Multiple sequence alignment - TraesCS4D01G286000

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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 TraesCS4D01G286000 chr4D 100.000 5114 0 0 1 5114 456489512 456494625 0.000000e+00 9444.0
1 TraesCS4D01G286000 chr4B 93.909 3612 139 38 1 3581 570731538 570735099 0.000000e+00 5376.0
2 TraesCS4D01G286000 chr4B 95.961 1238 38 5 3878 5114 570735398 570736624 0.000000e+00 1999.0
3 TraesCS4D01G286000 chr4B 96.283 269 9 1 3582 3849 570735130 570735398 1.690000e-119 440.0
4 TraesCS4D01G286000 chr4A 95.791 974 38 2 2609 3581 11366022 11365051 0.000000e+00 1568.0
5 TraesCS4D01G286000 chr4A 96.141 881 34 0 1727 2607 11367080 11366200 0.000000e+00 1439.0
6 TraesCS4D01G286000 chr4A 94.356 939 43 6 3582 4516 11365019 11364087 0.000000e+00 1432.0
7 TraesCS4D01G286000 chr4A 92.602 757 41 7 956 1707 11367932 11367186 0.000000e+00 1074.0
8 TraesCS4D01G286000 chr4A 89.556 766 72 7 22 781 11368762 11367999 0.000000e+00 965.0
9 TraesCS4D01G286000 chr4A 97.282 515 14 0 4600 5114 11364044 11363530 0.000000e+00 874.0
10 TraesCS4D01G286000 chr4A 100.000 37 0 0 1727 1763 11367143 11367107 9.190000e-08 69.4
11 TraesCS4D01G286000 chr5D 88.325 394 34 9 1708 2098 494069922 494069538 3.610000e-126 462.0
12 TraesCS4D01G286000 chr5D 87.692 390 41 5 1712 2098 493898465 493898850 1.010000e-121 448.0
13 TraesCS4D01G286000 chr6B 90.572 297 22 4 1708 2003 96647215 96647506 6.210000e-104 388.0


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 TraesCS4D01G286000 chr4D 456489512 456494625 5113 False 9444.0 9444 100.000000 1 5114 1 chr4D.!!$F1 5113
1 TraesCS4D01G286000 chr4B 570731538 570736624 5086 False 2605.0 5376 95.384333 1 5114 3 chr4B.!!$F1 5113
2 TraesCS4D01G286000 chr4A 11363530 11368762 5232 True 1060.2 1568 95.104000 22 5114 7 chr4A.!!$R1 5092

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
610 621 0.395311 TCCTCTTGGACGCCGTCTAT 60.395 55.000 17.76 0.0 37.46 1.98 F
1027 1045 0.459489 CTCCTGCTCTTCTTCCTCCG 59.541 60.000 0.00 0.0 0.00 4.63 F
1140 1158 0.796927 GAGTTTTCGCAGTACAGGGC 59.203 55.000 0.00 0.0 0.00 5.19 F
1925 2041 1.067283 CAGGTCAGACAATCGAGCACT 60.067 52.381 2.17 0.0 32.05 4.40 F
3852 4207 0.179103 CGTGGGGGTATCGTACAACC 60.179 60.000 0.00 0.0 34.85 3.77 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1638 1668 0.036010 ATCCCTGCTTGGAACAGTCG 60.036 55.000 0.00 0.00 42.39 4.18 R
2315 2431 0.465097 CTCCAGCGCATCCTTGGAAT 60.465 55.000 15.29 0.00 40.29 3.01 R
2334 2450 1.804151 TGTCGAAACAGCCAATACAGC 59.196 47.619 0.00 0.00 0.00 4.40 R
