1882 7.204496 TCTTCTATGTAGAAACTAGCCGATC 57.796 40.000 4.24 0.00 41.37 3.69
1802 1883 6.999272 TCTTCTATGTAGAAACTAGCCGATCT 59.001 38.462 4.24 0.00 41.37 2.75
1803 1884 8.155510 TCTTCTATGTAGAAACTAGCCGATCTA 58.844 37.037 4.24 0.00 41.37 1.98
1806 1887 5.752892 TGTAGAAACTAGCCGATCTACTG 57.247 43.478 18.08 0.00 42.90 2.74
1809 1890 3.067461 AGAAACTAGCCGATCTACTGCTG 59.933 47.826 6.27 0.00 39.29 4.41
1813 1894 0.103937 AGCCGATCTACTGCTGCTTC 59.896 55.000 0.00 0.00 37.65 3.86
1839 1920 7.693951 CGCAGAAAAGGAGAACATTTACATTAG 59.306 37.037 0.00 0.00 29.78 1.73
1864 1945 6.497785 TTTCTCAAACTACGTTCAAAACCA 57.502 33.333 0.00 0.00 0.00 3.67
1868 1954 6.149807 TCTCAAACTACGTTCAAAACCAGTTT 59.850 34.615 0.00 0.00 40.72 2.66
1869 1955 6.312645 CAAACTACGTTCAAAACCAGTTTG 57.687 37.500 17.16 17.16 44.89 2.93
1999 2085 7.642071 TTTTCGTGTCCACTAACATAGTAAC 57.358 36.000 0.00 0.00 37.23 2.50
2004 2090 6.034577 CGTGTCCACTAACATAGTAACATGTG 59.965 42.308 0.00 0.00 39.10 3.21
2037 2124 9.770097 CTGAGCTTACAGATGATTCCTTTATAA 57.230 33.333 0.00 0.00 39.94 0.98
2106 2193 5.041951 TCATTTTGTAGCAGCTAAAACGG 57.958 39.130 4.34 1.93 0.00 4.44
2108 2195 1.161843 TTGTAGCAGCTAAAACGGGC 58.838 50.000 2.87 0.00 0.00 6.13
2152 2240 5.954153 ACAATGGAGAGAGACTTGATCAT 57.046 39.130 0.00 0.00 0.00 2.45
2206 2295 3.884091 TCGTTTTTAGCAGCCTTAAACCA 59.116 39.130 7.78 0.00 0.00 3.67
2304 2403 2.511659 AGACTGCATTGCAATGTGTCT 58.488 42.857 36.29 36.29 42.03 3.41
2305 2404 2.889045 AGACTGCATTGCAATGTGTCTT 59.111 40.909 36.29 27.85 43.05 3.01
2306 2405 3.057736 AGACTGCATTGCAATGTGTCTTC 60.058 43.478 36.29 26.64 43.05 2.87
2307 2406 2.889045 ACTGCATTGCAATGTGTCTTCT 59.111 40.909 33.67 12.88 38.41 2.85
2308 2407 3.319972 ACTGCATTGCAATGTGTCTTCTT 59.680 39.130 33.67 12.23 38.41 2.52
2309 2408 4.520111 ACTGCATTGCAATGTGTCTTCTTA 59.480 37.500 33.67 12.78 38.41 2.10
2310 2409 5.009911 ACTGCATTGCAATGTGTCTTCTTAA 59.990 36.000 33.67 11.06 38.41 1.85
2311 2410 6.028146 TGCATTGCAATGTGTCTTCTTAAT 57.972 33.333 33.67 0.00 38.65 1.40
2476 2590 2.058798 CATGCTGCAGCTGAAAAAGTG 58.941 47.619 36.61 18.29 42.66 3.16
2842 2962 6.003950 TCCCAGAAAATCTTCAGGTTAGTTG 58.996 40.000 0.00 0.00 36.68 3.16
