Multiple sequence alignment - TraesCS4A01G204800

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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 TraesCS4A01G204800 chr4A 100.000 4560 0 0 1 4560 497009610 497014169 0.000000e+00 8421
1 TraesCS4A01G204800 chr4A 88.462 780 56 19 2 756 487544822 487544052 0.000000e+00 911
2 TraesCS4A01G204800 chr4A 84.561 421 41 14 1200 1602 661867027 661866613 3.310000e-106 396
3 TraesCS4A01G204800 chr4D 93.617 3384 127 40 750 4089 84276585 84279923 0.000000e+00 4970
4 TraesCS4A01G204800 chr4D 86.667 420 43 7 4138 4547 84280083 84280499 1.930000e-123 453
5 TraesCS4A01G204800 chr4B 90.826 1526 86 20 1867 3364 119274714 119276213 0.000000e+00 1993
6 TraesCS4A01G204800 chr4B 83.305 1186 83 45 750 1878 119273514 119274641 0.000000e+00 987
7 TraesCS4A01G204800 chr4B 86.418 670 52 19 3403 4044 119276204 119276862 0.000000e+00 697
8 TraesCS4A01G204800 chr2A 91.157 769 51 13 1 756 749965441 749966205 0.000000e+00 1027
9 TraesCS4A01G204800 chr2A 88.129 775 64 18 2 756 702125909 702126675 0.000000e+00 896
10 TraesCS4A01G204800 chr1A 89.740 770 57 16 5 756 52218655 52217890 0.000000e+00 965
11 TraesCS4A01G204800 chr1A 86.628 516 67 2 2289 2803 114545530 114546044 1.840000e-158 569
12 TraesCS4A01G204800 chr5A 89.235 771 61 15 1 756 501353638 501354401 0.000000e+00 944
13 TraesCS4A01G204800 chr2D 88.990 772 61 20 1 756 497917578 497918341 0.000000e+00 933
14 TraesCS4A01G204800 chr7A 88.963 752 67 11 18 755 660557808 660558557 0.000000e+00 915
15 TraesCS4A01G204800 chr3D 88.472 772 60 21 1 756 182343106 182343864 0.000000e+00 905
16 TraesCS4A01G204800 chr7D 88.312 770 61 21 1 759 431340122 431339371 0.000000e+00 896
17 TraesCS4A01G204800 chr1B 86.434 516 68 2 2289 2803 167713497 167714011 8.560000e-157 564
18 TraesCS4A01G204800 chr1D 86.240 516 69 2 2289 2803 110335417 110335931 3.980000e-155 558


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 TraesCS4A01G204800 chr4A 497009610 497014169 4559 False 8421.000000 8421 100.000000 1 4560 1 chr4A.!!$F1 4559
1 TraesCS4A01G204800 chr4A 487544052 487544822 770 True 911.000000 911 88.462000 2 756 1 chr4A.!!$R1 754
2 TraesCS4A01G204800 chr4D 84276585 84280499 3914 False 2711.500000 4970 90.142000 750 4547 2 chr4D.!!$F1 3797
3 TraesCS4A01G204800 chr4B 119273514 119276862 3348 False 1225.666667 1993 86.849667 750 4044 3 chr4B.!!$F1 3294
4 TraesCS4A01G204800 chr2A 749965441 749966205 764 False 1027.000000 1027 91.157000 1 756 1 chr2A.!!$F2 755
5 TraesCS4A01G204800 chr2A 702125909 702126675 766 False 896.000000 896 88.129000 2 756 1 chr2A.!!$F1 754
6 TraesCS4A01G204800 chr1A 52217890 52218655 765 True 965.000000 965 89.740000 5 756 1 chr1A.!!$R1 751
7 TraesCS4A01G204800 chr1A 114545530 114546044 514 False 569.000000 569 86.628000 2289 2803 1 chr1A.!!$F1 514
8 TraesCS4A01G204800 chr5A 501353638 501354401 763 False 944.000000 944 89.235000 1 756 1 chr5A.!!$F1 755