3867 4222 2.364002 GGGGAGTATCAGAGAACTCAGC 59.636 54.545 14.66 2.38 43.21 4.26 R
4912 5272 3.758554 GCTCCAAGACTCCAAAAGCAATA 59.241 43.478 0.00 0.00 0.00 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
34 35 3.073274 AGGTTTGAAGCACCATAGTCC 57.927 47.619 0.00 0.00 36.67 3.85
82 84 0.899019 GACCTCAGTCAAGGGAGTCC 59.101 60.000 0.00 0.00 42.99 3.85
104 106 2.766828 CCTTCTTTCTCACCGGGATACT 59.233 50.000 6.32 0.00 0.00 2.12
121 123 1.151908 CTACCTAGAGCCTCCGCCT 59.848 63.158 0.00 0.00 34.57 5.52
146 148 1.786937 AGAGACGATGCCTTCATCCT 58.213 50.000 0.00 0.00 44.83 3.24
170 172 2.534903 GCCGCCAAGAATACCTCGC 61.535 63.158 0.00 0.00 0.00 5.03
275 278 4.053295 CCAAACAACTTCAGCAAATGGAG 58.947 43.478 0.00 0.00 40.83 3.86
277 280 4.574599 AACAACTTCAGCAAATGGAGTC 57.425 40.909 0.00 0.00 45.33 3.36
278 281 3.825328 ACAACTTCAGCAAATGGAGTCT 58.175 40.909 0.00 0.00 45.33 3.24
279 282 4.210331 ACAACTTCAGCAAATGGAGTCTT 58.790 39.130 0.00 0.00 45.33 3.01
280 283 4.276926 ACAACTTCAGCAAATGGAGTCTTC 59.723 41.667 0.00 0.00 45.33 2.87
318 327 1.536418 CACCAGGTGTCCTCCTCCA 60.536 63.158 11.99 0.00 35.37 3.86
321 330 0.545309 CCAGGTGTCCTCCTCCAAGA 60.545 60.000 0.00 0.00 35.37 3.02
353 364 2.745884 CCCAAAGCGCCACATCGA 60.746 61.111 2.29 0.00 0.00 3.59
549 560 2.938451 GTCATCAGCATCCAATCAACGA 59.062 45.455 0.00 0.00 0.00 3.85
603 614 0.951040 CACAACCTCCTCTTGGACGC 60.951 60.000 0.00 0.00 37.46 5.19
610 621 0.395311 TCCTCTTGGACGCCGTCTAT 60.395 55.000 17.76 0.00 37.46 1.98
644 655 2.227865 TGATAAACCAAGCGGCAGTTTC 59.772 45.455 15.83 7.02 35.45 2.78
646 657 0.755327 AAACCAAGCGGCAGTTTCCT 60.755 50.000 1.45 0.00 34.57 3.36
695 706 2.794350 CGAAAAAGCGTGGCAAAAGATT 59.206 40.909 0.00 0.00 0.00 2.40
758 772 5.413499 GTGTAACAAAAGGCTCGAGGTATA 58.587 41.667 15.58 0.00 36.32 1.47
769 783 1.002201 TCGAGGTATAGGCTCCTCTCG 59.998 57.143 16.20 16.85 45.57 4.04
850 868 1.476085 TGTCCCTATTTTTGCCATGCG 59.524 47.619 0.00 0.00 0.00 4.73
865 883 2.023673 CATGCGAAAATTGCCTCCCTA 58.976 47.619 0.00 0.00 0.00 3.53
912 930 1.339291 GCAGGGCAAAGCATCTAATCC 59.661 52.381 0.00 0.00 0.00 3.01
940 958 2.767960 AGGGTCAAATGATCAAATGCCC 59.232 45.455 22.24 22.24 32.61 5.36
1017 1035 1.674764 CGATGGCTGTCTCCTGCTCT 61.675 60.000 0.00 0.00 35.96 4.09
1027 1045 0.459489 CTCCTGCTCTTCTTCCTCCG 59.541 60.000 0.00 0.00 0.00 4.63
1140 1158 0.796927 GAGTTTTCGCAGTACAGGGC 59.203 55.000 0.00 0.00 0.00 5.19
1159 1180 1.870055 CTCTTGCCCATGCGCAGTTT 61.870 55.000 18.32 0.00 40.53 2.66
1209 1233 9.161629 TGGATAAATCTTGTAGTACACAACATG 57.838 33.333 1.43 0.00 42.29 3.21