2856 2976 5.817816 CAGGTTAGTTGACAAGTTTCTCAGT 59.182 40.000 0.00 0.00 0.00 3.41
2880 3000 8.680903 AGTTTCCTATGTGCTCTGAATTAATTG 58.319 33.333 5.17 0.00 0.00 2.32
2951 3071 9.471084 CCCTGTTAATTTACGTTTTCTTTTGAT 57.529 29.630 0.00 0.00 0.00 2.57
3015 3135 1.315690 CATATGAGCCTGGCTGTTGG 58.684 55.000 28.82 7.74 39.88 3.77
3058 3178 8.669946 ATTCCAATGATTTTAAAACGTGGTTT 57.330 26.923 1.97 0.00 37.34 3.27
3254 3374 5.802465 ACTACTTTTAGTTAGTTCCCTGCC 58.198 41.667 0.00 0.00 34.66 4.85
3595 3721 8.919145 TCTACAGGAACCATTTAATGTTGTTTT 58.081 29.630 4.15 0.00 0.00 2.43
3845 3980 6.942005 TGAAGATGATCTTAAGCAAACCTTCA 59.058 34.615 7.82 17.45 36.73 3.02
3880 4015 5.109500 AGATTTCCTCTGTGAAGATTCCC 57.891 43.478 0.00 0.00 31.12 3.97
3940 4075 3.577848 GGTATGGATTATTGGCCATGCAA 59.422 43.478 6.09 0.67 45.53 4.08
3943 4078 4.339872 TGGATTATTGGCCATGCAATTC 57.660 40.909 6.09 6.04 0.00 2.17
3982 4118 5.931724 CCTCCCCACATACAATTTTTGTTTC 59.068 40.000 0.00 0.00 42.22 2.78
3986 4122 6.292596 CCCCACATACAATTTTTGTTTCGTTG 60.293 38.462 0.00 0.00 42.22 4.10
3987 4123 6.126079 CCACATACAATTTTTGTTTCGTTGC 58.874 36.000 0.00 0.00 42.22 4.17
4027 4163 6.036577 TGATGGAATCCGATCGATTAATGA 57.963 37.500 18.66 4.11 44.73 2.57
4034 4170 6.957984 ATCCGATCGATTAATGATGTCAAG 57.042 37.500 18.66 0.00 0.00 3.02
4085 4221 3.036091 AGATGCATTGCAAGGGCTAAAT 58.964 40.909 16.46 10.80 43.62 1.40
4200 4336 7.240194 TCCCTCCCTCCTTAAACAGTAAAATTA 59.760 37.037 0.00 0.00 0.00 1.40
4559 4702 7.817478 TGACTGGTCATGTAAAGTACATTACTG 59.183 37.037 18.76 14.52 46.69 2.74
4560 4703 6.594159 ACTGGTCATGTAAAGTACATTACTGC 59.406 38.462 18.76 11.38 46.69 4.40
4561 4704 6.707290 TGGTCATGTAAAGTACATTACTGCT 58.293 36.000 18.76 4.64 46.69 4.24
4772 4918 1.694150 TGTTGAGCTGAGCAAGTAGGT 59.306 47.619 7.39 0.00 0.00 3.08
4813 4959 5.900865 TGCAAACAATCAATAGCTCATCA 57.099 34.783 0.00 0.00 0.00 3.07
4976 8260 8.607459 CAATTATTATGAAGCTAATAGGGAGCG 58.393 37.037 0.00 0.00 44.98 5.03
4984 8268 2.866762 GCTAATAGGGAGCGTCAAACAG 59.133 50.000 0.00 0.00 0.00 3.16
4989 8273 2.180276 AGGGAGCGTCAAACAGAGTAT 58.820 47.619 0.00 0.00 0.00 2.12
5037 8321 0.321653 AGGGCTGTACCAAAAGCTCG 60.322 55.000 3.26 0.00 44.98 5.03
