Multiple sequence alignment - TraesCS5D01G421700

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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 TraesCS5D01G421700 chr5D 100.000 4698 0 0 1 4698 481809618 481814315 0.000000e+00 8676
1 TraesCS5D01G421700 chr5D 88.636 88 7 3 4141 4227 128577657 128577572 2.310000e-18 104
2 TraesCS5D01G421700 chr5A 93.874 2530 127 15 1430 3951 601431303 601433812 0.000000e+00 3788
3 TraesCS5D01G421700 chr5A 90.591 1456 80 24 1 1422 601429835 601431267 0.000000e+00 1877
4 TraesCS5D01G421700 chr5A 90.104 192 12 1 4514 4698 601434534 601434725 4.700000e-60 243
5 TraesCS5D01G421700 chr5B 92.933 2533 142 16 1430 3952 591106972 591109477 0.000000e+00 3651
6 TraesCS5D01G421700 chr5B 89.139 976 77 18 1 951 591061482 591062453 0.000000e+00 1188
7 TraesCS5D01G421700 chr5B 91.954 609 31 9 834 1428 591106327 591106931 0.000000e+00 837
8 TraesCS5D01G421700 chr5B 86.305 701 65 17 1 676 591100623 591101317 0.000000e+00 734
9 TraesCS5D01G421700 chr5B 85.519 732 71 14 1 713 591066221 591066936 0.000000e+00 732
10 TraesCS5D01G421700 chr5B 88.961 462 21 6 4073 4526 591109475 591109914 1.150000e-150 544
11 TraesCS5D01G421700 chr5B 76.275 843 149 35 416 1230 590238422 590239241 7.320000e-108 401
12 TraesCS5D01G421700 chr5B 91.000 200 18 0 1007 1206 591062462 591062661 2.150000e-68 270
13 TraesCS5D01G421700 chr5B 75.856 584 100 27 415 981 591060774 591061333 4.660000e-65 259
14 TraesCS5D01G421700 chr5B 80.805 323 48 6 1110 1430 591103274 591103584 1.690000e-59 241
15 TraesCS5D01G421700 chr5B 89.189 185 18 2 4514 4697 591109932 591110115 3.660000e-56 230
16 TraesCS5D01G421700 chr5B 91.250 80 4 3 4141 4218 62940392 62940314 6.430000e-19 106
17 TraesCS5D01G421700 chr5B 92.000 75 5 1 4141 4215 140965999 140965926 2.310000e-18 104
18 TraesCS5D01G421700 chr5B 92.000 75 5 1 4141 4215 411034937 411035010 2.310000e-18 104
19 TraesCS5D01G421700 chr4B 81.339 911 133 21 2730 3627 5780157 5779271 0.000000e+00 706
20 TraesCS5D01G421700 chr4B 80.153 262 42 4 1762 2014 5781567 5781307 2.230000e-43 187
21 TraesCS5D01G421700 chr4B 76.174 298 42 19 1063 1347 5781914 5781633 3.820000e-26 130
22 TraesCS5D01G421700 chr1B 87.960 598 47 11 1430 2014 519300556 519301141 0.000000e+00 682
23 TraesCS5D01G421700 chrUn 80.858 909 136 21 2732 3627 60987385 60986502 0.000000e+00 680
24 TraesCS5D01G421700 chr4A 82.642 795 113 19 2730 3520 601243794 601243021 0.000000e+00 680
25 TraesCS5D01G421700 chr4A 77.948 916 144 45 1766 2642 601248271 601247375 1.940000e-143 520
26 TraesCS5D01G421700 chr7B 91.283 413 32 2 1606 2014 627290736 627290324 1.140000e-155 560
27 TraesCS5D01G421700 chr7B 93.237 207 14 0 1808 2014 630108859 630108653 5.910000e-79 305
28 TraesCS5D01G421700 chr6A 92.330 352 26 1 1664 2014 429227470 429227821 2.520000e-137 499
