Multiple sequence alignment - TraesCS4D01G083100

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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 TraesCS4D01G083100 chr4D 100.000 4677 0 0 1 4677 56950706 56946030 0.000000e+00 8637.0
1 TraesCS4D01G083100 chr4B 92.753 4029 172 50 3 3975 85585854 85581890 0.000000e+00 5712.0
2 TraesCS4D01G083100 chr4A 94.509 2422 99 14 1568 3975 540015143 540017544 0.000000e+00 3705.0
3 TraesCS4D01G083100 chr4A 90.141 1491 75 39 3 1464 540013465 540014912 0.000000e+00 1873.0
4 TraesCS4D01G083100 chr4A 95.886 1118 38 5 1779 2896 540081807 540082916 0.000000e+00 1803.0
5 TraesCS4D01G083100 chr4A 95.886 1118 38 5 1779 2896 540084030 540085139 0.000000e+00 1803.0
6 TraesCS4D01G083100 chr4A 95.796 1118 39 5 1779 2896 540086234 540087343 0.000000e+00 1797.0
7 TraesCS4D01G083100 chr4A 95.528 1118 41 6 1779 2896 540082919 540084027 0.000000e+00 1779.0
8 TraesCS4D01G083100 chr4A 93.918 1118 40 10 1779 2896 540085142 540086231 0.000000e+00 1663.0
9 TraesCS4D01G083100 chr4A 95.524 916 33 5 1779 2694 540080172 540081079 0.000000e+00 1458.0
10 TraesCS4D01G083100 chr4A 95.989 723 21 5 2174 2896 540081090 540081804 0.000000e+00 1168.0
11 TraesCS4D01G083100 chr4A 92.587 715 30 5 3140 3832 540087454 540088167 0.000000e+00 1005.0
12 TraesCS4D01G083100 chr4A 91.946 149 9 2 3828 3975 540093690 540093836 6.130000e-49 206.0
13 TraesCS4D01G083100 chr4A 97.196 107 3 0 1779 1885 540087346 540087452 1.030000e-41 182.0
14 TraesCS4D01G083100 chr4A 100.000 40 0 0 1522 1561 540015015 540015054 1.800000e-09 75.0
15 TraesCS4D01G083100 chr5A 96.423 643 19 4 4035 4673 580927868 580928510 0.000000e+00 1057.0
16 TraesCS4D01G083100 chr1D 96.401 639 19 4 4035 4669 433907783 433908421 0.000000e+00 1050.0
17 TraesCS4D01G083100 chr1D 95.625 640 22 6 4035 4669 457215318 457215956 0.000000e+00 1022.0
18 TraesCS4D01G083100 chr1D 95.618 639 23 5 4035 4669 469095739 469096376 0.000000e+00 1020.0
19 TraesCS4D01G083100 chr1D 95.745 47 2 0 3990 4036 310856166 310856120 5.020000e-10 76.8
20 TraesCS4D01G083100 chr1D 100.000 31 0 0 3993 4023 99701532 99701562 1.820000e-04 58.4
21 TraesCS4D01G083100 chr5D 95.827 647 23 4 4035 4677 135516887 135516241 0.000000e+00 1042.0
22 TraesCS4D01G083100 chr5D 95.231 650 23 6 4035 4677 525595223 525594575 0.000000e+00 1022.0
23 TraesCS4D01G083100 chr2D 95.639 642 24 4 4035 4672 318350484 318349843 0.000000e+00 1027.0
24 TraesCS4D01G083100 chr2D 95.356 646 25 5 4036 4677 386482094 386482738 0.000000e+00 1022.0
25 TraesCS4D01G083100 chr2D 95.077 650 24 6 4035 4677 562895529 562894881 0.000000e+00 1016.0
26 TraesCS4D01G083100 chr7A 95.447 593 23 4 4089 4677 162587508 162588100 0.000000e+00 942.0