5071 8355 2.141535 AATGAGCGCTCGATAGTTCC 57.858 50.000 30.75 6.47 37.40 3.62
5075 8359 2.011881 GCGCTCGATAGTTCCGCTC 61.012 63.158 0.00 0.00 41.67 5.03
5080 8364 2.906153 CTCGATAGTTCCGCTCGTTAG 58.094 52.381 0.00 0.00 34.19 2.34
5084 8368 0.737219 TAGTTCCGCTCGTTAGGCTC 59.263 55.000 0.00 0.00 0.00 4.70
5096 8380 2.558554 TTAGGCTCGTGGCTCGCTTC 62.559 60.000 17.39 0.00 46.86 3.86
5110 8394 3.848582 GCTCGCTTCTTAATGAACAAAGC 59.151 43.478 0.00 0.00 39.10 3.51
5129 8413 7.256286 ACAAAGCTAATCATCAATTTCAGCTC 58.744 34.615 0.00 0.00 36.91 4.09
5171 8455 2.088664 CGAACGAGCTAACGAGTTTCAC 59.911 50.000 1.33 0.00 37.03 3.18
5201 8485 4.475944 TCGGTAAGCTCGTTAGTAACAAC 58.524 43.478 13.33 1.88 0.00 3.32
5282 8567 9.547753 TTCAATCTAATCTACATAAGAGGCAAC 57.452 33.333 0.00 0.00 37.74 4.17
5283 8568 8.704668 TCAATCTAATCTACATAAGAGGCAACA 58.295 33.333 0.00 0.00 37.74 3.33
5284 8569 9.330063 CAATCTAATCTACATAAGAGGCAACAA 57.670 33.333 0.00 0.00 37.74 2.83
5285 8570 9.905713 AATCTAATCTACATAAGAGGCAACAAA 57.094 29.630 0.00 0.00 37.74 2.83
5286 8571 8.718102 TCTAATCTACATAAGAGGCAACAAAC 57.282 34.615 0.00 0.00 37.74 2.93
5287 8572 8.540388 TCTAATCTACATAAGAGGCAACAAACT 58.460 33.333 0.00 0.00 37.74 2.66
5288 8573 9.817809 CTAATCTACATAAGAGGCAACAAACTA 57.182 33.333 0.00 0.00 37.74 2.24
5298 8583 3.891366 AGGCAACAAACTAGTGCATTTCT 59.109 39.130 0.00 0.00 41.41 2.52
5364 8882 2.894257 ATGGCTGCACCCTTGACGA 61.894 57.895 0.50 0.00 37.83 4.20
5387 8905 1.571460 CAGTGTGCGGTTCTTGAGC 59.429 57.895 0.00 0.00 0.00 4.26
5388 8906 1.146041 AGTGTGCGGTTCTTGAGCA 59.854 52.632 0.00 0.00 38.71 4.26
5389 8907 0.250467 AGTGTGCGGTTCTTGAGCAT 60.250 50.000 0.00 0.00 43.17 3.79
5390 8908 0.593128 GTGTGCGGTTCTTGAGCATT 59.407 50.000 0.00 0.00 43.17 3.56
5391 8909 1.001378 GTGTGCGGTTCTTGAGCATTT 60.001 47.619 0.00 0.00 43.17 2.32
5400 8918 3.476295 TCTTGAGCATTTCATGAACGC 57.524 42.857 17.50 17.50 37.12 4.84
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 2.031191 ACCTACGTTTTGTGCTTTGACG 59.969 45.455 0.00 0.00 39.43 4.35
25 26 6.031471 CAGTTTTAACCTACGTTTTGTGCTT 58.969 36.000 0.00 0.00 33.17 3.91
35 36 3.615496 CCGGTGATCAGTTTTAACCTACG 59.385 47.826 0.00 0.00 0.00 3.51