29 TraesCS5D01G421700 chr2A 93.333 300 19 1 1716 2014 21730964 21730665 4.310000e-120 442
30 TraesCS5D01G421700 chr6B 93.421 76 4 1 4141 4216 359864650 359864724 1.380000e-20 111
31 TraesCS5D01G421700 chr2D 93.243 74 4 1 4141 4214 589522268 589522340 1.790000e-19 108
32 TraesCS5D01G421700 chr7A 93.151 73 4 1 4141 4213 246710899 246710828 6.430000e-19 106
33 TraesCS5D01G421700 chr7D 88.372 86 8 2 4141 4225 563608948 563608864 8.320000e-18 102
34 TraesCS5D01G421700 chr3D 88.372 86 8 2 4142 4227 582105805 582105888 8.320000e-18 102


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 TraesCS5D01G421700 chr5D 481809618 481814315 4697 False 8676.000000 8676 100.000000 1 4698 1 chr5D.!!$F1 4697
1 TraesCS5D01G421700 chr5A 601429835 601434725 4890 False 1969.333333 3788 91.523000 1 4698 3 chr5A.!!$F1 4697
2 TraesCS5D01G421700 chr5B 591100623 591110115 9492 False 1039.500000 3651 88.357833 1 4697 6 chr5B.!!$F4 4696
3 TraesCS5D01G421700 chr5B 591060774 591066936 6162 False 612.250000 1188 85.378500 1 1206 4 chr5B.!!$F3 1205
4 TraesCS5D01G421700 chr5B 590238422 590239241 819 False 401.000000 401 76.275000 416 1230 1 chr5B.!!$F2 814
5 TraesCS5D01G421700 chr4B 5779271 5781914 2643 True 341.000000 706 79.222000 1063 3627 3 chr4B.!!$R1 2564
6 TraesCS5D01G421700 chr1B 519300556 519301141 585 False 682.000000 682 87.960000 1430 2014 1 chr1B.!!$F1 584
7 TraesCS5D01G421700 chrUn 60986502 60987385 883 True 680.000000 680 80.858000 2732 3627 1 chrUn.!!$R1 895
8 TraesCS5D01G421700 chr4A 601243021 601248271 5250 True 600.000000 680 80.295000 1766 3520 2 chr4A.!!$R1 1754

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
339 1056 0.248054 CACTTTGTGCACACGACACC 60.248 55.0 21.56 0.00 37.22 4.16 F
864 6476 0.255318 AGGCTTTCCTGAGATGGCAG 59.745 55.0 0.00 0.00 42.34 4.85 F
1532 7234 0.734889 CGCGATTTGGCCTTCATCTT 59.265 50.0 0.00 0.00 0.00 2.40 F
3051 14102 0.736053 TTTTGACAAGGACACGTGCC 59.264 50.0 17.22 17.61 0.00 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1513 7215 0.734889 AAGATGAAGGCCAAATCGCG 59.265 50.0 5.01 0.0 0.00 5.87 R
2848 13899 2.282555 CGTAGGAGCGACATTTCACATG 59.717 50.0 0.00 0.0 0.00 3.21 R
3451 15376 0.172803 CGGACTTCGGACCAAGGTAG 59.827 60.0 0.00 0.0 34.75 3.18 R
3953 15889 0.332632 TGCTGCCCCAAGAATAAGCT 59.667 50.0 0.00 0.0 0.00 3.74 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
23 732 1.547820 TGCTGAAACACAAACCTTGCA 59.452 42.857 0.00 0.00 0.00 4.08
33 742 2.029649 ACAAACCTTGCAGATCATGTGC 60.030 45.455 0.00 0.00 41.59 4.57
123 835 1.529010 CCAGCTCAGTGGGCAAACA 60.529 57.895 19.27 0.00 33.46 2.83
209 922 4.202202 CCAAGGCTCCAGATCTTAGTACTG 60.202 50.000 5.39 0.00 0.00 2.74
213 926 3.005367 GCTCCAGATCTTAGTACTGCTCC 59.995 52.174 5.39 0.00 0.00 4.70
222 939 1.472188 AGTACTGCTCCCGTCTTACC 58.528 55.000 0.00 0.00 0.00 2.85