1277 1302 1.206132 TGCCACATTGGTACCTACTCG 59.794 52.381 14.36 0.65 40.46 4.18
1303 1332 3.559384 CCCAAGAACTCAGGAACCCTAAC 60.559 52.174 0.00 0.00 29.64 2.34
1321 1350 5.653769 CCCTAACAATCCACTGTGATTTCAT 59.346 40.000 9.86 0.00 32.71 2.57
1325 1354 7.765695 AACAATCCACTGTGATTTCATTAGT 57.234 32.000 9.86 0.00 32.71 2.24
1337 1366 8.952278 TGTGATTTCATTAGTTATTAGCCGTTT 58.048 29.630 0.00 0.00 0.00 3.60
1430 1460 5.957842 TTGCGATATTTGAACCTGAGTTT 57.042 34.783 0.00 0.00 35.94 2.66
1638 1668 5.125100 TGGTCATGTGAGAGCAAATTTTC 57.875 39.130 0.00 0.00 42.45 2.29
1640 1670 4.083324 GGTCATGTGAGAGCAAATTTTCGA 60.083 41.667 0.00 0.00 36.11 3.71
1670 1700 5.829924 CCAAGCAGGGATACTATGTCATTTT 59.170 40.000 0.00 0.00 0.00 1.82
1683 1713 6.714810 ACTATGTCATTTTGTTGAACTAGGCA 59.285 34.615 0.00 0.00 0.00 4.75
1692 1722 5.689383 TGTTGAACTAGGCAAATGTCTTC 57.311 39.130 0.00 0.00 0.00 2.87
1707 1737 2.007608 GTCTTCGTTACCCAATGCCTC 58.992 52.381 0.00 0.00 0.00 4.70
1710 1757 1.202099 TCGTTACCCAATGCCTCCCA 61.202 55.000 0.00 0.00 0.00 4.37
1717 1764 3.734926 ACCCAATGCCTCCCAAATTAAT 58.265 40.909 0.00 0.00 0.00 1.40
1787 1903 3.091545 TGATGGCCTGGAGATTTTTGAC 58.908 45.455 3.32 0.00 0.00 3.18
1879 1995 5.527214 CAGACAATGTGGAAGTACAGAACAA 59.473 40.000 0.00 0.00 33.44 2.83
1925 2041 1.067283 CAGGTCAGACAATCGAGCACT 60.067 52.381 2.17 0.00 32.05 4.40
1966 2082 4.220382 TGTTTGCATCTCTAACCCATTTGG 59.780 41.667 0.00 0.00 41.37 3.28
2095 2211 6.939132 TTTAGTCATCCTCTACCGTCTTAG 57.061 41.667 0.00 0.00 0.00 2.18
2185 2301 6.427853 TGTCTATGAAATTGTGTGTCCTCTTG 59.572 38.462 0.00 0.00 0.00 3.02
2212 2328 2.114670 CATGCCTGCCCGGTAACTG 61.115 63.158 0.00 0.00 34.25 3.16
2330 2446 1.378911 TGCATTCCAAGGATGCGCT 60.379 52.632 9.73 0.00 43.69 5.92
2334 2450 0.465097 ATTCCAAGGATGCGCTGGAG 60.465 55.000 14.16 0.00 40.29 3.86
2630 2922 7.771361 TGTTTAACAAGTAAATCTGTGTCTGGA 59.229 33.333 0.00 0.00 34.23 3.86
2691 2983 7.575365 TCGCTATGTGCACATATCTAAATTTG 58.425 34.615 33.66 21.46 43.06 2.32
2692 2984 6.798476 CGCTATGTGCACATATCTAAATTTGG 59.202 38.462 33.66 20.85 43.06 3.28
2714 3006 5.364157 TGGGTGTACAAAAGGCAGTATTTTT 59.636 36.000 0.00 0.00 0.00 1.94
3023 3315 7.938715 ACTCCTACTATACACGATTGGTTAAG 58.061 38.462 0.00 0.00 0.00 1.85
3278 3570 2.421388 GCATATGTTACAGTCCCTGGCA 60.421 50.000 4.29 0.00 35.51 4.92
3741 4066 1.327303 GCAACACTGGGAATCCACAA 58.673 50.000 0.09 0.00 38.32 3.33
3753 4078 5.048364 TGGGAATCCACAATACAAAGTTTCG 60.048 40.000 0.09 0.00 38.32 3.46
3849 4204 1.034356 CATCGTGGGGGTATCGTACA 58.966 55.000 0.00 0.00 0.00 2.90
3850 4205 1.409790 CATCGTGGGGGTATCGTACAA 59.590 52.381 0.00 0.00 0.00 2.41