43 44 1.611673 CCTGCTCCGGTGATCAGTTTT 60.612 52.381 7.92 0.00 33.77 2.43
141 154 3.255395 TGGTTGTGTCATGCTGGTAATTG 59.745 43.478 0.00 0.00 0.00 2.32
234 252 2.288948 GCTGGTCAAACATTGCATGGAA 60.289 45.455 0.79 0.79 33.60 3.53
265 284 1.421268 AGTGAACCAGAGCCAATGTGA 59.579 47.619 0.00 0.00 0.00 3.58
274 293 6.040278 TGCTCTGATATTCTAGTGAACCAGAG 59.960 42.308 19.76 19.76 34.71 3.35
297 316 2.526304 TGCATCCGTAGTAATCCTGC 57.474 50.000 0.00 0.00 0.00 4.85
370 389 8.463607 CCCGTAAATAAATAAATGAACACTGGT 58.536 33.333 0.00 0.00 0.00 4.00
371 390 7.434013 GCCCGTAAATAAATAAATGAACACTGG 59.566 37.037 0.00 0.00 0.00 4.00
372 391 7.971168 TGCCCGTAAATAAATAAATGAACACTG 59.029 33.333 0.00 0.00 0.00 3.66
373 392 8.057536 TGCCCGTAAATAAATAAATGAACACT 57.942 30.769 0.00 0.00 0.00 3.55
374 393 7.434013 CCTGCCCGTAAATAAATAAATGAACAC 59.566 37.037 0.00 0.00 0.00 3.32
375 394 7.122948 ACCTGCCCGTAAATAAATAAATGAACA 59.877 33.333 0.00 0.00 0.00 3.18
443 483 1.434696 CCGCGGGTTACACGTAGAT 59.565 57.895 20.10 0.00 0.00 1.98
638 684 0.336737 GAGGGAAGAGGTGGAGGAGA 59.663 60.000 0.00 0.00 0.00 3.71
658 714 2.368875 GGAGATAATTTGGAGGCGAGGA 59.631 50.000 0.00 0.00 0.00 3.71
704 767 0.313987 CGCAAAACCAAACCTCTCCC 59.686 55.000 0.00 0.00 0.00 4.30
793 856 2.255554 CTGTTGCTGCTGCTGCTG 59.744 61.111 27.67 16.73 40.48 4.41
794 857 2.984155 CCTGTTGCTGCTGCTGCT 60.984 61.111 27.67 0.00 40.48 4.24
796 859 2.643272 CACCTGTTGCTGCTGCTG 59.357 61.111 17.00 0.77 40.48 4.41
797 860 2.596631 CCACCTGTTGCTGCTGCT 60.597 61.111 17.00 0.00 40.48 4.24
799 862 2.558286 CCACCACCTGTTGCTGCTG 61.558 63.158 0.00 0.00 0.00 4.41
800 863 2.203394 CCACCACCTGTTGCTGCT 60.203 61.111 0.00 0.00 0.00 4.24
802 865 3.663176 CGCCACCACCTGTTGCTG 61.663 66.667 0.00 0.00 33.56 4.41
803 866 4.954970 CCGCCACCACCTGTTGCT 62.955 66.667 0.00 0.00 33.56 3.91
1147 1213 3.990141 ATCTGGGGTTGGGGGAGGG 62.990 68.421 0.00 0.00 0.00 4.30
1245 1311 3.256631 CACATCCAAGAAAAGGGTTCCTG 59.743 47.826 0.00 0.00 32.13 3.86
1435 1511 3.121030 CTGCGCTACCCACTGCAC 61.121 66.667 9.73 0.00 33.12 4.57
1468 1544 3.088532 TGACCCAATCATTTGTACTGCC 58.911 45.455 0.00 0.00 29.99 4.85
1589 1666 1.306296 GGGGTATCTTGCCTTGCCA 59.694 57.895 0.00 0.00 0.00 4.92