257 974 7.597288 TTTCTATCATCCCGTGAGATTTCTA 57.403 36.000 0.00 0.00 40.92 2.10
339 1056 0.248054 CACTTTGTGCACACGACACC 60.248 55.000 21.56 0.00 37.22 4.16
347 1064 0.949105 GCACACGACACCCTTCGATT 60.949 55.000 0.00 0.00 41.78 3.34
348 1065 0.790207 CACACGACACCCTTCGATTG 59.210 55.000 0.00 0.00 41.78 2.67
357 1074 1.420138 ACCCTTCGATTGGACTGTTGT 59.580 47.619 7.67 0.00 0.00 3.32
394 1111 5.190925 TGCCTACCATTCCTAACACATTACT 59.809 40.000 0.00 0.00 0.00 2.24
417 1151 0.958382 TCCTGTTAATGTGCCCGCAC 60.958 55.000 12.90 12.90 46.33 5.34
481 1215 9.166222 ACCTATTTATAACTCCATCCATGTACA 57.834 33.333 0.00 0.00 0.00 2.90
519 1255 5.806502 CACAGTTATGCCATTTATTGTGTGG 59.193 40.000 6.85 0.00 36.09 4.17
521 1257 6.035843 CAGTTATGCCATTTATTGTGTGGAC 58.964 40.000 0.00 0.00 34.94 4.02
568 1304 3.798337 GCACATGTGTCTGGTTTTTCTTG 59.202 43.478 26.01 0.00 0.00 3.02
577 1313 6.308041 GTGTCTGGTTTTTCTTGAAACTTCAC 59.692 38.462 0.00 0.00 39.05 3.18
608 1351 4.681074 TCAAGTCACCATCACACTGTAA 57.319 40.909 0.00 0.00 0.00 2.41
666 1409 0.614979 TCTCCTTGGCCGACTTAGCT 60.615 55.000 0.00 0.00 0.00 3.32
724 3078 0.820226 GAGGAGGAAGGGCAAATTGC 59.180 55.000 9.87 9.87 44.08 3.56
764 3118 5.049267 CACAATTCAAATTCAAAGGGCTTGG 60.049 40.000 0.00 0.00 35.56 3.61
864 6476 0.255318 AGGCTTTCCTGAGATGGCAG 59.745 55.000 0.00 0.00 42.34 4.85
916 6533 1.203287 GCAAGATCCAAAAGGCCAGAC 59.797 52.381 5.01 0.00 0.00 3.51
990 6622 4.083862 AAGCTCGAGCCGTTCCCC 62.084 66.667 32.94 3.92 43.38 4.81
1209 6862 3.710722 CTCCAGTTCCTGCCGGCT 61.711 66.667 29.70 1.94 0.00 5.52
1212 6865 2.662596 CAGTTCCTGCCGGCTACA 59.337 61.111 29.70 6.34 0.00 2.74
1342 7004 3.838271 CTTCCGGCTCCAGCGCTA 61.838 66.667 10.99 0.00 43.26 4.26
1372 7034 1.302033 CGCTCTTGGGCTTGACTGT 60.302 57.895 0.00 0.00 0.00 3.55
1393 7055 1.968540 GGAGCGATATTGCCTGCCC 60.969 63.158 11.53 4.66 34.65 5.36
1506 7208 3.773560 TCTTTCACGGATGGGGAAATTT 58.226 40.909 0.00 0.00 30.88 1.82
1513 7215 1.831106 GGATGGGGAAATTTGGTGGAC 59.169 52.381 0.00 0.00 0.00 4.02
1526 7228 2.033448 TGGACGCGATTTGGCCTT 59.967 55.556 15.93 0.00 0.00 4.35
1532 7234 0.734889 CGCGATTTGGCCTTCATCTT 59.265 50.000 0.00 0.00 0.00 2.40
1539 7241 2.425143 TGGCCTTCATCTTGTGGATC 57.575 50.000 3.32 0.00 31.27 3.36
1584 7294 5.738909 AGTCCAAATGTAGGATCAGAACTG 58.261 41.667 0.00 0.00 37.52 3.16
1597 7307 6.508777 GGATCAGAACTGAACCTGATACTAC 58.491 44.000 19.20 0.00 46.64 2.73
1599 7309 6.761099 TCAGAACTGAACCTGATACTACTC 57.239 41.667 1.79 0.00 36.53 2.59
1600 7310 5.652891 TCAGAACTGAACCTGATACTACTCC 59.347 44.000 1.79 0.00 36.53 3.85
1602 7312 5.654650 AGAACTGAACCTGATACTACTCCTG 59.345 44.000 0.00 0.00 0.00 3.86
1603 7313 3.702045 ACTGAACCTGATACTACTCCTGC 59.298 47.826 0.00 0.00 0.00 4.85
1604 7314 3.031736 TGAACCTGATACTACTCCTGCC 58.968 50.000 0.00 0.00 0.00 4.85
1620 7330 6.142498 ACTCCTGCCTAGTAGACTAGTAGTA 58.858 44.000 18.86 9.67 43.34 1.82