27 TraesCS4D01G083100 chr7A 97.872 47 1 0 3990 4036 461791213 461791259 1.080000e-11 82.4
28 TraesCS4D01G083100 chr1A 93.750 48 3 0 3989 4036 154018484 154018437 6.490000e-09 73.1
29 TraesCS4D01G083100 chr1A 88.889 54 4 2 3984 4036 535730277 535730329 1.090000e-06 65.8
30 TraesCS4D01G083100 chr7D 95.455 44 2 0 3993 4036 586893091 586893134 2.330000e-08 71.3
31 TraesCS4D01G083100 chr1B 100.000 29 0 0 3988 4016 662204804 662204776 2.000000e-03 54.7
32 TraesCS4D01G083100 chr6A 100.000 28 0 0 3989 4016 59960229 59960202 8.000000e-03 52.8


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 TraesCS4D01G083100 chr4D 56946030 56950706 4676 True 8637.000000 8637 100.000000 1 4677 1 chr4D.!!$R1 4676
1 TraesCS4D01G083100 chr4B 85581890 85585854 3964 True 5712.000000 5712 92.753000 3 3975 1 chr4B.!!$R1 3972
2 TraesCS4D01G083100 chr4A 540013465 540017544 4079 False 1884.333333 3705 94.883333 3 3975 3 chr4A.!!$F2 3972
3 TraesCS4D01G083100 chr4A 540080172 540088167 7995 False 1406.444444 1803 95.367778 1779 3832 9 chr4A.!!$F3 2053
4 TraesCS4D01G083100 chr5A 580927868 580928510 642 False 1057.000000 1057 96.423000 4035 4673 1 chr5A.!!$F1 638
5 TraesCS4D01G083100 chr1D 433907783 433908421 638 False 1050.000000 1050 96.401000 4035 4669 1 chr1D.!!$F2 634
6 TraesCS4D01G083100 chr1D 457215318 457215956 638 False 1022.000000 1022 95.625000 4035 4669 1 chr1D.!!$F3 634
7 TraesCS4D01G083100 chr1D 469095739 469096376 637 False 1020.000000 1020 95.618000 4035 4669 1 chr1D.!!$F4 634
8 TraesCS4D01G083100 chr5D 135516241 135516887 646 True 1042.000000 1042 95.827000 4035 4677 1 chr5D.!!$R1 642
9 TraesCS4D01G083100 chr5D 525594575 525595223 648 True 1022.000000 1022 95.231000 4035 4677 1 chr5D.!!$R2 642
10 TraesCS4D01G083100 chr2D 318349843 318350484 641 True 1027.000000 1027 95.639000 4035 4672 1 chr2D.!!$R1 637
11 TraesCS4D01G083100 chr2D 386482094 386482738 644 False 1022.000000 1022 95.356000 4036 4677 1 chr2D.!!$F1 641
12 TraesCS4D01G083100 chr2D 562894881 562895529 648 True 1016.000000 1016 95.077000 4035 4677 1 chr2D.!!$R2 642
13 TraesCS4D01G083100 chr7A 162587508 162588100 592 False 942.000000 942 95.447000 4089 4677 1 chr7A.!!$F1 588

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
241 252 0.254178 TGATCCTCCCTTTGCTCTGC 59.746 55.0 0.0 0.0 0.00 4.26 F
1143 1172 0.037303 ACAATGGAGCAGGTGAGTGG 59.963 55.0 0.0 0.0 0.00 4.00 F
1288 1325 0.953727 TTGCCTGTGTTGATCAGTGC 59.046 50.0 0.0 0.0 33.27 4.40 F
2433 3746 0.093705 GTGACGCTGAATCTTGTCGC 59.906 55.0 0.0 0.0 35.08 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1288 1325 0.109412 GTCTCCGACAACACCCTACG 60.109 60.000 0.00 0.0 32.09 3.51 R