1595 1672 1.424612 GGGGTAGGGGGTATCTTGCC 61.425 65.000 0.00 0.00 0.00 4.52
1611 1688 4.410400 GACCAGCACGGGAAGGGG 62.410 72.222 0.00 0.00 40.22 4.79
1743 1820 0.041090 ACATCCCAATCCCCAACACC 59.959 55.000 0.00 0.00 0.00 4.16
1813 1894 5.356882 TGTAAATGTTCTCCTTTTCTGCG 57.643 39.130 0.00 0.00 0.00 5.18
1864 1945 5.306114 AGTGTAAAGCCCTAACTCAAACT 57.694 39.130 0.00 0.00 0.00 2.66
1868 1954 6.675413 TCTAAAGTGTAAAGCCCTAACTCA 57.325 37.500 0.00 0.00 0.00 3.41
1869 1955 7.384477 TCTTCTAAAGTGTAAAGCCCTAACTC 58.616 38.462 0.00 0.00 0.00 3.01
1870 1956 7.312415 TCTTCTAAAGTGTAAAGCCCTAACT 57.688 36.000 0.00 0.00 0.00 2.24
1871 1957 7.660617 AGTTCTTCTAAAGTGTAAAGCCCTAAC 59.339 37.037 0.00 0.00 0.00 2.34
1872 1958 7.660208 CAGTTCTTCTAAAGTGTAAAGCCCTAA 59.340 37.037 0.00 0.00 0.00 2.69
1873 1959 7.015877 TCAGTTCTTCTAAAGTGTAAAGCCCTA 59.984 37.037 0.00 0.00 32.49 3.53
2022 2108 8.457238 AAACTGGAGCTTATAAAGGAATCATC 57.543 34.615 0.00 0.00 0.00 2.92
2037 2124 3.580458 AGACAGTACATGAAACTGGAGCT 59.420 43.478 25.86 19.40 46.97 4.09
2108 2195 3.499737 GAGGTGACAATGCCGCGG 61.500 66.667 24.05 24.05 0.00 6.46
2140 2228 4.696479 ACCCCATGTATGATCAAGTCTC 57.304 45.455 0.00 0.00 0.00 3.36
2152 2240 6.833346 TTGTCCTCATATAAACCCCATGTA 57.167 37.500 0.00 0.00 0.00 2.29
2206 2295 3.487879 CGAAACAGCCCAGTAAAACGTTT 60.488 43.478 7.96 7.96 0.00 3.60
2234 2323 7.770201 TCAGAATTTCAATTGTCAAGACACAA 58.230 30.769 5.13 0.00 41.67 3.33
2378 2492 1.238439 ACCTTGATTGCGACAACCTG 58.762 50.000 0.00 0.00 0.00 4.00
2476 2590 0.671472 GCCCAGCAAAACCATCAAGC 60.671 55.000 0.00 0.00 0.00 4.01
2842 2962 6.566753 GCACATAGGAAACTGAGAAACTTGTC 60.567 42.308 0.00 0.00 43.88 3.18
2856 2976 8.579850 ACAATTAATTCAGAGCACATAGGAAA 57.420 30.769 0.00 0.00 0.00 3.13
2880 3000 0.890683 CTCCATTCAGTTGGGCCAAC 59.109 55.000 36.51 36.51 43.83 3.77
2951 3071 9.431887 GTTGTGTGGATTTAGTTTCAGACTATA 57.568 33.333 0.00 0.00 40.44 1.31
3015 3135 3.330267 GAATCTCGCCCCATCAGTAATC 58.670 50.000 0.00 0.00 0.00 1.75
3254 3374 3.350833 AGTGGCAAAGAGATGCTAAAGG 58.649 45.455 0.00 0.00 45.68 3.11
3298 3418 6.114187 ACAAGTCCAGATGTGTGATAAAGA 57.886 37.500 0.00 0.00 0.00 2.52