1623 8175 6.558014 TCCTGCCTAGTAGACTAGTAGTACAT 59.442 42.308 18.86 0.00 43.34 2.29
1750 8985 7.494952 AGTCCGAATTACCAAAATAAGCTCTAC 59.505 37.037 0.00 0.00 0.00 2.59
1801 9036 6.406370 CCATGAGGTTGAAACTGTAGATGTA 58.594 40.000 0.00 0.00 0.00 2.29
1893 9133 2.876550 GGTGCTGTTTCTCCGTTTTACT 59.123 45.455 0.00 0.00 0.00 2.24
1962 9208 6.699366 AGAGCCTTAACTACCAGAACTTTAC 58.301 40.000 0.00 0.00 0.00 2.01
2056 9537 6.183360 TGGTGACTGCAAAACATAAAGTGATT 60.183 34.615 0.00 0.00 0.00 2.57
2064 9545 6.088883 GCAAAACATAAAGTGATTAACCACCG 59.911 38.462 0.00 0.00 37.76 4.94
2229 9744 5.142265 CGCATCATGTATCCTTCAATTTCG 58.858 41.667 0.00 0.00 0.00 3.46
2521 10045 8.604640 ATGTTTATATCTCAGCAGACTCAATG 57.395 34.615 0.00 0.00 0.00 2.82
2603 10131 7.282224 CGAGAGATAACCATTTGTCCCATTAAA 59.718 37.037 0.00 0.00 0.00 1.52
2665 10194 1.888215 TGGCTTGTTTGCTCTCTCAG 58.112 50.000 0.00 0.00 0.00 3.35
2724 13774 3.254166 CCAGGGTTGTGAGTTCTTTGATG 59.746 47.826 0.00 0.00 0.00 3.07
2737 13787 8.049117 TGAGTTCTTTGATGAATTAGGCATAGT 58.951 33.333 0.00 0.00 0.00 2.12
2832 13883 4.431661 AGCAAAGTAGCATTTTCTCAGC 57.568 40.909 0.00 0.00 36.85 4.26
2839 13890 5.494724 AGTAGCATTTTCTCAGCATCTTCA 58.505 37.500 0.00 0.00 0.00 3.02
2848 13899 3.449018 TCTCAGCATCTTCAGGTTACCTC 59.551 47.826 0.00 0.00 0.00 3.85
2946 13997 3.604582 GGTGCTTCTGAAGATTGTAGCT 58.395 45.455 21.06 0.00 0.00 3.32
2947 13998 3.620821 GGTGCTTCTGAAGATTGTAGCTC 59.379 47.826 21.06 5.33 0.00 4.09
3051 14102 0.736053 TTTTGACAAGGACACGTGCC 59.264 50.000 17.22 17.61 0.00 5.01
3249 14823 7.093465 ACCTAGGTATATGATAACACCATTCCG 60.093 40.741 14.41 0.00 33.27 4.30
3370 15295 5.111989 GCAGATGCTAACACAGACATTCTA 58.888 41.667 0.00 0.00 38.21 2.10
3451 15376 2.894387 GGCGAGATCTGGCAGCAC 60.894 66.667 27.93 9.62 35.94 4.40
3552 15487 2.032550 CAGCATTTGAGATAGGGCGTTG 59.967 50.000 0.00 0.00 0.00 4.10
3589 15524 3.384789 AGCACAAGATATAAGAGGACGCA 59.615 43.478 0.00 0.00 0.00 5.24
3627 15562 5.004821 CGTATCACACATAGCAGTGAAAGAC 59.995 44.000 10.38 5.11 46.62 3.01
3674 15610 5.600484 ACCAAAGGATCACCAAAATGTTGTA 59.400 36.000 0.00 0.00 38.94 2.41
3716 15652 0.240945 GGCAAGTCAAACCCATGTCG 59.759 55.000 0.00 0.00 0.00 4.35
3725 15661 3.312973 TCAAACCCATGTCGTGTTTGTAC 59.687 43.478 18.61 0.00 45.55 2.90
3752 15688 8.059798 ACAATGTTTTAGAAGCATCTAAGCAT 57.940 30.769 17.46 17.46 46.15 3.79
3832 15768 2.359169 GGGAGGGACAGACGATGCA 61.359 63.158 0.00 0.00 0.00 3.96
3836 15772 3.188786 GGACAGACGATGCACGCC 61.189 66.667 8.31 0.00 46.94 5.68
3844 15780 4.796231 GATGCACGCCGTCGGTCT 62.796 66.667 13.94 0.00 40.69 3.85
3846 15782 3.695022 ATGCACGCCGTCGGTCTAC 62.695 63.158 13.94 1.35 40.69 2.59
3856 15792 2.803670 CGGTCTACCACACACGCG 60.804 66.667 3.53 3.53 35.14 6.01
3951 15887 0.991920 TCCCATCTTCCTCCACCAAC 59.008 55.000 0.00 0.00 0.00 3.77