3851 4206 0.817013 TCGTGGGGGTATCGTACAAC 59.183 55.000 0.00 0.00 0.00 3.32
3852 4207 0.179103 CGTGGGGGTATCGTACAACC 60.179 60.000 0.00 0.00 34.85 3.77
3853 4208 0.903942 GTGGGGGTATCGTACAACCA 59.096 55.000 10.29 0.00 37.51 3.67
3854 4209 0.903942 TGGGGGTATCGTACAACCAC 59.096 55.000 10.29 6.97 38.54 4.16
3855 4210 1.197812 GGGGGTATCGTACAACCACT 58.802 55.000 10.24 0.00 39.29 4.00
3856 4211 1.134610 GGGGGTATCGTACAACCACTG 60.135 57.143 10.24 0.00 39.29 3.66
3857 4212 1.648504 GGGTATCGTACAACCACTGC 58.351 55.000 10.29 0.00 37.51 4.40
3858 4213 1.066716 GGGTATCGTACAACCACTGCA 60.067 52.381 10.29 0.00 37.51 4.41
3859 4214 2.613474 GGGTATCGTACAACCACTGCAA 60.613 50.000 10.29 0.00 37.51 4.08
3860 4215 3.267483 GGTATCGTACAACCACTGCAAT 58.733 45.455 4.57 0.00 35.73 3.56
3861 4216 3.063452 GGTATCGTACAACCACTGCAATG 59.937 47.826 4.57 0.00 35.73 2.82
3862 4217 2.248280 TCGTACAACCACTGCAATGT 57.752 45.000 0.00 0.00 0.00 2.71
3863 4218 2.566913 TCGTACAACCACTGCAATGTT 58.433 42.857 0.00 0.00 0.00 2.71
3864 4219 2.946329 TCGTACAACCACTGCAATGTTT 59.054 40.909 0.00 0.00 0.00 2.83
3865 4220 3.378742 TCGTACAACCACTGCAATGTTTT 59.621 39.130 0.00 0.00 0.00 2.43
3866 4221 4.109050 CGTACAACCACTGCAATGTTTTT 58.891 39.130 0.00 0.00 0.00 1.94
3867 4222 4.026968 CGTACAACCACTGCAATGTTTTTG 60.027 41.667 0.00 0.00 0.00 2.44
3868 4223 2.677337 ACAACCACTGCAATGTTTTTGC 59.323 40.909 3.44 3.44 45.11 3.68
3869 4224 2.937799 CAACCACTGCAATGTTTTTGCT 59.062 40.909 11.18 0.00 45.13 3.91
3870 4225 2.553086 ACCACTGCAATGTTTTTGCTG 58.447 42.857 13.44 13.44 45.13 4.41
3871 4226 2.168106 ACCACTGCAATGTTTTTGCTGA 59.832 40.909 19.57 0.00 45.13 4.26
3872 4227 2.798283 CCACTGCAATGTTTTTGCTGAG 59.202 45.455 19.57 13.34 45.13 3.35
3873 4228 3.450578 CACTGCAATGTTTTTGCTGAGT 58.549 40.909 19.57 9.85 45.13 3.41
3874 4229 3.866910 CACTGCAATGTTTTTGCTGAGTT 59.133 39.130 19.57 0.22 45.13 3.01
3875 4230 4.026310 CACTGCAATGTTTTTGCTGAGTTC 60.026 41.667 19.57 0.00 45.13 3.01
3876 4231 4.142093 ACTGCAATGTTTTTGCTGAGTTCT 60.142 37.500 19.57 0.00 45.13 3.01
3877 4232 4.362279 TGCAATGTTTTTGCTGAGTTCTC 58.638 39.130 11.18 0.00 45.13 2.87
3968 4323 2.005370 TGACCAACTTACTCCCGAGT 57.995 50.000 2.41 2.41 45.02 4.18
4124 4479 3.426859 GTCGAGAAATGAGACACACTGTG 59.573 47.826 7.68 7.68 39.75 3.66
4125 4480 3.317993 TCGAGAAATGAGACACACTGTGA 59.682 43.478 16.30 0.00 36.96 3.58
4231 4586 5.068234 TCACTAAACCCAAGAGACATACG 57.932 43.478 0.00 0.00 0.00 3.06
4284 4639 9.223099 CAAGGCTCATTTTTCCATTTTATCTTT 57.777 29.630 0.00 0.00 0.00 2.52