3595 3721 7.161404 ACAGAAATAAACAGTCACAGCTATGA 58.839 34.615 0.00 0.00 0.00 2.15
3720 3847 6.779115 TGTATATTGCATAAGTTACAGCCG 57.221 37.500 6.68 0.00 0.00 5.52
3845 3980 3.456277 GAGGAAATCTCACCATACTGGGT 59.544 47.826 0.00 0.00 43.56 4.51
3880 4015 0.750182 ACCCACACTGTTTCCCAACG 60.750 55.000 0.00 0.00 35.40 4.10
3895 4030 1.305201 GAAGAAACTGCACGAACCCA 58.695 50.000 0.00 0.00 0.00 4.51
3940 4075 6.447084 TGGGGAGGAACTGAAAAGTATAGAAT 59.553 38.462 0.00 0.00 41.55 2.40
3943 4078 5.045869 TGTGGGGAGGAACTGAAAAGTATAG 60.046 44.000 0.00 0.00 41.55 1.31
3982 4118 0.110056 GTGACAGAGCCAATGCAACG 60.110 55.000 0.00 0.00 41.13 4.10
3986 4122 4.402851 TGGTGACAGAGCCAATGC 57.597 55.556 0.00 0.00 35.01 3.56
4034 4170 6.465439 TTCTTTCTGAGAAAGGGAAAAACC 57.535 37.500 28.78 0.00 41.34 3.27
4200 4336 1.826720 CTTGGGTTATGTTGGCTGCAT 59.173 47.619 0.50 0.00 0.00 3.96
4481 4624 3.622163 TCGTCTACCTTCTTTCTCTAGCG 59.378 47.826 0.00 0.00 0.00 4.26
4559 4702 4.503370 GTGGTGCTAGTTCTTCGTAATAGC 59.497 45.833 0.00 0.00 39.41 2.97
4560 4703 5.892568 AGTGGTGCTAGTTCTTCGTAATAG 58.107 41.667 0.00 0.00 0.00 1.73
4561 4704 5.909621 AGTGGTGCTAGTTCTTCGTAATA 57.090 39.130 0.00 0.00 0.00 0.98
4697 4843 1.021390 ATCAGAAACCGCGCAGAAGG 61.021 55.000 8.75 2.12 0.00 3.46
4740 4886 4.126437 TCAGCTCAACATCAGTTCGAAAA 58.874 39.130 0.00 0.00 35.28 2.29
4772 4918 7.336679 TGTTTGCAAAATATTCTAGCAGCTAGA 59.663 33.333 25.81 25.81 40.78 2.43
4813 4959 7.786178 TTTATGTGACGAAATTGCTAGCTAT 57.214 32.000 17.23 11.42 0.00 2.97
4970 8254 2.674796 ATACTCTGTTTGACGCTCCC 57.325 50.000 0.00 0.00 0.00 4.30
4984 8268 9.771915 GGCTACTACTAAATGTCGATTATACTC 57.228 37.037 0.00 0.00 0.00 2.59
4989 8273 5.563475 GCGGGCTACTACTAAATGTCGATTA 60.563 44.000 0.00 0.00 0.00 1.75
5071 8355 2.579787 CCACGAGCCTAACGAGCG 60.580 66.667 0.00 0.00 34.64 5.03
5075 8359 2.579787 CGAGCCACGAGCCTAACG 60.580 66.667 0.00 0.00 45.47 3.18
5080 8364 2.558554 TAAGAAGCGAGCCACGAGCC 62.559 60.000 5.11 0.00 45.47 4.70
5084 8368 1.640428 TCATTAAGAAGCGAGCCACG 58.360 50.000 0.00 0.00 45.66 4.94
5110 8394 8.984482 CTTAACGAGCTGAAATTGATGATTAG 57.016 34.615 0.00 0.00 0.00 1.73
5137 8421 2.658325 GCTCGTTCGTTAAGCTCGTTAA 59.342 45.455 0.00 0.00 33.23 2.01