9 TraesCS4A01G204800 chr2D 497917578 497918341 763 False 933.000000 933 88.990000 1 756 1 chr2D.!!$F1 755
10 TraesCS4A01G204800 chr7A 660557808 660558557 749 False 915.000000 915 88.963000 18 755 1 chr7A.!!$F1 737
11 TraesCS4A01G204800 chr3D 182343106 182343864 758 False 905.000000 905 88.472000 1 756 1 chr3D.!!$F1 755
12 TraesCS4A01G204800 chr7D 431339371 431340122 751 True 896.000000 896 88.312000 1 759 1 chr7D.!!$R1 758
13 TraesCS4A01G204800 chr1B 167713497 167714011 514 False 564.000000 564 86.434000 2289 2803 1 chr1B.!!$F1 514
14 TraesCS4A01G204800 chr1D 110335417 110335931 514 False 558.000000 558 86.240000 2289 2803 1 chr1D.!!$F1 514

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
911 966 1.079127 CGCATATAAGCCCTCCCCG 60.079 63.158 0.00 0.0 0.00 5.73 F
1202 1272 0.250513 GCGAGTTCCCTTGAGATGGT 59.749 55.000 0.00 0.0 0.00 3.55 F
1301 1373 1.113788 AAATTGGATGGATGCCGTGG 58.886 50.000 0.00 0.0 0.00 4.94 F
2689 2907 1.880221 CGTGTGGACATTGGCCAAGTA 60.880 52.381 24.94 0.0 37.12 2.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2689 2907 1.142748 GCAGCGCACAGATAGGAGT 59.857 57.895 11.47 0.00 0.00 3.85 R
3127 3345 2.829741 AACTGGAGCTCAGACTTGAC 57.170 50.000 17.19 0.00 46.18 3.18 R
3131 3349 4.899352 ACAATAAACTGGAGCTCAGACT 57.101 40.909 17.19 6.54 46.18 3.24 R
3636 3863 1.202879 ACTCGTTCAAGCATGGGGAAA 60.203 47.619 0.00 0.00 0.00 3.13 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
245 261 1.227527 CACAACCGTGCCTCTCACA 60.228 57.895 0.00 0.00 45.92 3.58
719 772 1.585267 AAATGGCGCTGATCGTTGCA 61.585 50.000 7.64 0.00 41.07 4.08
721 774 1.378882 ATGGCGCTGATCGTTGCAAT 61.379 50.000 7.64 0.00 41.07 3.56
756 809 2.415625 CGCTCGTTAACTAGTTGCTCCT 60.416 50.000 18.56 0.00 0.00 3.69
911 966 1.079127 CGCATATAAGCCCTCCCCG 60.079 63.158 0.00 0.00 0.00 5.73
912 967 1.299976 GCATATAAGCCCTCCCCGG 59.700 63.158 0.00 0.00 0.00 5.73
970 1040 2.835895 GTCGCCTCCTCCTCTCCC 60.836 72.222 0.00 0.00 0.00 4.30
971 1041 4.507916 TCGCCTCCTCCTCTCCCG 62.508 72.222 0.00 0.00 0.00 5.14
975 1045 2.837291 CTCCTCCTCTCCCGCCTG 60.837 72.222 0.00 0.00 0.00 4.85
1057 1127 1.907255 CGTTCCCTACCTCCCTTTTCT 59.093 52.381 0.00 0.00 0.00 2.52
1060 1130 2.999928 TCCCTACCTCCCTTTTCTTGT 58.000 47.619 0.00 0.00 0.00 3.16
1099 1169 1.421410 GATCCGTGCGATGTGTGGAC 61.421 60.000 0.00 0.00 0.00 4.02
1127 1197 0.675837 GCGGTAGGGTTTTGTCTCCC 60.676 60.000 0.00 0.00 43.71 4.30
1132 1202 2.265904 GGGTTTTGTCTCCCGTGCC 61.266 63.158 0.00 0.00 33.97 5.01
1133 1203 1.228154 GGTTTTGTCTCCCGTGCCT 60.228 57.895 0.00 0.00 0.00 4.75
1134 1204 0.822121 GGTTTTGTCTCCCGTGCCTT 60.822 55.000 0.00 0.00 0.00 4.35
1135 1205 0.310854 GTTTTGTCTCCCGTGCCTTG 59.689 55.000 0.00 0.00 0.00 3.61
1136 1206 0.821711 TTTTGTCTCCCGTGCCTTGG 60.822 55.000 0.00 0.00 0.00 3.61
1169 1239 2.646175 GCGGTCTAGCCCTGTGTGA 61.646 63.158 0.00 0.00 0.00 3.58
1178 1248 0.737715 GCCCTGTGTGAGATGTCGAC 60.738 60.000 9.11 9.11 0.00 4.20