2433 3746 0.608640 ACCTAGCAAGACAAGGACCG 59.391 55.000 0.00 0.0 34.34 4.79 R
2841 5269 1.227089 ATCGTGCAGGATGACGCTC 60.227 57.895 20.52 0.0 39.69 5.03 R
3991 8512 0.036010 CGTCCCATTGGAGTTGCTCT 60.036 55.000 3.62 0.0 42.85 4.09 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
91 99 5.104067 AGGTGGGAGTTACTCTGTTCTTTTT 60.104 40.000 12.41 0.00 0.00 1.94
114 122 5.523438 TGGGTCAGTTTGGTGTAAAAATC 57.477 39.130 0.00 0.00 0.00 2.17
183 191 0.387202 AGCACGATCGAGGATGAAGG 59.613 55.000 24.34 0.63 0.00 3.46
197 205 3.507622 GGATGAAGGGTTCCACTTGAAAG 59.492 47.826 0.00 0.00 33.94 2.62
241 252 0.254178 TGATCCTCCCTTTGCTCTGC 59.746 55.000 0.00 0.00 0.00 4.26
242 253 0.254178 GATCCTCCCTTTGCTCTGCA 59.746 55.000 0.00 0.00 36.47 4.41
243 254 0.924823 ATCCTCCCTTTGCTCTGCAT 59.075 50.000 0.00 0.00 38.76 3.96
245 256 0.323178 CCTCCCTTTGCTCTGCATGT 60.323 55.000 0.00 0.00 38.76 3.21
249 260 2.699846 TCCCTTTGCTCTGCATGTTTTT 59.300 40.909 0.00 0.00 38.76 1.94
411 425 5.351740 TGGCATCGTAAATTCGTAATCACAA 59.648 36.000 0.00 0.00 0.00 3.33
545 565 1.412079 TGTCCAAAGCCTGCACAATT 58.588 45.000 0.00 0.00 0.00 2.32
547 567 2.224018 TGTCCAAAGCCTGCACAATTTC 60.224 45.455 0.00 0.00 0.00 2.17
577 597 7.172019 GTCTGACTCAGAAACCGGTAATTAAAA 59.828 37.037 8.00 0.00 42.46 1.52
588 608 4.095334 CCGGTAATTAAAACTAGCCACACC 59.905 45.833 0.00 0.00 0.00 4.16
736 756 2.693267 AGACCAGAAATTAGGCCGAC 57.307 50.000 0.00 0.00 0.00 4.79
745 765 0.745468 ATTAGGCCGACGAGGAAGAC 59.255 55.000 0.00 0.00 45.00 3.01
831 860 1.398390 GTTGATCTGCGGATTGTCACC 59.602 52.381 9.98 0.00 31.46 4.02
930 959 7.631594 GCCTTTTGGTTTCTTCTTCTTCTTCTT 60.632 37.037 0.00 0.00 42.99 2.52
931 960 7.918033 CCTTTTGGTTTCTTCTTCTTCTTCTTC 59.082 37.037 0.00 0.00 34.07 2.87
932 961 8.581253 TTTTGGTTTCTTCTTCTTCTTCTTCT 57.419 30.769 0.00 0.00 0.00 2.85
939 968 7.234661 TCTTCTTCTTCTTCTTCTACCTTCC 57.765 40.000 0.00 0.00 0.00 3.46
1045 1074 1.206072 GTGTTTCTGCTCTGCTGCG 59.794 57.895 0.00 0.00 35.36 5.18
1046 1075 1.227645 TGTTTCTGCTCTGCTGCGT 60.228 52.632 0.00 0.00 35.36 5.24
1111 1140 2.618053 CCACTCTACGACAACAATCCC 58.382 52.381 0.00 0.00 0.00 3.85
1143 1172 0.037303 ACAATGGAGCAGGTGAGTGG 59.963 55.000 0.00 0.00 0.00 4.00
1172 1201 5.104776 TCCTCATCTACCACCTCATGAAAAG 60.105 44.000 0.00 0.00 0.00 2.27
1173 1202 4.517285 TCATCTACCACCTCATGAAAAGC 58.483 43.478 0.00 0.00 0.00 3.51
1174 1203 4.225942 TCATCTACCACCTCATGAAAAGCT 59.774 41.667 0.00 0.00 0.00 3.74
1176 1205 5.755409 TCTACCACCTCATGAAAAGCTTA 57.245 39.130 0.00 0.00 0.00 3.09
1177 1206 6.313519 TCTACCACCTCATGAAAAGCTTAT 57.686 37.500 0.00 0.00 0.00 1.73
1178 1207 6.115446 TCTACCACCTCATGAAAAGCTTATG 58.885 40.000 0.00 0.00 0.00 1.90