5138 8422 2.095567 AGCTCGTTCGTTAAGCTCGTTA 60.096 45.455 0.00 0.00 42.58 3.18
5139 8423 1.058404 GCTCGTTCGTTAAGCTCGTT 58.942 50.000 0.00 0.00 33.23 3.85
5140 8424 0.240411 AGCTCGTTCGTTAAGCTCGT 59.760 50.000 0.00 0.00 42.58 4.18
5141 8425 2.169663 TAGCTCGTTCGTTAAGCTCG 57.830 50.000 9.48 0.00 44.89 5.03
5142 8426 2.275767 CGTTAGCTCGTTCGTTAAGCTC 59.724 50.000 9.48 0.00 44.89 4.09
5144 8428 2.245096 TCGTTAGCTCGTTCGTTAAGC 58.755 47.619 0.00 0.00 36.27 3.09
5145 8429 3.486584 ACTCGTTAGCTCGTTCGTTAAG 58.513 45.455 0.00 0.00 0.00 1.85
5151 8435 2.088664 CGTGAAACTCGTTAGCTCGTTC 59.911 50.000 0.00 0.00 31.75 3.95
5155 8439 2.931228 ACTCGTGAAACTCGTTAGCTC 58.069 47.619 0.00 0.00 31.75 4.09
5182 8466 6.019640 TGTTGTGTTGTTACTAACGAGCTTAC 60.020 38.462 0.00 0.00 33.28 2.34
5189 8473 8.996988 AAATATGTGTTGTGTTGTTACTAACG 57.003 30.769 0.00 0.00 33.28 3.18
5234 8519 5.720371 ATAGATAAGCTGAGGTGCTACAG 57.280 43.478 0.00 0.00 43.24 2.74
5270 8555 4.455533 TGCACTAGTTTGTTGCCTCTTATG 59.544 41.667 0.00 0.00 0.00 1.90
5274 8559 2.638480 TGCACTAGTTTGTTGCCTCT 57.362 45.000 0.00 0.00 0.00 3.69
5279 8564 7.962917 ACAAAAAGAAATGCACTAGTTTGTTG 58.037 30.769 0.00 0.00 34.82 3.33
5280 8565 9.646427 TTACAAAAAGAAATGCACTAGTTTGTT 57.354 25.926 16.20 5.40 37.18 2.83
5281 8566 9.816354 ATTACAAAAAGAAATGCACTAGTTTGT 57.184 25.926 15.68 15.68 38.29 2.83
5325 8843 6.348458 GCCATGTAATCGTGCATGTAATATGT 60.348 38.462 5.68 0.00 44.00 2.29
5333 8851 1.598676 GCAGCCATGTAATCGTGCATG 60.599 52.381 0.00 0.00 44.81 4.06
5376 8894 4.424061 TTCATGAAATGCTCAAGAACCG 57.576 40.909 5.45 0.00 46.21 4.44
5384 8902 2.744787 ATCGCGTTCATGAAATGCTC 57.255 45.000 23.70 7.44 46.21 4.26
5387 8905 7.252078 CGAGTAGAAATCGCGTTCATGAAATG 61.252 42.308 10.35 7.14 38.43 2.32
5388 8906 5.276395 CGAGTAGAAATCGCGTTCATGAAAT 60.276 40.000 10.35 0.00 32.81 2.17
5389 8907 4.031314 CGAGTAGAAATCGCGTTCATGAAA 59.969 41.667 10.35 0.00 32.81 2.69
5390 8908 3.546271 CGAGTAGAAATCGCGTTCATGAA 59.454 43.478 5.77 3.38 32.81 2.57
5391 8909 3.105937 CGAGTAGAAATCGCGTTCATGA 58.894 45.455 5.77 0.00 32.81 3.07


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

AutoCloner maintained by Alex Coulton.