1179 1249 0.456824 CCCTGTGTGAGATGTCGACG 60.457 60.000 11.62 0.00 0.00 5.12
1180 1250 1.073216 CCTGTGTGAGATGTCGACGC 61.073 60.000 11.62 5.56 0.00 5.19
1181 1251 1.398762 CTGTGTGAGATGTCGACGCG 61.399 60.000 11.62 3.53 0.00 6.01
1198 1268 2.261671 GCGCGAGTTCCCTTGAGA 59.738 61.111 12.10 0.00 0.00 3.27
1202 1272 0.250513 GCGAGTTCCCTTGAGATGGT 59.749 55.000 0.00 0.00 0.00 3.55
1207 1277 4.039730 CGAGTTCCCTTGAGATGGTATCAT 59.960 45.833 0.00 0.00 36.09 2.45
1218 1288 7.062749 TGAGATGGTATCATGTTAGGGTTAC 57.937 40.000 0.00 0.00 32.98 2.50
1244 1316 1.597027 CCCACCGCTGTCGAGTTTT 60.597 57.895 0.00 0.00 38.10 2.43
1301 1373 1.113788 AAATTGGATGGATGCCGTGG 58.886 50.000 0.00 0.00 0.00 4.94
1341 1414 3.431207 GGCAATGCTGGTTCTATTTGCAT 60.431 43.478 4.82 0.00 44.86 3.96
1415 1488 5.353956 TGTTGTATGATGTAGATTGTGTGGC 59.646 40.000 0.00 0.00 0.00 5.01
1444 1517 5.730550 TCGGCTGTTGTCTATACAAATCTT 58.269 37.500 0.00 0.00 46.84 2.40
1509 1595 4.777896 TCTTCAGAACTAGGGCAACAGTAT 59.222 41.667 0.00 0.00 39.74 2.12
1515 1601 5.720041 AGAACTAGGGCAACAGTATTGTCTA 59.280 40.000 0.00 0.00 36.23 2.59
1520 1606 4.459337 AGGGCAACAGTATTGTCTAAAAGC 59.541 41.667 0.00 0.00 36.23 3.51
1527 1613 5.989777 ACAGTATTGTCTAAAAGCTGTTCGT 59.010 36.000 0.00 0.00 32.62 3.85
1611 1697 5.186603 TGATTGCCAATTTGTAACCATGCTA 59.813 36.000 0.00 0.00 0.00 3.49
1634 1724 6.749923 ACTCTGCAATACCTCTGATTTTTC 57.250 37.500 0.00 0.00 0.00 2.29
1696 1791 4.801330 AGGTTTCAGATGTGACGTATGA 57.199 40.909 0.00 0.00 30.10 2.15
1705 1800 6.530181 TCAGATGTGACGTATGATGTTGTTAC 59.470 38.462 0.00 0.00 0.00 2.50
1841 1955 3.502979 CCCCATTCCATTTTTGTTGCTTG 59.497 43.478 0.00 0.00 0.00 4.01
2057 2254 2.715046 TCTATTTCTGCTGCCACCTTG 58.285 47.619 0.00 0.00 0.00 3.61
2097 2311 5.689068 GTGCTGATTTTCTGAGAAGTTTTGG 59.311 40.000 0.00 0.00 0.00 3.28
2102 2316 8.519799 TGATTTTCTGAGAAGTTTTGGTTAGT 57.480 30.769 0.00 0.00 0.00 2.24
2470 2688 3.308046 GCTGGGAAAAGGAGAATGTCTCT 60.308 47.826 5.31 0.00 42.95 3.10
2689 2907 1.880221 CGTGTGGACATTGGCCAAGTA 60.880 52.381 24.94 0.00 37.12 2.24
2878 3096 7.721842 AGTCGGAAATTCTATGAGATGACTAGA 59.278 37.037 0.00 0.00 31.72 2.43
2933 3151 2.296190 GGGGCTTTACCAAGTTCAACAG 59.704 50.000 0.00 0.00 42.05 3.16
2937 3155 3.222603 CTTTACCAAGTTCAACAGGGCT 58.777 45.455 4.29 0.00 0.00 5.19
3127 3345 6.734137 TCCACATTTTTACTGCTTGTTACAG 58.266 36.000 0.00 0.00 41.08 2.74
3131 3349 7.700234 CACATTTTTACTGCTTGTTACAGTCAA 59.300 33.333 0.00 0.00 45.06 3.18
3161 3379 6.003950 AGCTCCAGTTTATTGTTGTGTGTAT 58.996 36.000 0.00 0.00 0.00 2.29
3338 3561 9.015367 TCCTATATACTGCTTGTCATAGTTCTC 57.985 37.037 0.00 0.00 0.00 2.87
3394 3619 6.146216 TGTATTGTTTGCTGGTATGTTTTCG 58.854 36.000 0.00 0.00 0.00 3.46
3398 3623 3.907894 TTGCTGGTATGTTTTCGTTCC 57.092 42.857 0.00 0.00 0.00 3.62
3401 3626 3.190327 TGCTGGTATGTTTTCGTTCCATG 59.810 43.478 0.00 0.00 36.07 3.66
3420 3645 6.506147 TCCATGTACTTGCATATTGAATTGC 58.494 36.000 3.24 5.70 39.33 3.56