3952 15888 0.698238 CCCATCTTCCTCCACCAACA 59.302 55.000 0.00 0.00 0.00 3.33
3953 15889 1.075374 CCCATCTTCCTCCACCAACAA 59.925 52.381 0.00 0.00 0.00 2.83
3964 15956 4.082571 CCTCCACCAACAAGCTTATTCTTG 60.083 45.833 0.00 2.33 46.57 3.02
3968 15960 2.094026 CCAACAAGCTTATTCTTGGGGC 60.094 50.000 0.00 0.00 45.72 5.80
3971 15963 1.135721 CAAGCTTATTCTTGGGGCAGC 59.864 52.381 0.00 0.00 39.68 5.25
3972 15964 0.332632 AGCTTATTCTTGGGGCAGCA 59.667 50.000 0.00 0.00 0.00 4.41
3973 15965 0.743097 GCTTATTCTTGGGGCAGCAG 59.257 55.000 0.00 0.00 0.00 4.24
3974 15966 1.396653 CTTATTCTTGGGGCAGCAGG 58.603 55.000 0.00 0.00 0.00 4.85
3975 15967 0.704076 TTATTCTTGGGGCAGCAGGT 59.296 50.000 0.00 0.00 0.00 4.00
3976 15968 0.034186 TATTCTTGGGGCAGCAGGTG 60.034 55.000 0.00 0.00 0.00 4.00
3977 15969 2.793317 ATTCTTGGGGCAGCAGGTGG 62.793 60.000 0.86 0.00 0.00 4.61
3978 15970 4.290622 CTTGGGGCAGCAGGTGGT 62.291 66.667 0.86 0.00 0.00 4.16
3979 15971 4.601794 TTGGGGCAGCAGGTGGTG 62.602 66.667 4.77 4.77 45.58 4.17
3981 15973 4.284550 GGGGCAGCAGGTGGTGAA 62.285 66.667 13.25 0.00 45.66 3.18
3982 15974 2.036256 GGGCAGCAGGTGGTGAAT 59.964 61.111 13.25 0.00 45.66 2.57
3983 15975 2.048603 GGGCAGCAGGTGGTGAATC 61.049 63.158 13.25 1.95 45.66 2.52
3984 15976 2.048603 GGCAGCAGGTGGTGAATCC 61.049 63.158 13.25 1.33 45.66 3.01
3985 15977 2.048603 GCAGCAGGTGGTGAATCCC 61.049 63.158 13.25 0.00 45.66 3.85
3996 15988 1.308746 TGAATCCCCCTCCCCCTTC 60.309 63.158 0.00 0.00 0.00 3.46
4006 15998 3.878667 CCCCCTTCGGCTCCCATC 61.879 72.222 0.00 0.00 0.00 3.51
4007 15999 2.770048 CCCCTTCGGCTCCCATCT 60.770 66.667 0.00 0.00 0.00 2.90
4045 16038 0.753479 AATGCCACCACCAAACGTCA 60.753 50.000 0.00 0.00 0.00 4.35
4123 16116 4.013267 CCATCAAGGCAAGTCCTATAGG 57.987 50.000 13.07 13.07 46.94 2.57
4209 16209 6.756221 TCTTATATTTCTTTACGGAGGGAGC 58.244 40.000 0.00 0.00 0.00 4.70
4211 16211 2.467566 TTTCTTTACGGAGGGAGCAC 57.532 50.000 0.00 0.00 0.00 4.40
4239 16239 1.954362 CTCTCCTTAGCTGCTGCCGT 61.954 60.000 13.43 0.00 40.80 5.68
4456 16572 6.869913 ACATTGCTATTGGTTGAGTGAAATTG 59.130 34.615 0.00 0.00 0.00 2.32
4546 16693 1.517257 GGACGACTGTGATCCAGCG 60.517 63.158 17.48 17.48 45.68 5.18
4547 16694 2.125912 ACGACTGTGATCCAGCGC 60.126 61.111 0.00 0.00 45.68 5.92
4580 16734 2.489938 ACATGGTCGCCAATACAAGT 57.510 45.000 0.00 0.00 36.95 3.16
4582 16736 2.487762 ACATGGTCGCCAATACAAGTTG 59.512 45.455 0.00 0.00 36.95 3.16
4587 16741 3.243267 GGTCGCCAATACAAGTTGTTGTT 60.243 43.478 14.90 7.14 45.00 2.83
4628 16782 1.645710 AAGGATCACACGGGAAGAGT 58.354 50.000 0.00 0.00 0.00 3.24
4636 16790 1.003580 ACACGGGAAGAGTGCAATCAT 59.996 47.619 17.53 3.76 42.94 2.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 732 1.065636 CACTGACCTGGCACATGATCT 60.066 52.381 0.00 0.00 38.20 2.75
33 742 2.804572 CGGATATGCTTCACTGACCTGG 60.805 54.545 0.00 0.00 0.00 4.45