1183 1212 6.127535 CCACCTCATGAAAAGCTTATGAATGT 60.128 38.462 10.75 8.51 31.11 2.71
1184 1213 7.318141 CACCTCATGAAAAGCTTATGAATGTT 58.682 34.615 10.75 0.00 31.11 2.71
1231 1265 2.175878 AGTGTGCCTCTGATGTGTTC 57.824 50.000 0.00 0.00 0.00 3.18
1268 1305 3.270877 GCCTGTGAGGTAATTGATCGTT 58.729 45.455 0.00 0.00 37.80 3.85
1288 1325 0.953727 TTGCCTGTGTTGATCAGTGC 59.046 50.000 0.00 0.00 33.27 4.40
1407 1444 4.039124 GGAGGGTTCAACATCACAAACAAT 59.961 41.667 0.00 0.00 0.00 2.71
1504 1545 5.698545 AGATAGACTGACTTGCTCACAAAAC 59.301 40.000 0.00 0.00 34.74 2.43
1505 1546 3.878778 AGACTGACTTGCTCACAAAACT 58.121 40.909 0.00 0.00 34.74 2.66
1615 1816 5.091261 AGTTGACTGAACAAAGTGAGAGT 57.909 39.130 0.00 0.00 36.98 3.24
1618 1819 3.197766 TGACTGAACAAAGTGAGAGTGGT 59.802 43.478 0.00 0.00 0.00 4.16
1639 1840 1.538047 AACCATATGCATCCATCGGC 58.462 50.000 0.19 0.00 32.85 5.54
1681 1883 4.936411 TGTGTTTACTTTTTCAGTCGACCA 59.064 37.500 13.01 0.00 36.88 4.02
1730 1932 3.731652 TGGTGCATTATGGCTTATTGC 57.268 42.857 16.09 16.09 37.58 3.56
1851 2053 3.979101 TGCCATCTTGTGTCTGTCATA 57.021 42.857 0.00 0.00 0.00 2.15
1902 2104 2.543777 AAGTTTCAGCTCAGCGGTAA 57.456 45.000 0.00 0.00 0.00 2.85
2075 2277 3.579709 CATCAAAGATATCGTCGGGAGG 58.420 50.000 0.00 0.00 0.00 4.30
2128 2330 2.306805 ACATCACAGGAGCCATTGAGAA 59.693 45.455 0.00 0.00 0.00 2.87
2186 3499 5.455872 AGCCAATCCTTTGATCATCTGAAT 58.544 37.500 0.00 0.00 34.60 2.57
2286 3599 6.594788 AAGGCATCAACACATTGTAAGAAT 57.405 33.333 0.00 0.00 37.11 2.40
2287 3600 6.199937 AGGCATCAACACATTGTAAGAATC 57.800 37.500 0.00 0.00 37.11 2.52
2353 3666 7.602517 AGTTCTTGAATCTTATGAAACCTCG 57.397 36.000 0.00 0.00 0.00 4.63
2433 3746 0.093705 GTGACGCTGAATCTTGTCGC 59.906 55.000 0.00 0.00 35.08 5.19
2626 3942 3.758554 ACATCCACCACAATAAGCTGAAC 59.241 43.478 0.00 0.00 0.00 3.18
2841 5269 1.227089 CAGCGAGAAGATGTCCGGG 60.227 63.158 0.00 0.00 0.00 5.73
2899 6419 6.070251 ACATGACATCATAGACCAGGTAACAA 60.070 38.462 0.00 0.00 34.60 2.83
2903 6423 7.552687 TGACATCATAGACCAGGTAACAAATTC 59.447 37.037 0.00 0.00 41.41 2.17
2904 6424 7.402054 ACATCATAGACCAGGTAACAAATTCA 58.598 34.615 0.00 0.00 41.41 2.57
2905 6425 7.554118 ACATCATAGACCAGGTAACAAATTCAG 59.446 37.037 0.00 0.00 41.41 3.02
2907 6427 7.103641 TCATAGACCAGGTAACAAATTCAGAC 58.896 38.462 0.00 0.00 41.41 3.51
2908 6428 5.304686 AGACCAGGTAACAAATTCAGACA 57.695 39.130 0.00 0.00 41.41 3.41
2911 6431 5.063880 ACCAGGTAACAAATTCAGACAGAC 58.936 41.667 0.00 0.00 41.41 3.51
2912 6432 5.163195 ACCAGGTAACAAATTCAGACAGACT 60.163 40.000 0.00 0.00 41.41 3.24
2913 6433 5.409826 CCAGGTAACAAATTCAGACAGACTC 59.590 44.000 0.00 0.00 41.41 3.36
2914 6434 6.226787 CAGGTAACAAATTCAGACAGACTCT 58.773 40.000 0.00 0.00 41.41 3.24