4392 4748 4.135306 CCTGAGAAATATGCAGCTGTGAT 58.865 43.478 16.64 10.39 0.00 3.06
4393 4749 4.579340 CCTGAGAAATATGCAGCTGTGATT 59.421 41.667 16.64 9.56 0.00 2.57
4475 4835 4.399978 CGACGAATTTGGTAACCAATGAC 58.600 43.478 0.00 0.00 43.55 3.06
4476 4836 4.083749 CGACGAATTTGGTAACCAATGACA 60.084 41.667 0.00 0.00 43.55 3.58
4492 4852 1.202915 TGACAAGCCTGGAAATGCTCA 60.203 47.619 0.00 0.00 36.66 4.26
4521 4881 6.204688 TCCACAGTTTCTATCATGTCAACAAC 59.795 38.462 0.00 0.00 0.00 3.32
4522 4882 6.017192 CCACAGTTTCTATCATGTCAACAACA 60.017 38.462 0.00 0.00 43.51 3.33
4523 4883 7.416817 CACAGTTTCTATCATGTCAACAACAA 58.583 34.615 0.00 0.00 42.37 2.83
4534 4894 5.850557 TGTCAACAACAAATCATCCAGTT 57.149 34.783 0.00 0.00 34.03 3.16
4537 4897 6.096705 TGTCAACAACAAATCATCCAGTTTCT 59.903 34.615 0.00 0.00 34.03 2.52
4538 4898 7.284261 TGTCAACAACAAATCATCCAGTTTCTA 59.716 33.333 0.00 0.00 34.03 2.10
4539 4899 8.299570 GTCAACAACAAATCATCCAGTTTCTAT 58.700 33.333 0.00 0.00 0.00 1.98
4540 4900 8.514594 TCAACAACAAATCATCCAGTTTCTATC 58.485 33.333 0.00 0.00 0.00 2.08
4541 4901 8.298854 CAACAACAAATCATCCAGTTTCTATCA 58.701 33.333 0.00 0.00 0.00 2.15
4543 4903 8.464404 ACAACAAATCATCCAGTTTCTATCATG 58.536 33.333 0.00 0.00 0.00 3.07
4544 4904 8.464404 CAACAAATCATCCAGTTTCTATCATGT 58.536 33.333 0.00 0.00 0.00 3.21
4545 4905 8.218338 ACAAATCATCCAGTTTCTATCATGTC 57.782 34.615 0.00 0.00 0.00 3.06
4636 4996 5.055812 GGCTTGGTGAAAAACAATTCATCA 58.944 37.500 0.00 0.00 46.00 3.07
4912 5272 1.447838 CAACCTGCGGCGACACTAT 60.448 57.895 12.98 0.00 0.00 2.12
5078 5438 1.334160 TGTCCATGACACGGTACAGT 58.666 50.000 0.00 0.00 37.67 3.55
5090 5450 0.038159 GGTACAGTCTGCGCTTGTCT 60.038 55.000 9.73 1.74 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 2.558359 ACTATGGTGCTTCAAACCTTGC 59.442 45.455 0.00 0.00 38.60 4.01
82 84 0.912486 ATCCCGGTGAGAAAGAAGGG 59.088 55.000 0.00 0.00 40.16 3.95
121 123 4.736126 TGAAGGCATCGTCTCTTTGATA 57.264 40.909 0.00 0.00 0.00 2.15
146 148 0.392461 GTATTCTTGGCGGCACCTCA 60.392 55.000 12.92 0.00 40.22 3.86
170 172 2.365582 CAAGACGGGGACTTAATTGGG 58.634 52.381 0.00 0.00 0.00 4.12
234 237 3.797039 TGGTGGAGCTTCGATGATAAAG 58.203 45.455 1.89 0.00 0.00 1.85
242 245 1.134220 AGTTGTTTGGTGGAGCTTCGA 60.134 47.619 0.00 0.00 0.00 3.71
275 278 7.381377 TCATTCTGATGACGGAGACGAAGAC 62.381 48.000 0.00 0.00 46.79 3.01
276 279 5.400589 TCATTCTGATGACGGAGACGAAGA 61.401 45.833 0.00 0.00 46.79 2.87
277 280 3.181496 TCATTCTGATGACGGAGACGAAG 60.181 47.826 0.00 0.00 46.79 3.79
278 281 2.752903 TCATTCTGATGACGGAGACGAA 59.247 45.455 0.00 0.00 46.79 3.85
279 282 2.365582 TCATTCTGATGACGGAGACGA 58.634 47.619 0.00 0.00 46.79 4.20