123 835 7.811282 TGGGTCACCAATAATATTCACATAGT 58.189 34.615 0.00 0.00 45.87 2.12
209 922 1.138464 CCTTAAGGGTAAGACGGGAGC 59.862 57.143 14.25 0.00 39.36 4.70
213 926 7.063934 AGAAATATCCTTAAGGGTAAGACGG 57.936 40.000 18.45 0.00 39.36 4.79
222 939 7.766278 CACGGGATGATAGAAATATCCTTAAGG 59.234 40.741 15.98 15.98 40.17 2.69
339 1056 1.726791 CGACAACAGTCCAATCGAAGG 59.273 52.381 0.00 0.00 34.77 3.46
347 1064 3.858868 GAGCGCCGACAACAGTCCA 62.859 63.158 2.29 0.00 0.00 4.02
348 1065 3.112709 GAGCGCCGACAACAGTCC 61.113 66.667 2.29 0.00 0.00 3.85
394 1111 2.937873 GCGGGCACATTAACAGGAAGTA 60.938 50.000 0.00 0.00 0.00 2.24
452 1186 8.164070 ACATGGATGGAGTTATAAATAGGTTCC 58.836 37.037 0.00 0.00 0.00 3.62
481 1215 5.180117 GCATAACTGTGTGTGTCAATTCTCT 59.820 40.000 0.00 0.00 0.00 3.10
519 1255 8.813643 ATATATAACCAGCTCAACTAAACGTC 57.186 34.615 0.00 0.00 0.00 4.34
521 1257 8.861101 GCTATATATAACCAGCTCAACTAAACG 58.139 37.037 6.96 0.00 0.00 3.60
568 1304 7.032377 ACTTGAAAGGAATGAGTGAAGTTTC 57.968 36.000 0.00 0.00 0.00 2.78
577 1313 5.005740 TGATGGTGACTTGAAAGGAATGAG 58.994 41.667 0.00 0.00 0.00 2.90
724 3078 6.550843 TGAATTGTGGTTTTGCTATGTATCG 58.449 36.000 0.00 0.00 0.00 2.92
764 3118 6.220930 GGGTTTCCCACAAGAAATTTTAGAC 58.779 40.000 0.00 0.00 44.65 2.59
817 3171 1.803289 GCCTTGTCCTCGGCAAATC 59.197 57.895 0.00 0.00 45.59 2.17
824 3178 2.162338 TACCAACGGCCTTGTCCTCG 62.162 60.000 0.00 0.00 0.00 4.63
864 6476 1.363885 GGTCCGGTTTATGTGCGTCC 61.364 60.000 0.00 0.00 0.00 4.79
916 6533 2.332654 CGGGGGCTCCTGTTTTTCG 61.333 63.158 2.03 0.00 34.69 3.46
941 6558 2.281622 CCGGGCGTGGGTTTGTAA 60.282 61.111 0.00 0.00 0.00 2.41
1209 6862 2.745037 GGGTGGCGGAAGTGTGTA 59.255 61.111 0.00 0.00 0.00 2.90
1363 7025 3.782244 CGCTCCGCACAGTCAAGC 61.782 66.667 0.00 0.00 0.00 4.01
1369 7031 1.566563 GCAATATCGCTCCGCACAG 59.433 57.895 0.00 0.00 0.00 3.66
1372 7034 1.595109 CAGGCAATATCGCTCCGCA 60.595 57.895 0.00 0.00 0.00 5.69
1393 7055 7.301054 GTGAAATATGGAGAAATCAATAGGCG 58.699 38.462 0.00 0.00 0.00 5.52
1423 7085 4.989279 AATGGGAATCTCAATTGGAACG 57.011 40.909 5.42 0.00 0.00 3.95
1424 7086 6.700352 TGAAAATGGGAATCTCAATTGGAAC 58.300 36.000 5.42 1.81 0.00 3.62
1426 7088 6.441284 ACATGAAAATGGGAATCTCAATTGGA 59.559 34.615 5.42 2.32 0.00 3.53
1427 7089 6.646267 ACATGAAAATGGGAATCTCAATTGG 58.354 36.000 5.42 0.00 0.00 3.16
1434 7134 9.710900 GTTAGAAAAACATGAAAATGGGAATCT 57.289 29.630 0.00 0.00 0.00 2.40
1506 7208 3.053291 GCCAAATCGCGTCCACCA 61.053 61.111 5.77 0.00 0.00 4.17
1513 7215 0.734889 AAGATGAAGGCCAAATCGCG 59.265 50.000 5.01 0.00 0.00 5.87
1526 7228 7.669304 TGTAAATTTCAAGGATCCACAAGATGA 59.331 33.333 15.82 5.49 34.42 2.92
1532 7234 9.613428 CTATACTGTAAATTTCAAGGATCCACA 57.387 33.333 15.82 5.05 0.00 4.17
1539 7241 9.110502 GGACTTCCTATACTGTAAATTTCAAGG 57.889 37.037 0.00 0.00 0.00 3.61
1584 7294 3.301274 AGGCAGGAGTAGTATCAGGTTC 58.699 50.000 0.00 0.00 0.00 3.62