3441 3666 6.554334 TGCTTGTCTATTGTTGGTTCTTAC 57.446 37.500 0.00 0.00 0.00 2.34
3450 3677 9.048446 TCTATTGTTGGTTCTTACACTTGTAAC 57.952 33.333 0.00 0.00 35.75 2.50
3452 3679 7.633193 TTGTTGGTTCTTACACTTGTAACAT 57.367 32.000 0.00 0.00 35.75 2.71
3454 3681 8.057536 TGTTGGTTCTTACACTTGTAACATTT 57.942 30.769 0.00 0.00 35.75 2.32
3470 3697 6.806739 TGTAACATTTATCTCACACAGTCTCG 59.193 38.462 0.00 0.00 0.00 4.04
3629 3856 6.257630 TCATGAGTTTTGTTTTTGCTTTAGCC 59.742 34.615 0.00 0.00 41.18 3.93
3636 3863 9.203421 GTTTTGTTTTTGCTTTAGCCAGTATAT 57.797 29.630 0.00 0.00 41.18 0.86
3668 3895 6.044046 TGCTTGAACGAGTGTTAAGTAAAGA 58.956 36.000 0.00 0.00 38.78 2.52
3673 3900 4.890088 ACGAGTGTTAAGTAAAGATGGCA 58.110 39.130 0.00 0.00 0.00 4.92
3738 3965 1.806542 CGTTTCTCATGGTGGAGGTTG 59.193 52.381 0.00 0.00 35.58 3.77
3877 4117 4.576053 TCATTGATGTGTGGCTAGTTATGC 59.424 41.667 0.00 0.00 0.00 3.14
3887 4127 5.068460 TGTGGCTAGTTATGCTTGTTTGTTT 59.932 36.000 0.00 0.00 0.00 2.83
3888 4128 5.402270 GTGGCTAGTTATGCTTGTTTGTTTG 59.598 40.000 0.00 0.00 0.00 2.93
3889 4129 5.068460 TGGCTAGTTATGCTTGTTTGTTTGT 59.932 36.000 0.00 0.00 0.00 2.83
3891 4131 6.143919 GGCTAGTTATGCTTGTTTGTTTGTTC 59.856 38.462 0.00 0.00 0.00 3.18
3892 4132 6.918022 GCTAGTTATGCTTGTTTGTTTGTTCT 59.082 34.615 0.00 0.00 0.00 3.01
3893 4133 7.096477 GCTAGTTATGCTTGTTTGTTTGTTCTG 60.096 37.037 0.00 0.00 0.00 3.02
3955 4196 5.163622 GCTCAAATTGCACCTAATCTGCTTA 60.164 40.000 0.00 0.00 35.53 3.09
3956 4197 6.460676 GCTCAAATTGCACCTAATCTGCTTAT 60.461 38.462 0.00 0.00 35.53 1.73
3968 4226 9.601217 ACCTAATCTGCTTATAACAGTTTAGTG 57.399 33.333 23.50 20.17 41.55 2.74
4039 4297 6.718912 TGATTGTATTTCCACAATGTTCTCCA 59.281 34.615 6.22 0.00 46.53 3.86
4065 4323 1.977129 TCCCAATTTTCCTTGGCCTTG 59.023 47.619 3.32 0.00 43.66 3.61
4068 4326 2.368221 CCAATTTTCCTTGGCCTTGACA 59.632 45.455 3.32 0.00 39.32 3.58
4071 4329 4.541973 ATTTTCCTTGGCCTTGACAATC 57.458 40.909 3.32 0.00 26.61 2.67
4116 4463 2.432628 CGACAGTCAGGGCGGTTC 60.433 66.667 0.41 0.00 0.00 3.62
4119 4466 2.100879 GACAGTCAGGGCGGTTCTGT 62.101 60.000 0.00 0.00 41.18 3.41
4136 4483 1.154150 GTGCACTTGCGGCAATCTC 60.154 57.895 16.80 8.37 43.91 2.75
4142 4512 4.695993 TGCGGCAATCTCACGGCA 62.696 61.111 0.00 0.00 39.45 5.69
4144 4514 2.125552 CGGCAATCTCACGGCAGA 60.126 61.111 0.00 0.00 0.00 4.26
4155 4525 1.078214 ACGGCAGATCCATGTGGTG 60.078 57.895 0.00 0.00 36.34 4.17
4166 4536 1.457346 CATGTGGTGGGCTTCTTCTC 58.543 55.000 0.00 0.00 0.00 2.87
4177 4547 6.122964 GTGGGCTTCTTCTCCACTAATAAAT 58.877 40.000 0.00 0.00 45.36 1.40
4180 4550 8.333235 TGGGCTTCTTCTCCACTAATAAATTTA 58.667 33.333 0.00 0.00 0.00 1.40
4181 4551 8.622157 GGGCTTCTTCTCCACTAATAAATTTAC 58.378 37.037 0.00 0.00 0.00 2.01
4182 4552 9.174166 GGCTTCTTCTCCACTAATAAATTTACA 57.826 33.333 0.00 0.00 0.00 2.41
4285 4657 9.802039 ACATAAATCTAAACAGTTAACCTTCCA 57.198 29.630 0.88 0.00 0.00 3.53