280 283 2.851805 TCATTCTGATGACGGAGACG 57.148 50.000 0.00 0.00 45.47 4.18
309 318 1.258445 GCGGAGTTCTTGGAGGAGGA 61.258 60.000 0.00 0.00 0.00 3.71
318 327 1.292541 GGACGAAGGCGGAGTTCTT 59.707 57.895 0.00 0.00 43.17 2.52
321 330 3.703127 GGGGACGAAGGCGGAGTT 61.703 66.667 0.00 0.00 43.17 3.01
353 364 1.228154 GACCGGGTTTGCTGGAGTT 60.228 57.895 6.32 0.00 0.00 3.01
603 614 5.011090 TCACAGAGGATCAAAATAGACGG 57.989 43.478 0.00 0.00 37.82 4.79
610 621 6.071952 GCTTGGTTTATCACAGAGGATCAAAA 60.072 38.462 0.00 0.00 37.82 2.44
769 783 5.796424 ATCAAATTTCCATATGGCACCTC 57.204 39.130 17.58 0.00 34.44 3.85
817 831 9.372369 CAAAAATAGGGACAAAACAGTAAACAA 57.628 29.630 0.00 0.00 0.00 2.83
818 832 7.492994 GCAAAAATAGGGACAAAACAGTAAACA 59.507 33.333 0.00 0.00 0.00 2.83
819 833 7.042321 GGCAAAAATAGGGACAAAACAGTAAAC 60.042 37.037 0.00 0.00 0.00 2.01
823 837 4.407296 TGGCAAAAATAGGGACAAAACAGT 59.593 37.500 0.00 0.00 0.00 3.55
824 838 4.954875 TGGCAAAAATAGGGACAAAACAG 58.045 39.130 0.00 0.00 0.00 3.16
850 868 4.743057 ATTTGCTAGGGAGGCAATTTTC 57.257 40.909 2.01 0.00 46.81 2.29
912 930 7.423199 CATTTGATCATTTGACCCTCTACATG 58.577 38.462 0.00 0.00 0.00 3.21
940 958 7.670009 TTGATCATTTGCCCTGTTTTATTTG 57.330 32.000 0.00 0.00 0.00 2.32
1057 1075 1.749334 GCGAGGTGGGAGGTATGGAG 61.749 65.000 0.00 0.00 0.00 3.86
1140 1158 1.870055 AAACTGCGCATGGGCAAGAG 61.870 55.000 33.40 25.06 43.39 2.85
1159 1180 0.618458 CCCGAGAAACAGATTGGGGA 59.382 55.000 0.00 0.00 36.58 4.81
1209 1233 8.711457 CAAGTGTGAAATAAATTTGACCCAATC 58.289 33.333 0.00 0.00 33.76 2.67
1277 1302 3.409570 GGTTCCTGAGTTCTTGGGTTAC 58.590 50.000 0.00 0.00 0.00 2.50
1386 1416 7.322222 CGCAATCGAAATCCTAAATTCTTCATC 59.678 37.037 0.00 0.00 38.10 2.92
1430 1460 3.007473 TGATGCTGCATCAAGAATCCA 57.993 42.857 35.71 15.97 46.17 3.41
1603 1633 2.047179 GACCAGTCCTTGCCGACC 60.047 66.667 0.00 0.00 32.91 4.79
1638 1668 0.036010 ATCCCTGCTTGGAACAGTCG 60.036 55.000 0.00 0.00 42.39 4.18
1640 1670 2.269940 AGTATCCCTGCTTGGAACAGT 58.730 47.619 0.00 0.00 42.39 3.55
1670 1700 4.213270 CGAAGACATTTGCCTAGTTCAACA 59.787 41.667 0.00 0.00 0.00 3.33
1681 1711 3.907894 TTGGGTAACGAAGACATTTGC 57.092 42.857 0.00 0.00 37.60 3.68
1683 1713 3.192633 GGCATTGGGTAACGAAGACATTT 59.807 43.478 0.00 0.00 37.86 2.32
1692 1722 0.322997 TTGGGAGGCATTGGGTAACG 60.323 55.000 0.00 0.00 37.60 3.18
1879 1995 0.966920 ACCTCGGAAGTGAATCACGT 59.033 50.000 7.83 4.38 39.64 4.49
1925 2041 8.235359 TGCAAACATGATATGGTGATATTGAA 57.765 30.769 0.00 0.00 33.60 2.69
2095 2211 7.923414 ATAAGGGAGTTCTTGAAACACATAC 57.077 36.000 0.00 0.00 0.00 2.39