1588 7298 5.935789 GTCTACTAGGCAGGAGTAGTATCAG 59.064 48.000 16.19 0.00 44.53 2.90
1620 7330 5.338300 GGCAGGAATTCCAATTTAACCATGT 60.338 40.000 26.22 0.00 38.89 3.21
1623 8175 4.424842 AGGCAGGAATTCCAATTTAACCA 58.575 39.130 26.22 0.00 38.89 3.67
1750 8985 3.244033 TCCTGCGGGCAAAATAAAATG 57.756 42.857 6.73 0.00 0.00 2.32
1801 9036 5.133941 TCCAGACAGCTTATCGAAGAGTAT 58.866 41.667 0.00 0.00 43.63 2.12
1893 9133 8.081633 CCTCACAGCAAAATTACTGAAATACAA 58.918 33.333 9.36 0.00 37.35 2.41
1962 9208 8.818141 AATGACATTATTCTACATCAGGTACG 57.182 34.615 0.00 0.00 0.00 3.67
2064 9545 7.556635 AGAGGTAAAACTATCCAATACCAAAGC 59.443 37.037 0.00 0.00 38.76 3.51
2195 9710 3.103447 ACATGATGCGGATCACTGTAG 57.897 47.619 22.58 11.77 41.52 2.74
2229 9744 3.118261 TCATTGCCTCCTTCAGGTATCAC 60.118 47.826 0.00 0.00 45.61 3.06
2388 9909 7.013655 TGGCAAGATTTAGCTTATCCTTGATTC 59.986 37.037 17.23 9.49 0.00 2.52
2436 9957 4.006989 TGACAGTTCATTGGGGAATAACG 58.993 43.478 0.00 0.00 0.00 3.18
2665 10194 7.698130 GCTCACCATCATCACAAGTTAAATTAC 59.302 37.037 0.00 0.00 0.00 1.89
2724 13774 6.299141 TCTTCCATGGAACTATGCCTAATTC 58.701 40.000 23.63 0.00 0.00 2.17
2737 13787 5.018149 TCATGCTCAAAATCTTCCATGGAA 58.982 37.500 25.53 25.53 32.96 3.53
2832 13883 5.089970 TCACATGAGGTAACCTGAAGATG 57.910 43.478 0.00 0.00 31.76 2.90
2839 13890 4.253685 CGACATTTCACATGAGGTAACCT 58.746 43.478 0.00 0.00 36.03 3.50
2848 13899 2.282555 CGTAGGAGCGACATTTCACATG 59.717 50.000 0.00 0.00 0.00 3.21
2946 13997 0.464036 ATGTAATCTCCAAGGCGCGA 59.536 50.000 12.10 0.00 0.00 5.87
2947 13998 0.861837 GATGTAATCTCCAAGGCGCG 59.138 55.000 0.00 0.00 41.17 6.86
3051 14102 6.072286 ACCAGAAGCACATCAAAATCAAGTAG 60.072 38.462 0.00 0.00 0.00 2.57
3114 14165 1.956802 CCTTGGTCCAAAAGGCGAC 59.043 57.895 5.64 0.00 37.96 5.19
3249 14823 1.560505 ATGGATGTTTGGCAGGAACC 58.439 50.000 0.00 0.00 0.00 3.62
3370 15295 4.654262 ACATTCTTGGGTCCGTCATAGTAT 59.346 41.667 0.00 0.00 0.00 2.12
3451 15376 0.172803 CGGACTTCGGACCAAGGTAG 59.827 60.000 0.00 0.00 34.75 3.18
3494 15422 2.880890 AGAACATAGGATGAAATGCCGC 59.119 45.455 0.00 0.00 33.77 6.53
3552 15487 2.494059 TGTGCTACAGCTGAAAGGTTC 58.506 47.619 23.35 5.49 46.63 3.62
3589 15524 7.408756 TGTGTGATACGTTAATAGGTAACCT 57.591 36.000 0.00 0.00 39.22 3.50
3647 15583 6.933514 ACATTTTGGTGATCCTTTGGTAAT 57.066 33.333 0.00 0.00 34.23 1.89
3695 15631 1.541588 GACATGGGTTTGACTTGCCTC 59.458 52.381 0.00 0.00 0.00 4.70
3716 15652 8.318167 GCTTCTAAAACATTGTTGTACAAACAC 58.682 33.333 10.51 0.00 41.96 3.32
3725 15661 7.809331 TGCTTAGATGCTTCTAAAACATTGTTG 59.191 33.333 19.30 8.55 42.46 3.33
3779 15715 8.940768 TTTTTCTTCTTACCTCAACATTTTGG 57.059 30.769 0.00 0.00 33.06 3.28
3832 15768 3.741476 GTGGTAGACCGACGGCGT 61.741 66.667 14.65 14.65 39.43 5.68
3836 15772 1.441515 CGTGTGTGGTAGACCGACG 60.442 63.158 0.00 0.00 39.43 5.12