4303 4675 4.383931 TCCATCTATAAGGTAGAGCGGT 57.616 45.455 0.00 0.00 0.00 5.68
4316 4688 2.760385 GCGGTGGCTACTCCTCCT 60.760 66.667 0.00 0.00 44.51 3.69
4326 4698 3.898741 GGCTACTCCTCCTATGCTAAAGT 59.101 47.826 0.00 0.00 0.00 2.66
4345 4717 5.726980 AAGTAATTGTGCACCATTCACAT 57.273 34.783 18.57 7.13 43.12 3.21
4346 4718 6.832520 AAGTAATTGTGCACCATTCACATA 57.167 33.333 18.57 0.00 43.12 2.29
4347 4719 6.441093 AGTAATTGTGCACCATTCACATAG 57.559 37.500 18.57 0.00 43.12 2.23
4355 4727 5.815222 GTGCACCATTCACATAGTACATGTA 59.185 40.000 5.22 0.08 34.73 2.29
4400 4772 5.782893 TGTTTACCCACTTTGAATTGAGG 57.217 39.130 0.00 0.00 0.00 3.86
4413 4785 3.206964 GAATTGAGGATCCGTTTCCCTC 58.793 50.000 5.98 0.00 45.07 4.30
4417 4789 0.535797 AGGATCCGTTTCCCTCGTTC 59.464 55.000 5.98 0.00 36.35 3.95
4419 4791 1.471153 GGATCCGTTTCCCTCGTTCTC 60.471 57.143 0.00 0.00 0.00 2.87
4422 4794 1.542187 CCGTTTCCCTCGTTCTCCCT 61.542 60.000 0.00 0.00 0.00 4.20
4445 4817 6.500751 CCTTTAGGGCCAGAAGTCCTATATTA 59.499 42.308 6.18 0.00 33.65 0.98
4446 4818 7.017254 CCTTTAGGGCCAGAAGTCCTATATTAA 59.983 40.741 6.18 0.00 33.65 1.40
4447 4819 8.520119 TTTAGGGCCAGAAGTCCTATATTAAT 57.480 34.615 6.18 0.00 33.65 1.40
4448 4820 6.628644 AGGGCCAGAAGTCCTATATTAATC 57.371 41.667 6.18 0.00 0.00 1.75
4449 4821 5.187967 AGGGCCAGAAGTCCTATATTAATCG 59.812 44.000 6.18 0.00 0.00 3.34
4451 4823 6.295688 GGGCCAGAAGTCCTATATTAATCGAA 60.296 42.308 4.39 0.00 0.00 3.71
4452 4824 6.814146 GGCCAGAAGTCCTATATTAATCGAAG 59.186 42.308 0.00 0.00 0.00 3.79
4453 4825 7.379750 GCCAGAAGTCCTATATTAATCGAAGT 58.620 38.462 0.00 0.00 0.00 3.01
4455 4827 7.329717 CCAGAAGTCCTATATTAATCGAAGTGC 59.670 40.741 0.00 0.00 0.00 4.40
4468 4844 1.906966 CGAAGTGCGTCAAATCATTGC 59.093 47.619 0.00 0.00 36.45 3.56
4470 4846 3.181521 CGAAGTGCGTCAAATCATTGCTA 60.182 43.478 0.00 0.00 36.45 3.49
4485 4861 5.181009 TCATTGCTATTTGACTCTGGACTG 58.819 41.667 0.00 0.00 0.00 3.51
4494 4870 5.825593 TTGACTCTGGACTGGTTCTAAAT 57.174 39.130 0.00 0.00 0.00 1.40
4500 4876 5.962433 TCTGGACTGGTTCTAAATAAGTCG 58.038 41.667 0.00 0.00 38.50 4.18
4509 4885 8.937634 TGGTTCTAAATAAGTCGAGGTATTTC 57.062 34.615 13.77 3.84 33.20 2.17
4510 4886 8.533657 TGGTTCTAAATAAGTCGAGGTATTTCA 58.466 33.333 13.77 6.04 33.20 2.69
4558 4938 7.015226 GGGAAAACCTTTGAACAAATTTCTG 57.985 36.000 16.83 2.54 32.07 3.02
4559 4939 6.597672 GGGAAAACCTTTGAACAAATTTCTGT 59.402 34.615 16.83 0.00 32.07 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
63 67 4.866921 AGGGAAAAATACGTGTTTTCTGC 58.133 39.130 25.66 18.94 42.22 4.26
178 194 6.097696 CCTCTAGGAAAGGGAAAAACAAAACA 59.902 38.462 0.00 0.00 37.39 2.83
243 259 1.940613 GAGTCACGGTTTTGCTTCTGT 59.059 47.619 0.00 0.00 0.00 3.41
245 261 2.158957 TGAGAGTCACGGTTTTGCTTCT 60.159 45.455 0.00 0.00 0.00 2.85
289 307 3.927758 CGGAAAAGGGAAAAACAAAACGT 59.072 39.130 0.00 0.00 0.00 3.99
410 436 1.305201 GGCCGTGACTTTCAGAAACA 58.695 50.000 0.00 0.00 0.00 2.83