2915 6435 6.146837 CAGGTAACAAATTCAGACAGACTCTG 59.853 42.308 4.36 4.36 43.92 3.35
2916 6436 6.183361 AGGTAACAAATTCAGACAGACTCTGT 60.183 38.462 11.69 11.69 44.19 3.41
2918 6438 7.656137 GGTAACAAATTCAGACAGACTCTGTAA 59.344 37.037 11.84 3.70 45.44 2.41
2919 6439 7.484035 AACAAATTCAGACAGACTCTGTAAC 57.516 36.000 11.84 0.92 45.44 2.50
2944 6868 3.986970 TGAAGCTGCGTTCAGAAGA 57.013 47.368 9.45 0.00 42.95 2.87
2975 6909 7.547019 CAGACAGAGTTAGCATGATTGTTTCTA 59.453 37.037 0.00 0.00 0.00 2.10
3016 7321 6.402118 CGACAGGTGAATTCGAACATTTACAT 60.402 38.462 0.00 0.00 34.62 2.29
3017 7322 6.611381 ACAGGTGAATTCGAACATTTACATG 58.389 36.000 15.26 15.26 39.21 3.21
3161 7660 2.360801 TCAGGTAAACAAACAAGCAGCC 59.639 45.455 0.00 0.00 0.00 4.85
3331 7852 0.317479 ACTACGACAAGGTGCAGACC 59.683 55.000 0.00 0.00 43.52 3.85
3639 8160 2.956964 CGAGTTCGCCGAGATGCC 60.957 66.667 0.00 0.00 0.00 4.40
3640 8161 2.956964 GAGTTCGCCGAGATGCCG 60.957 66.667 0.00 0.00 0.00 5.69
3975 8496 9.066892 TCATGGCCTGATTTATAATCTTACAAC 57.933 33.333 3.32 0.00 0.00 3.32
3976 8497 7.490962 TGGCCTGATTTATAATCTTACAACG 57.509 36.000 3.32 0.00 0.00 4.10
3977 8498 6.017440 TGGCCTGATTTATAATCTTACAACGC 60.017 38.462 3.32 0.00 0.00 4.84
3978 8499 6.017440 GGCCTGATTTATAATCTTACAACGCA 60.017 38.462 0.00 0.00 0.00 5.24
3979 8500 7.308589 GGCCTGATTTATAATCTTACAACGCAT 60.309 37.037 0.00 0.00 0.00 4.73
3980 8501 8.717821 GCCTGATTTATAATCTTACAACGCATA 58.282 33.333 0.00 0.00 0.00 3.14
4001 8522 9.760660 CGCATATATTTTATTTAGAGCAACTCC 57.239 33.333 0.00 0.00 0.00 3.85
4007 8528 6.773976 TTTATTTAGAGCAACTCCAATGGG 57.226 37.500 0.00 0.00 0.00 4.00
4008 8529 4.591321 ATTTAGAGCAACTCCAATGGGA 57.409 40.909 0.00 0.00 42.29 4.37
4009 8530 3.350219 TTAGAGCAACTCCAATGGGAC 57.650 47.619 0.00 0.00 38.64 4.46
4010 8531 0.036010 AGAGCAACTCCAATGGGACG 60.036 55.000 0.00 0.00 38.64 4.79
4011 8532 0.036388 GAGCAACTCCAATGGGACGA 60.036 55.000 0.00 0.00 38.64 4.20
4012 8533 0.321653 AGCAACTCCAATGGGACGAC 60.322 55.000 0.00 0.00 38.64 4.34
4013 8534 1.305930 GCAACTCCAATGGGACGACC 61.306 60.000 0.00 0.00 38.64 4.79
4030 8551 3.732892 CCAAACGGACGGCGCATT 61.733 61.111 10.83 0.00 0.00 3.56
4031 8552 2.254051 CAAACGGACGGCGCATTT 59.746 55.556 10.83 0.00 0.00 2.32
4032 8553 2.080062 CAAACGGACGGCGCATTTG 61.080 57.895 10.83 9.01 0.00 2.32
4033 8554 2.548295 AAACGGACGGCGCATTTGT 61.548 52.632 10.83 0.74 0.00 2.83
4107 8629 2.223641 CCCATTTCATGTCCGCATTCAG 60.224 50.000 0.00 0.00 31.99 3.02
4162 8685 2.190313 GGCCATGTCTCATGCCGA 59.810 61.111 0.00 0.00 33.59 5.54
4170 8693 0.391661 GTCTCATGCCGACACCATGT 60.392 55.000 9.30 0.00 40.63 3.21
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.953686 CCGCCCAAGAACTCAAGAAAA 59.046 47.619 0.00 0.00 0.00 2.29