2185 2301 1.080298 GGCAGGCATGAAACAGCAC 60.080 57.895 0.62 0.00 0.00 4.40
2212 2328 2.555325 GGTTTGCAGGGTACTGTTTACC 59.445 50.000 0.00 0.00 46.62 2.85
2315 2431 0.465097 CTCCAGCGCATCCTTGGAAT 60.465 55.000 15.29 0.00 40.29 3.01
2330 2446 2.436417 GAAACAGCCAATACAGCTCCA 58.564 47.619 0.00 0.00 38.95 3.86
2334 2450 1.804151 TGTCGAAACAGCCAATACAGC 59.196 47.619 0.00 0.00 0.00 4.40
2389 2505 6.978659 TGTTGTATGTCCAAATCTCTCGATAC 59.021 38.462 0.00 0.00 0.00 2.24
2630 2922 7.902920 AATTTTACATGAGGCCATTCTATGT 57.097 32.000 5.01 10.26 36.15 2.29
2691 2983 5.462530 AAAATACTGCCTTTTGTACACCC 57.537 39.130 0.00 0.00 0.00 4.61
2692 2984 6.745116 AGAAAAATACTGCCTTTTGTACACC 58.255 36.000 0.00 0.00 0.00 4.16
3008 3300 5.808540 GTGTATGCTCTTAACCAATCGTGTA 59.191 40.000 0.00 0.00 0.00 2.90
3278 3570 4.924625 TCTGAGAGGTAGCTAGTCTTGTT 58.075 43.478 6.94 0.00 0.00 2.83
3425 3717 4.565652 GCAGAACCATTAAGAGGAAGACCA 60.566 45.833 3.90 0.00 38.94 4.02
3435 3727 5.587388 AATGGATGTGCAGAACCATTAAG 57.413 39.130 29.60 0.00 46.77 1.85
3736 4061 3.252215 TCTGGCGAAACTTTGTATTGTGG 59.748 43.478 0.00 0.00 0.00 4.17
3741 4066 6.325919 TCATTTTCTGGCGAAACTTTGTAT 57.674 33.333 4.44 0.00 38.77 2.29
3753 4078 5.643379 TGTATGAGGTTTCATTTTCTGGC 57.357 39.130 0.00 0.00 41.24 4.85
3856 4211 4.443394 CAGAGAACTCAGCAAAAACATTGC 59.557 41.667 5.06 5.06 45.22 3.56
3857 4212 5.824429 TCAGAGAACTCAGCAAAAACATTG 58.176 37.500 4.64 0.00 0.00 2.82
3858 4213 6.645790 ATCAGAGAACTCAGCAAAAACATT 57.354 33.333 4.64 0.00 0.00 2.71
3859 4214 6.939163 AGTATCAGAGAACTCAGCAAAAACAT 59.061 34.615 4.64 0.00 0.00 2.71
3860 4215 6.291377 AGTATCAGAGAACTCAGCAAAAACA 58.709 36.000 4.64 0.00 0.00 2.83
3861 4216 6.128418 GGAGTATCAGAGAACTCAGCAAAAAC 60.128 42.308 14.66 0.00 43.21 2.43
3862 4217 5.934625 GGAGTATCAGAGAACTCAGCAAAAA 59.065 40.000 14.66 0.00 43.21 1.94
3863 4218 5.482908 GGAGTATCAGAGAACTCAGCAAAA 58.517 41.667 14.66 0.00 43.21 2.44
3864 4219 4.081420 GGGAGTATCAGAGAACTCAGCAAA 60.081 45.833 14.66 0.00 43.21 3.68
3865 4220 3.449018 GGGAGTATCAGAGAACTCAGCAA 59.551 47.826 14.66 0.00 43.21 3.91
3866 4221 3.027412 GGGAGTATCAGAGAACTCAGCA 58.973 50.000 14.66 0.00 43.21 4.41
3867 4222 2.364002 GGGGAGTATCAGAGAACTCAGC 59.636 54.545 14.66 2.38 43.21 4.26
3868 4223 3.909732 AGGGGAGTATCAGAGAACTCAG 58.090 50.000 14.66 0.00 43.21 3.35
3869 4224 4.727332 TCTAGGGGAGTATCAGAGAACTCA 59.273 45.833 14.66 0.00 43.21 3.41
3870 4225 5.313280 TCTAGGGGAGTATCAGAGAACTC 57.687 47.826 7.04 7.04 41.16 3.01
3871 4226 5.941146 ATCTAGGGGAGTATCAGAGAACT 57.059 43.478 0.00 0.00 36.25 3.01