464 491 3.431856 GCGAAAGTCACGGTTTTTCTTT 58.568 40.909 0.00 0.00 0.00 2.52
553 588 2.027469 TCCCCGGTCTTTCTTAGCTTTC 60.027 50.000 0.00 0.00 0.00 2.62
688 740 4.228097 CCATTTGGCGCGCTCTCG 62.228 66.667 32.29 15.43 39.07 4.04
702 755 1.378882 ATTGCAACGATCAGCGCCAT 61.379 50.000 2.29 0.00 46.04 4.40
756 809 2.044793 AATCCTCTCCTGGTGACCAA 57.955 50.000 5.53 0.00 30.80 3.67
911 966 1.222113 GAGCAGTAGGGTTGGAGCC 59.778 63.158 0.00 0.00 35.59 4.70
912 967 1.222113 GGAGCAGTAGGGTTGGAGC 59.778 63.158 0.00 0.00 0.00 4.70
913 968 0.539051 CAGGAGCAGTAGGGTTGGAG 59.461 60.000 0.00 0.00 0.00 3.86
1057 1127 6.257423 TCGAAACGTAGCGAGATTATTACAA 58.743 36.000 8.38 0.00 32.13 2.41
1060 1130 6.082338 GGATCGAAACGTAGCGAGATTATTA 58.918 40.000 16.08 0.00 40.14 0.98
1127 1197 2.281761 AGGCAAGACCAAGGCACG 60.282 61.111 0.00 0.00 43.14 5.34
1128 1198 0.610232 ATCAGGCAAGACCAAGGCAC 60.610 55.000 0.00 0.00 43.14 5.01
1129 1199 0.322816 GATCAGGCAAGACCAAGGCA 60.323 55.000 0.00 0.00 43.14 4.75
1130 1200 0.034670 AGATCAGGCAAGACCAAGGC 60.035 55.000 0.00 0.00 43.14 4.35
1132 1202 2.559440 GCTAGATCAGGCAAGACCAAG 58.441 52.381 0.00 0.00 43.14 3.61
1133 1203 1.134699 CGCTAGATCAGGCAAGACCAA 60.135 52.381 9.87 0.00 43.14 3.67
1134 1204 0.461548 CGCTAGATCAGGCAAGACCA 59.538 55.000 9.87 0.00 43.14 4.02
1135 1205 0.249657 CCGCTAGATCAGGCAAGACC 60.250 60.000 9.87 0.00 39.61 3.85
1136 1206 0.461961 ACCGCTAGATCAGGCAAGAC 59.538 55.000 9.87 0.00 0.00 3.01
1180 1250 2.890847 ATCTCAAGGGAACTCGCGCG 62.891 60.000 26.76 26.76 42.68 6.86
1181 1251 1.153549 ATCTCAAGGGAACTCGCGC 60.154 57.895 0.00 0.00 42.68 6.86
1192 1262 6.179906 ACCCTAACATGATACCATCTCAAG 57.820 41.667 0.00 0.00 0.00 3.02
1193 1263 6.575244 AACCCTAACATGATACCATCTCAA 57.425 37.500 0.00 0.00 0.00 3.02
1198 1268 5.601313 AGACGTAACCCTAACATGATACCAT 59.399 40.000 0.00 0.00 0.00 3.55
1202 1272 5.221185 GCAGAGACGTAACCCTAACATGATA 60.221 44.000 0.00 0.00 0.00 2.15
1207 1277 1.547372 GGCAGAGACGTAACCCTAACA 59.453 52.381 0.00 0.00 0.00 2.41
1244 1316 0.955428 GCAGAGATGCCAAACACCGA 60.955 55.000 0.00 0.00 0.00 4.69
1276 1348 2.035832 GGCATCCATCCAATTTTACCCG 59.964 50.000 0.00 0.00 0.00 5.28
1301 1373 6.564328 CATTGCCAAGTCTAAAGGGAATAAC 58.436 40.000 0.00 0.00 40.83 1.89
1369 1442 2.354805 CGGGGAAAAACTCTAGGACCAG 60.355 54.545 0.00 0.00 0.00 4.00
1415 1488 5.109210 TGTATAGACAACAGCCGATCAAAG 58.891 41.667 0.00 0.00 30.68 2.77
1509 1595 4.732355 GCCAAACGAACAGCTTTTAGACAA 60.732 41.667 0.00 0.00 0.00 3.18
1515 1601 2.472816 CATGCCAAACGAACAGCTTTT 58.527 42.857 0.00 0.00 0.00 2.27
1520 1606 2.393764 GAAACCATGCCAAACGAACAG 58.606 47.619 0.00 0.00 0.00 3.16
1527 1613 0.189574 TCCCTGGAAACCATGCCAAA 59.810 50.000 0.00 0.00 32.95 3.28
1611 1697 6.479884 AGAAAAATCAGAGGTATTGCAGAGT 58.520 36.000 0.00 0.00 0.00 3.24
1634 1724 4.789012 ATTACAACAAGACCCATGCAAG 57.211 40.909 0.00 0.00 0.00 4.01
2057 2254 9.520204 AAAATCAGCACACAGTTTATAATATGC 57.480 29.630 0.00 0.00 0.00 3.14