1 2 1.133915 ACCGCCCAAGAACTCAAGAAA 60.134 47.619 0.00 0.00 0.00 2.52
57 61 2.830651 ACTCCCACCTGAGGTACTAG 57.169 55.000 2.59 4.23 41.55 2.57
62 66 1.433592 AGAGTAACTCCCACCTGAGGT 59.566 52.381 0.00 0.00 36.66 3.85
66 70 2.900546 AGAACAGAGTAACTCCCACCTG 59.099 50.000 0.00 0.00 0.00 4.00
67 71 3.261818 AGAACAGAGTAACTCCCACCT 57.738 47.619 0.00 0.00 0.00 4.00
68 72 4.353383 AAAGAACAGAGTAACTCCCACC 57.647 45.455 0.00 0.00 0.00 4.61
91 99 5.163395 GGATTTTTACACCAAACTGACCCAA 60.163 40.000 0.00 0.00 0.00 4.12
103 111 5.801531 AAACCCTCTTGGATTTTTACACC 57.198 39.130 0.00 0.00 38.00 4.16
108 116 7.234577 TGCTATGTAAAACCCTCTTGGATTTTT 59.765 33.333 0.00 0.00 39.58 1.94
114 122 5.765182 CCTATGCTATGTAAAACCCTCTTGG 59.235 44.000 0.00 0.00 41.37 3.61
154 162 0.368227 CGATCGTGCTGCAACTCTTC 59.632 55.000 2.77 0.00 0.00 2.87
161 169 1.227060 CATCCTCGATCGTGCTGCA 60.227 57.895 15.94 0.00 0.00 4.41
183 191 4.759516 TTTATCGCTTTCAAGTGGAACC 57.240 40.909 0.35 0.00 37.80 3.62
197 205 7.900352 CACAAGTAATTCAGAGTCTTTTATCGC 59.100 37.037 0.00 0.00 0.00 4.58
249 260 4.832266 TCAGAGAAGCCAAAAATAAGCCAA 59.168 37.500 0.00 0.00 0.00 4.52
250 261 4.406456 TCAGAGAAGCCAAAAATAAGCCA 58.594 39.130 0.00 0.00 0.00 4.75
251 262 5.183904 TCTTCAGAGAAGCCAAAAATAAGCC 59.816 40.000 1.96 0.00 0.00 4.35
545 565 3.550233 CGGTTTCTGAGTCAGACGAAGAA 60.550 47.826 22.57 10.94 40.46 2.52
547 567 2.320367 CGGTTTCTGAGTCAGACGAAG 58.680 52.381 22.57 10.79 40.46 3.79
577 597 1.754745 CTGTGGTGGTGTGGCTAGT 59.245 57.895 0.00 0.00 0.00 2.57
588 608 1.741525 CTTGGGTTTGCCTGTGGTG 59.258 57.895 0.00 0.00 34.45 4.17
736 756 0.241213 TGTCAGCTTCGTCTTCCTCG 59.759 55.000 0.00 0.00 0.00 4.63
745 765 1.156645 GGCTAGGCATGTCAGCTTCG 61.157 60.000 12.16 0.00 35.60 3.79
831 860 2.034254 CGACTAGATTTCTGCATGTGCG 60.034 50.000 0.00 0.00 45.83 5.34
930 959 4.007457 CCGACGTGGGAAGGTAGA 57.993 61.111 11.78 0.00 0.00 2.59
939 968 1.019278 CAATCTCAACCCCGACGTGG 61.019 60.000 0.00 0.00 37.55 4.94
1045 1074 4.759096 GCATGTGACGGCCGCAAC 62.759 66.667 28.58 23.94 38.96 4.17
1111 1140 1.252904 CCATTGTGGGGTGAGCCTTG 61.253 60.000 0.00 0.00 32.67 3.61
1143 1172 6.438741 TCATGAGGTGGTAGATGAGGATTATC 59.561 42.308 0.00 0.00 0.00 1.75
1184 1213 5.141182 TGCATGTTACTGGGAAGGTAAAAA 58.859 37.500 0.00 0.00 32.06 1.94
1268 1305 1.337703 GCACTGATCAACACAGGCAAA 59.662 47.619 0.00 0.00 39.38 3.68
1288 1325 0.109412 GTCTCCGACAACACCCTACG 60.109 60.000 0.00 0.00 32.09 3.51
1341 1378 4.035792 TCAAGAGGATCGATTCTTCTCGTC 59.964 45.833 7.87 1.85 39.72 4.20
1407 1444 7.451877 AGAAGAGAACTTACACTCCAGTAATGA 59.548 37.037 0.00 0.00 36.39 2.57
1618 1819 3.081061 GCCGATGGATGCATATGGTTTA 58.919 45.455 16.23 0.00 0.00 2.01