3842 15778 3.299977 AGGCGCGTGTGTGGTAGA 61.300 61.111 8.43 0.00 0.00 2.59
3951 15887 1.135721 GCTGCCCCAAGAATAAGCTTG 59.864 52.381 9.86 0.00 43.74 4.01
3952 15888 1.272648 TGCTGCCCCAAGAATAAGCTT 60.273 47.619 3.48 3.48 0.00 3.74
3953 15889 0.332632 TGCTGCCCCAAGAATAAGCT 59.667 50.000 0.00 0.00 0.00 3.74
3964 15956 3.590466 ATTCACCACCTGCTGCCCC 62.590 63.158 0.00 0.00 0.00 5.80
3968 15960 1.379044 GGGGATTCACCACCTGCTG 60.379 63.158 0.00 0.00 41.20 4.41
3974 15966 2.690734 GGGGAGGGGGATTCACCAC 61.691 68.421 7.39 0.00 38.06 4.16
3975 15967 2.286885 GGGGAGGGGGATTCACCA 60.287 66.667 7.39 0.00 38.06 4.17
3976 15968 3.103890 GGGGGAGGGGGATTCACC 61.104 72.222 0.00 0.00 37.40 4.02
3977 15969 1.622752 AAGGGGGAGGGGGATTCAC 60.623 63.158 0.00 0.00 0.00 3.18
3978 15970 1.308746 GAAGGGGGAGGGGGATTCA 60.309 63.158 0.00 0.00 0.00 2.57
3979 15971 2.452937 CGAAGGGGGAGGGGGATTC 61.453 68.421 0.00 0.00 0.00 2.52
3980 15972 2.368329 CGAAGGGGGAGGGGGATT 60.368 66.667 0.00 0.00 0.00 3.01
3996 15988 1.301558 GATGCTGAGATGGGAGCCG 60.302 63.158 0.00 0.00 34.04 5.52
4006 15998 3.606595 TTCTCCTCTTGTGATGCTGAG 57.393 47.619 0.00 0.00 0.00 3.35
4007 15999 4.259356 CATTTCTCCTCTTGTGATGCTGA 58.741 43.478 0.00 0.00 0.00 4.26
4063 16056 1.070786 GTGTGGAGTTCTTCGCCCA 59.929 57.895 0.00 0.00 35.07 5.36
4064 16057 0.534203 TTGTGTGGAGTTCTTCGCCC 60.534 55.000 0.00 0.00 35.07 6.13
4068 16061 1.604278 GCCAGTTGTGTGGAGTTCTTC 59.396 52.381 0.00 0.00 40.44 2.87
4140 16133 7.731054 AGTGATCCAGACCACTCTTATATTTC 58.269 38.462 0.00 0.00 39.19 2.17
4141 16134 7.682787 AGTGATCCAGACCACTCTTATATTT 57.317 36.000 0.00 0.00 39.19 1.40
4146 16139 6.017192 ACTTTAGTGATCCAGACCACTCTTA 58.983 40.000 0.00 0.00 42.12 2.10
4147 16140 4.841246 ACTTTAGTGATCCAGACCACTCTT 59.159 41.667 0.00 0.00 42.12 2.85
4149 16142 4.810191 ACTTTAGTGATCCAGACCACTC 57.190 45.455 0.00 0.00 42.12 3.51
4177 16177 9.585099 TCCGTAAAGAAATATAAGAGCGTTTAA 57.415 29.630 0.00 0.00 0.00 1.52
4195 16195 3.118738 ACAATAGTGCTCCCTCCGTAAAG 60.119 47.826 0.00 0.00 0.00 1.85
4209 16209 6.015519 AGCAGCTAAGGAGAGATACAATAGTG 60.016 42.308 0.00 0.00 0.00 2.74
4211 16211 6.389091 CAGCAGCTAAGGAGAGATACAATAG 58.611 44.000 0.00 0.00 0.00 1.73
4239 16239 1.079405 CTACGCCTTTTCTGCCGGA 60.079 57.895 5.05 0.00 0.00 5.14
4390 16506 1.333177 CCTGGGCCTAGTAGCTGTAG 58.667 60.000 15.86 0.00 0.00 2.74
4456 16572 5.107837 CGATTCGCTAGTACAACAATGATCC 60.108 44.000 0.00 0.00 0.00 3.36
4547 16694 3.490526 CGACCATGTTTCCTTTGCTTTTG 59.509 43.478 0.00 0.00 0.00 2.44
4580 16734 2.322658 ACTCCCGAGGTCTAACAACAA 58.677 47.619 0.00 0.00 0.00 2.83
4582 16736 4.492611 CTTTACTCCCGAGGTCTAACAAC 58.507 47.826 0.00 0.00 0.00 3.32
4587 16741 2.097825 GTGCTTTACTCCCGAGGTCTA 58.902 52.381 0.00 0.00 0.00 2.59


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

AutoCloner maintained by Alex Coulton.