3872 4227 6.987403 AAATCTAGGGGAGTATCAGAGAAC 57.013 41.667 0.00 0.00 36.25 3.01
3873 4228 7.827787 ACTAAATCTAGGGGAGTATCAGAGAA 58.172 38.462 0.00 0.00 36.25 2.87
3874 4229 7.409408 ACTAAATCTAGGGGAGTATCAGAGA 57.591 40.000 0.00 0.00 36.25 3.10
3875 4230 9.589461 TTAACTAAATCTAGGGGAGTATCAGAG 57.411 37.037 0.00 0.00 36.25 3.35
3876 4231 9.589461 CTTAACTAAATCTAGGGGAGTATCAGA 57.411 37.037 0.00 0.00 36.25 3.27
3877 4232 8.808092 CCTTAACTAAATCTAGGGGAGTATCAG 58.192 40.741 0.00 0.00 36.25 2.90
3968 4323 8.146412 CAGATCCTACATCAGACAATCATACAA 58.854 37.037 0.00 0.00 0.00 2.41
4045 4400 2.045536 GCCCTGCTTCCTCACCAG 60.046 66.667 0.00 0.00 0.00 4.00
4124 4479 1.940613 CTGCTAAGGCGGGTAAATGTC 59.059 52.381 0.00 0.00 40.90 3.06
4125 4480 2.038387 CTGCTAAGGCGGGTAAATGT 57.962 50.000 0.00 0.00 40.90 2.71
4239 4594 5.415701 GCCTTGAATTTCAGGAATGTACAGA 59.584 40.000 9.88 0.00 0.00 3.41
4240 4595 5.416952 AGCCTTGAATTTCAGGAATGTACAG 59.583 40.000 9.88 0.00 0.00 2.74
4475 4835 1.201647 CAGTGAGCATTTCCAGGCTTG 59.798 52.381 0.00 0.00 41.22 4.01
4476 4836 1.202976 ACAGTGAGCATTTCCAGGCTT 60.203 47.619 0.00 0.00 41.22 4.35
4508 4868 6.209986 ACTGGATGATTTGTTGTTGACATGAT 59.790 34.615 0.00 0.00 38.26 2.45
4521 4881 7.350467 CGACATGATAGAAACTGGATGATTTG 58.650 38.462 0.00 0.00 0.00 2.32
4522 4882 6.017605 GCGACATGATAGAAACTGGATGATTT 60.018 38.462 0.00 0.00 0.00 2.17
4523 4883 5.468072 GCGACATGATAGAAACTGGATGATT 59.532 40.000 0.00 0.00 0.00 2.57
4534 4894 6.701841 GGTTTATCTTCTGCGACATGATAGAA 59.298 38.462 0.00 2.90 0.00 2.10
4537 4897 5.297547 GGGTTTATCTTCTGCGACATGATA 58.702 41.667 0.00 0.00 0.00 2.15
4538 4898 4.130118 GGGTTTATCTTCTGCGACATGAT 58.870 43.478 0.00 0.00 0.00 2.45
4539 4899 3.531538 GGGTTTATCTTCTGCGACATGA 58.468 45.455 0.00 0.00 0.00 3.07
4540 4900 2.285220 CGGGTTTATCTTCTGCGACATG 59.715 50.000 0.00 0.00 0.00 3.21
4541 4901 2.550978 CGGGTTTATCTTCTGCGACAT 58.449 47.619 0.00 0.00 0.00 3.06
4543 4903 1.287425 CCGGGTTTATCTTCTGCGAC 58.713 55.000 0.00 0.00 0.00 5.19
4544 4904 0.461339 GCCGGGTTTATCTTCTGCGA 60.461 55.000 2.18 0.00 0.00 5.10
4545 4905 0.742990 TGCCGGGTTTATCTTCTGCG 60.743 55.000 2.18 0.00 0.00 5.18
4614 4974 5.523188 TGTGATGAATTGTTTTTCACCAAGC 59.477 36.000 0.00 0.00 38.37 4.01
4615 4975 6.979817 TCTGTGATGAATTGTTTTTCACCAAG 59.020 34.615 0.00 0.00 38.37 3.61
4636 4996 3.068307 GGAATATGACTACGGCACTCTGT 59.932 47.826 0.00 0.00 35.61 3.41
4912 5272 3.758554 GCTCCAAGACTCCAAAAGCAATA 59.241 43.478 0.00 0.00 0.00 1.90


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

AutoCloner maintained by Alex Coulton.