2097 2311 5.239525 ACACCTCAGAAATGCTTTCACTAAC 59.760 40.000 10.08 0.00 42.10 2.34
2102 2316 3.819368 TGACACCTCAGAAATGCTTTCA 58.181 40.909 10.08 0.00 42.10 2.69
2470 2688 1.380515 AGCCTCAAGAGCCTCGCTA 60.381 57.895 0.00 0.00 39.88 4.26
2689 2907 1.142748 GCAGCGCACAGATAGGAGT 59.857 57.895 11.47 0.00 0.00 3.85
2878 3096 4.994907 TGCAGATTAGCAATGCTTCAAT 57.005 36.364 14.85 8.13 42.46 2.57
3065 3283 9.432077 CAACCAACATTACATTTTAAGTTTTGC 57.568 29.630 0.00 0.00 0.00 3.68
3127 3345 2.829741 AACTGGAGCTCAGACTTGAC 57.170 50.000 17.19 0.00 46.18 3.18
3131 3349 4.899352 ACAATAAACTGGAGCTCAGACT 57.101 40.909 17.19 6.54 46.18 3.24
3192 3410 7.399191 TGACCAACTTAGTACCACTGATAGATT 59.601 37.037 0.00 0.00 0.00 2.40
3193 3411 6.895756 TGACCAACTTAGTACCACTGATAGAT 59.104 38.462 0.00 0.00 0.00 1.98
3194 3412 6.250711 TGACCAACTTAGTACCACTGATAGA 58.749 40.000 0.00 0.00 0.00 1.98
3250 3470 7.639378 TCAGGTTTAACTTGATATTAGCCCTT 58.361 34.615 5.80 0.00 28.69 3.95
3253 3473 9.120538 TCATTCAGGTTTAACTTGATATTAGCC 57.879 33.333 10.60 0.00 34.10 3.93
3371 3596 6.146898 ACGAAAACATACCAGCAAACAATAC 58.853 36.000 0.00 0.00 0.00 1.89
3388 3613 4.217754 TGCAAGTACATGGAACGAAAAC 57.782 40.909 0.00 0.00 0.00 2.43
3394 3619 7.043192 GCAATTCAATATGCAAGTACATGGAAC 60.043 37.037 0.00 0.00 42.12 3.62
3398 3623 7.490079 ACAAGCAATTCAATATGCAAGTACATG 59.510 33.333 0.00 0.00 44.95 3.21
3401 3626 7.253422 AGACAAGCAATTCAATATGCAAGTAC 58.747 34.615 0.00 0.00 44.95 2.73
3420 3645 7.730364 AGTGTAAGAACCAACAATAGACAAG 57.270 36.000 0.00 0.00 0.00 3.16
3441 3666 8.087982 ACTGTGTGAGATAAATGTTACAAGTG 57.912 34.615 0.00 0.00 0.00 3.16
3450 3677 6.556212 AGTACGAGACTGTGTGAGATAAATG 58.444 40.000 0.00 0.00 36.87 2.32
3470 3697 6.931840 ACAAGAGTTGGAAGAAGAATCAGTAC 59.068 38.462 0.00 0.00 34.12 2.73
3476 3703 4.464008 TGCACAAGAGTTGGAAGAAGAAT 58.536 39.130 0.00 0.00 34.12 2.40
3629 3856 5.277974 CGTTCAAGCATGGGGAAATATACTG 60.278 44.000 0.00 0.00 0.00 2.74
3636 3863 1.202879 ACTCGTTCAAGCATGGGGAAA 60.203 47.619 0.00 0.00 0.00 3.13
3673 3900 3.900601 AGTAGATTATACTGCAGCCAGCT 59.099 43.478 15.27 5.84 45.94 4.24
3843 4072 6.225318 CCACACATCAATGAAAGGTGATTTT 58.775 36.000 16.24 0.00 32.06 1.82
3844 4073 5.786311 CCACACATCAATGAAAGGTGATTT 58.214 37.500 16.24 0.00 32.06 2.17
3877 4117 8.020819 TCAAGTAGAACAGAACAAACAAACAAG 58.979 33.333 0.00 0.00 0.00 3.16
3887 4127 4.623932 ATGCCTCAAGTAGAACAGAACA 57.376 40.909 0.00 0.00 0.00 3.18
3888 4128 4.997395 TGAATGCCTCAAGTAGAACAGAAC 59.003 41.667 0.00 0.00 0.00 3.01
3889 4129 5.227569 TGAATGCCTCAAGTAGAACAGAA 57.772 39.130 0.00 0.00 0.00 3.02
3955 4196 7.724061 ACATTCCCTTGAACACTAAACTGTTAT 59.276 33.333 0.00 0.00 34.40 1.89
3956 4197 7.057894 ACATTCCCTTGAACACTAAACTGTTA 58.942 34.615 0.00 0.00 34.40 2.41
3968 4226 3.366374 GCAGTAGCAACATTCCCTTGAAC 60.366 47.826 0.00 0.00 41.58 3.18
4006 4264 8.522830 CATTGTGGAAATACAATCAAACTAGGT 58.477 33.333 1.46 0.00 45.49 3.08
