Multiple sequence alignment - TraesCS4D01G053000

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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 TraesCS4D01G053000 chr4D 100.000 4549 0 0 459 5007 29173070 29168522 0.000000e+00 8401.0
1 TraesCS4D01G053000 chr4D 100.000 187 0 0 1 187 29173528 29173342 3.710000e-91 346.0
2 TraesCS4D01G053000 chr4B 94.789 2111 68 13 2135 4226 41702798 41700711 0.000000e+00 3251.0
3 TraesCS4D01G053000 chr4B 91.995 1699 73 29 459 2138 41704489 41702835 0.000000e+00 2326.0
4 TraesCS4D01G053000 chr4B 86.608 687 59 21 4325 5007 41700634 41699977 0.000000e+00 728.0
5 TraesCS4D01G053000 chr4B 89.143 175 1 5 4 178 41704634 41704478 8.500000e-48 202.0
6 TraesCS4D01G053000 chr4A 91.654 1965 83 40 3073 5007 574391604 574393517 0.000000e+00 2645.0
7 TraesCS4D01G053000 chr4A 93.151 1679 60 23 495 2138 574388813 574390471 0.000000e+00 2412.0
8 TraesCS4D01G053000 chr4A 94.696 773 20 2 2135 2886 574390508 574391280 0.000000e+00 1181.0
9 TraesCS4D01G053000 chr4A 94.382 178 6 2 1 178 574388626 574388799 2.300000e-68 270.0
10 TraesCS4D01G053000 chr4A 100.000 28 0 0 459 486 574388788 574388815 9.000000e-03 52.8
11 TraesCS4D01G053000 chr4A 100.000 28 0 0 4211 4238 659629717 659629690 9.000000e-03 52.8
12 TraesCS4D01G053000 chr2B 83.820 377 48 9 4629 5004 412749936 412750300 3.710000e-91 346.0
13 TraesCS4D01G053000 chr2B 82.514 366 52 8 4636 5001 603349272 603349625 1.350000e-80 311.0
14 TraesCS4D01G053000 chr2B 74.865 557 85 30 3427 3964 629649439 629648919 8.500000e-48 202.0
15 TraesCS4D01G053000 chr3A 83.733 375 43 12 4638 5007 642344330 642343969 6.210000e-89 339.0
16 TraesCS4D01G053000 chr2D 83.196 363 55 5 4635 4996 505801344 505801701 1.340000e-85 327.0
17 TraesCS4D01G053000 chr7A 83.060 366 53 7 4638 5001 648521546 648521904 1.740000e-84 324.0
18 TraesCS4D01G053000 chr7A 81.383 376 56 9 4636 5007 664179358 664178993 1.360000e-75 294.0
19 TraesCS4D01G053000 chr1A 82.609 368 55 9 4636 5000 399594779 399594418 2.910000e-82 316.0
20 TraesCS4D01G053000 chr1A 100.000 33 0 0 4249 4281 28758889 28758921 1.510000e-05 62.1
21 TraesCS4D01G053000 chr1A 94.872 39 1 1 4244 4282 527694924 527694887 5.410000e-05 60.2
22 TraesCS4D01G053000 chr1A 100.000 28 0 0 4216 4243 276860703 276860676 9.000000e-03 52.8
23 TraesCS4D01G053000 chr5A 97.368 38 0 1 4244 4281 364712650 364712686 4.180000e-06 63.9
24 TraesCS4D01G053000 chr5A 100.000 33 0 0 4249 4281 436259193 436259225 1.510000e-05 62.1
25 TraesCS4D01G053000 chr7B 100.000 33 0 0 4249 4281 380716522 380716490 1.510000e-05 62.1
26 TraesCS4D01G053000 chr7B 100.000 28 0 0 4216 4243 264477833 264477860 9.000000e-03 52.8
27 TraesCS4D01G053000 chr5B 100.000 33 0 0 4249 4281 402737606 402737574 1.510000e-05 62.1
28 TraesCS4D01G053000 chr5B 100.000 30 0 0 4209 4238 596542285 596542256 7.000000e-04 56.5
29 TraesCS4D01G053000 chr5B 100.000 28 0 0 4211 4238 19675135 19675162 9.000000e-03 52.8
30 TraesCS4D01G053000 chr3D 100.000 33 0 0 4249 4281 293614204 293614236 1.510000e-05 62.1