1639 1840 6.241207 ACACAGGACAATCAGTTTTAATCG 57.759 37.500 0.00 0.00 0.00 3.34
1730 1932 1.750778 AGCCCGCAAAAATGATACCAG 59.249 47.619 0.00 0.00 0.00 4.00
1851 2053 8.807667 CAAAAACTGCAAGAAGAATGATAAGT 57.192 30.769 0.00 0.00 37.43 2.24
2027 2229 5.511571 TCTGCTCTAGAATGAAATCGTACG 58.488 41.667 9.53 9.53 30.84 3.67
2093 2295 3.322369 TGTGATGTTGTAAATCGTCGCT 58.678 40.909 0.00 0.00 33.12 4.93
2128 2330 4.333913 AGCTTCGATATGTTCTGCATCT 57.666 40.909 0.00 0.00 38.94 2.90
2186 3499 0.759959 TCAGTGCCTTTACCGTGGAA 59.240 50.000 0.00 0.00 0.00 3.53
2327 3640 9.151471 CGAGGTTTCATAAGATTCAAGAACTAA 57.849 33.333 0.00 0.00 0.00 2.24
2353 3666 7.446625 AGCTGTATTAGTTCCCATGATGATTTC 59.553 37.037 0.00 0.00 0.00 2.17
2433 3746 0.608640 ACCTAGCAAGACAAGGACCG 59.391 55.000 0.00 0.00 34.34 4.79
2519 3835 6.356977 CACTACAATAAAGAAGCAACGTGTTG 59.643 38.462 8.35 8.35 43.14 3.33
2587 3903 7.716560 TGGTGGATGTCTGAAGTAAATGATATG 59.283 37.037 0.00 0.00 0.00 1.78
2626 3942 9.338291 CTGTCATCAGAACATGAACTAAAATTG 57.662 33.333 0.00 0.00 42.53 2.32
2760 4076 4.435970 TACTCCTCGAGGGCCGCA 62.436 66.667 30.80 10.69 38.37 5.69
2841 5269 1.227089 ATCGTGCAGGATGACGCTC 60.227 57.895 20.52 0.00 39.69 5.03
2904 6424 5.594725 TCAGAGTTTGTTACAGAGTCTGTCT 59.405 40.000 28.70 18.03 41.21 3.41
2905 6425 5.833082 TCAGAGTTTGTTACAGAGTCTGTC 58.167 41.667 28.70 16.13 41.21 3.51
2907 6427 5.176590 GCTTCAGAGTTTGTTACAGAGTCTG 59.823 44.000 25.59 25.59 43.19 3.51
2908 6428 5.069781 AGCTTCAGAGTTTGTTACAGAGTCT 59.930 40.000 7.33 7.33 29.94 3.24
2911 6431 4.084118 GCAGCTTCAGAGTTTGTTACAGAG 60.084 45.833 0.00 0.00 0.00 3.35
2912 6432 3.809832 GCAGCTTCAGAGTTTGTTACAGA 59.190 43.478 0.00 0.00 0.00 3.41
2913 6433 3.363378 CGCAGCTTCAGAGTTTGTTACAG 60.363 47.826 0.00 0.00 0.00 2.74
2914 6434 2.543848 CGCAGCTTCAGAGTTTGTTACA 59.456 45.455 0.00 0.00 0.00 2.41
2915 6435 2.544267 ACGCAGCTTCAGAGTTTGTTAC 59.456 45.455 0.00 0.00 0.00 2.50
2916 6436 2.833794 ACGCAGCTTCAGAGTTTGTTA 58.166 42.857 0.00 0.00 0.00 2.41
2918 6438 1.599542 GAACGCAGCTTCAGAGTTTGT 59.400 47.619 0.00 0.00 0.00 2.83
2919 6439 1.599071 TGAACGCAGCTTCAGAGTTTG 59.401 47.619 3.87 0.00 0.00 2.93
2944 6868 3.513119 TCATGCTAACTCTGTCTGCTCTT 59.487 43.478 0.00 0.00 0.00 2.85
2975 6909 7.881142 TCACCTGTCGAAAACATGATTAATTT 58.119 30.769 0.00 0.00 37.23 1.82
2979 6913 7.447374 AATTCACCTGTCGAAAACATGATTA 57.553 32.000 0.00 0.00 37.23 1.75
2984 6918 4.062293 TCGAATTCACCTGTCGAAAACAT 58.938 39.130 6.22 0.00 40.59 2.71
3331 7852 1.393603 TCTGGATGGAGCTCGTGTAG 58.606 55.000 7.83 2.65 0.00 2.74
3639 8160 3.121030 CTCGCACCTTCTTGGCCG 61.121 66.667 0.00 0.00 40.22 6.13