4065 4323 3.987404 AGGCACGCCTTGATTGTC 58.013 55.556 4.27 0.00 45.70 3.18
4108 4455 2.594592 AAGTGCACAGAACCGCCC 60.595 61.111 21.04 0.00 0.00 6.13
4112 4459 2.639286 CCGCAAGTGCACAGAACC 59.361 61.111 21.04 1.31 42.21 3.62
4116 4463 1.443194 GATTGCCGCAAGTGCACAG 60.443 57.895 21.04 12.34 41.93 3.66
4119 4466 1.600356 TGAGATTGCCGCAAGTGCA 60.600 52.632 12.16 6.25 42.21 4.57
4155 4525 7.646548 AAATTTATTAGTGGAGAAGAAGCCC 57.353 36.000 0.00 0.00 0.00 5.19
4177 4547 8.539770 TTTTCAAAGCAAGTTGAACATGTAAA 57.460 26.923 7.16 3.62 44.96 2.01
4284 4656 3.367498 GCCACCGCTCTACCTTATAGATG 60.367 52.174 0.00 0.00 0.00 2.90
4285 4657 2.826725 GCCACCGCTCTACCTTATAGAT 59.173 50.000 0.00 0.00 0.00 1.98
4289 4661 1.962100 GTAGCCACCGCTCTACCTTAT 59.038 52.381 0.00 0.00 43.95 1.73
4303 4675 3.612795 TTAGCATAGGAGGAGTAGCCA 57.387 47.619 0.00 0.00 40.02 4.75
4316 4688 7.121907 TGAATGGTGCACAATTACTTTAGCATA 59.878 33.333 19.53 0.00 32.34 3.14
4345 4717 4.665833 ATTGAAGCCGCTACATGTACTA 57.334 40.909 0.08 0.00 0.00 1.82
4346 4718 3.543680 ATTGAAGCCGCTACATGTACT 57.456 42.857 0.08 0.00 0.00 2.73
4347 4719 6.036083 CCATATATTGAAGCCGCTACATGTAC 59.964 42.308 0.08 0.00 0.00 2.90
4355 4727 4.357918 AGTTCCATATATTGAAGCCGCT 57.642 40.909 0.00 0.00 0.00 5.52
4400 4772 1.471153 GGAGAACGAGGGAAACGGATC 60.471 57.143 0.00 0.00 34.93 3.36
4422 4794 7.941053 TTAATATAGGACTTCTGGCCCTAAA 57.059 36.000 0.00 0.00 36.28 1.85
4428 4800 7.329717 CACTTCGATTAATATAGGACTTCTGGC 59.670 40.741 0.00 0.00 0.00 4.85
4429 4801 7.329717 GCACTTCGATTAATATAGGACTTCTGG 59.670 40.741 0.00 0.00 0.00 3.86
4430 4802 7.061210 CGCACTTCGATTAATATAGGACTTCTG 59.939 40.741 0.00 0.00 41.67 3.02
4431 4803 7.085116 CGCACTTCGATTAATATAGGACTTCT 58.915 38.462 0.00 0.00 41.67 2.85
4445 4817 4.406069 CAATGATTTGACGCACTTCGATT 58.594 39.130 0.00 0.00 42.31 3.34
4446 4818 3.728864 GCAATGATTTGACGCACTTCGAT 60.729 43.478 0.00 0.00 36.13 3.59
4447 4819 2.412716 GCAATGATTTGACGCACTTCGA 60.413 45.455 0.00 0.00 36.13 3.71
4448 4820 1.906966 GCAATGATTTGACGCACTTCG 59.093 47.619 0.00 0.00 37.49 3.79
4449 4821 3.207474 AGCAATGATTTGACGCACTTC 57.793 42.857 0.00 0.00 34.60 3.01
4451 4823 4.970662 AATAGCAATGATTTGACGCACT 57.029 36.364 0.00 0.00 34.60 4.40
4452 4824 5.094812 TCAAATAGCAATGATTTGACGCAC 58.905 37.500 6.69 0.00 44.46 5.34
4453 4825 5.307926 TCAAATAGCAATGATTTGACGCA 57.692 34.783 6.69 0.00 44.46 5.24
4468 4844 5.413309 AGAACCAGTCCAGAGTCAAATAG 57.587 43.478 0.00 0.00 0.00 1.73
4470 4846 5.825593 TTAGAACCAGTCCAGAGTCAAAT 57.174 39.130 0.00 0.00 0.00 2.32
4485 4861 8.937634 TGAAATACCTCGACTTATTTAGAACC 57.062 34.615 6.52 0.00 29.81 3.62
4494 4870 9.715121 ACAAACTATTTGAAATACCTCGACTTA 57.285 29.630 8.24 0.00 43.26 2.24
4509 4885 9.398170 CCTTTGTCTATGTCAACAAACTATTTG 57.602 33.333 0.00 0.00 45.95 2.32
4510 4886 8.576442 CCCTTTGTCTATGTCAACAAACTATTT 58.424 33.333 0.00 0.00 39.70 1.40


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

AutoCloner maintained by Alex Coulton.