3640 8161 2.032681 ACTCGCACCTTCTTGGCC 59.967 61.111 0.00 0.00 40.22 5.36
3795 8316 2.113910 ACCAAACATTTCGCGTCAAC 57.886 45.000 5.77 0.00 0.00 3.18
3953 8474 6.017440 TGCGTTGTAAGATTATAAATCAGGCC 60.017 38.462 0.00 0.00 0.00 5.19
3975 8496 9.760660 GGAGTTGCTCTAAATAAAATATATGCG 57.239 33.333 0.00 0.00 0.00 4.73
3981 8502 8.912988 CCCATTGGAGTTGCTCTAAATAAAATA 58.087 33.333 3.62 0.00 34.82 1.40
3982 8503 7.619302 TCCCATTGGAGTTGCTCTAAATAAAAT 59.381 33.333 3.62 0.00 34.82 1.82
3983 8504 6.951198 TCCCATTGGAGTTGCTCTAAATAAAA 59.049 34.615 3.62 0.00 34.82 1.52
3984 8505 6.377146 GTCCCATTGGAGTTGCTCTAAATAAA 59.623 38.462 3.62 0.00 42.85 1.40
3985 8506 5.885912 GTCCCATTGGAGTTGCTCTAAATAA 59.114 40.000 3.62 0.00 42.85 1.40
3986 8507 5.437060 GTCCCATTGGAGTTGCTCTAAATA 58.563 41.667 3.62 0.00 42.85 1.40
3987 8508 4.273318 GTCCCATTGGAGTTGCTCTAAAT 58.727 43.478 3.62 0.00 42.85 1.40
3988 8509 3.686016 GTCCCATTGGAGTTGCTCTAAA 58.314 45.455 3.62 0.00 42.85 1.85
3989 8510 2.354704 CGTCCCATTGGAGTTGCTCTAA 60.355 50.000 3.62 0.00 42.85 2.10
3990 8511 1.207089 CGTCCCATTGGAGTTGCTCTA 59.793 52.381 3.62 0.00 42.85 2.43
3991 8512 0.036010 CGTCCCATTGGAGTTGCTCT 60.036 55.000 3.62 0.00 42.85 4.09
3992 8513 0.036388 TCGTCCCATTGGAGTTGCTC 60.036 55.000 3.62 0.00 42.85 4.26
3993 8514 0.321653 GTCGTCCCATTGGAGTTGCT 60.322 55.000 3.62 0.00 42.85 3.91
3994 8515 1.305930 GGTCGTCCCATTGGAGTTGC 61.306 60.000 3.62 0.00 42.85 4.17
3995 8516 2.854522 GGTCGTCCCATTGGAGTTG 58.145 57.895 3.62 0.00 42.85 3.16
4006 8527 2.735857 CGTCCGTTTGGGTCGTCC 60.736 66.667 0.00 0.00 41.57 4.79
4007 8528 2.735857 CCGTCCGTTTGGGTCGTC 60.736 66.667 0.00 0.00 44.42 4.20
4008 8529 4.974989 GCCGTCCGTTTGGGTCGT 62.975 66.667 0.00 0.00 44.42 4.34
4013 8534 3.262142 AAATGCGCCGTCCGTTTGG 62.262 57.895 4.18 0.00 39.71 3.28
4014 8535 2.080062 CAAATGCGCCGTCCGTTTG 61.080 57.895 4.18 3.18 39.71 2.93
4015 8536 2.254051 CAAATGCGCCGTCCGTTT 59.746 55.556 4.18 0.00 39.71 3.60
4016 8537 2.961669 GACAAATGCGCCGTCCGTT 61.962 57.895 4.18 0.00 39.71 4.44
4017 8538 3.419759 GACAAATGCGCCGTCCGT 61.420 61.111 4.18 0.00 39.71 4.69
4018 8539 4.160635 GGACAAATGCGCCGTCCG 62.161 66.667 16.42 0.29 39.86 4.79
4020 8541 4.160635 CGGGACAAATGCGCCGTC 62.161 66.667 4.18 6.37 0.00 4.79
4026 8547 3.810896 GGACGCCGGGACAAATGC 61.811 66.667 2.18 0.00 0.00 3.56
4027 8548 3.496131 CGGACGCCGGGACAAATG 61.496 66.667 2.18 0.00 44.15 2.32
4054 8575 1.095228 CGCACTGCCGACCCAAATAT 61.095 55.000 0.00 0.00 0.00 1.28
4170 8693 2.179547 CATTGTATGCCGGCGCTGA 61.180 57.895 23.90 3.74 35.36 4.26
4267 8793 0.666577 GTGGTCGAACTCAAGTCCCG 60.667 60.000 0.33 0.00 0.00 5.14


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

AutoCloner maintained by Alex Coulton.