31 TraesCS4D01G053000 chr1D 100.000 33 0 0 4249 4281 87661057 87661089 1.510000e-05 62.1
32 TraesCS4D01G053000 chr1B 100.000 33 0 0 4249 4281 616095638 616095606 1.510000e-05 62.1
33 TraesCS4D01G053000 chr6A 82.051 78 0 7 4204 4281 478526378 478526441 3.000000e-03 54.7
34 TraesCS4D01G053000 chr2A 94.444 36 0 2 4203 4238 728548786 728548753 3.000000e-03 54.7
35 TraesCS4D01G053000 chr7D 100.000 28 0 0 4216 4243 283700004 283699977 9.000000e-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 TraesCS4D01G053000 chr4D 29168522 29173528 5006 True 4373.50 8401 100.00000 1 5007 2 chr4D.!!$R1 5006
1 TraesCS4D01G053000 chr4B 41699977 41704634 4657 True 1626.75 3251 90.63375 4 5007 4 chr4B.!!$R1 5003
2 TraesCS4D01G053000 chr4A 574388626 574393517 4891 False 1312.16 2645 94.77660 1 5007 5 chr4A.!!$F1 5006
3 TraesCS4D01G053000 chr2B 629648919 629649439 520 True 202.00 202 74.86500 3427 3964 1 chr2B.!!$R1 537

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
174 175 0.172352 CACCACACCTGCAACGTTTT 59.828 50.000 0.00 0.0 0.00 2.43 F
175 176 0.454196 ACCACACCTGCAACGTTTTC 59.546 50.000 0.00 0.0 0.00 2.29 F
1040 1076 0.618968 TCTTTGCCTCTCCCCTCTCC 60.619 60.000 0.00 0.0 0.00 3.71 F
1947 2006 0.249073 CTGTCTACGCCGCTGCTATT 60.249 55.000 0.00 0.0 34.43 1.73 F
2013 2072 1.340889 TGTGTGGCCAATTCTTGCTTC 59.659 47.619 7.24 0.0 0.00 3.86 F
2459 2563 2.046023 CTGGGCGATGAACTGGCA 60.046 61.111 0.00 0.0 0.00 4.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1923 1982 0.457853 CAGCGGCGTAGACAGCTTAA 60.458 55.000 9.37 0.00 42.12 1.85 R
1939 1998 2.195922 CCCAAATTTCGCAATAGCAGC 58.804 47.619 0.00 0.00 42.27 5.25 R
2534 2638 1.374758 CAGGTCGGTGAGCAGAACC 60.375 63.158 0.00 0.00 31.89 3.62 R
3220 3529 0.820226 TGTGCACTGGCTAGCTAGAG 59.180 55.000 32.14 25.35 41.91 2.43 R
3949 4275 1.533731 ACACCAAACAAATAGCGTCGG 59.466 47.619 0.00 0.00 0.00 4.79 R
4451 4820 2.094026 TGCGTCTTCTGTATGTGCTGAT 60.094 45.455 0.00 0.00 0.00 2.90 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
73 74 2.511600 CACCCGGTCGCTGGATTC 60.512 66.667 0.00 0.00 29.82 2.52
74 75 3.782443 ACCCGGTCGCTGGATTCC 61.782 66.667 0.00 0.00 29.82 3.01
75 76 3.781307 CCCGGTCGCTGGATTCCA 61.781 66.667 5.05 5.05 29.82 3.53
159 160 4.555709 GTCGCCACACCCACACCA 62.556 66.667 0.00 0.00 0.00 4.17
166 167 2.906897 CACCCACACCACACCTGC 60.907 66.667 0.00 0.00 0.00 4.85
167 168 3.415983 ACCCACACCACACCTGCA 61.416 61.111 0.00 0.00 0.00 4.41
168 169 2.123939 CCCACACCACACCTGCAA 60.124 61.111 0.00 0.00 0.00 4.08
169 170 2.489275 CCCACACCACACCTGCAAC 61.489 63.158 0.00 0.00 0.00 4.17
170 171 2.715005 CACACCACACCTGCAACG 59.285 61.111 0.00 0.00 0.00 4.10
171 172 2.112198 CACACCACACCTGCAACGT 61.112 57.895 0.00 0.00 0.00 3.99
172 173 1.377987 ACACCACACCTGCAACGTT 60.378 52.632 0.00 0.00 0.00 3.99
173 174 0.963355 ACACCACACCTGCAACGTTT 60.963 50.000 0.00 0.00 0.00 3.60
174 175 0.172352 CACCACACCTGCAACGTTTT 59.828 50.000 0.00 0.00 0.00 2.43
175 176 0.454196 ACCACACCTGCAACGTTTTC 59.546 50.000 0.00 0.00 0.00 2.29
604 616 4.467107 GCCCTCCTCCTCCGTCCT 62.467 72.222 0.00 0.00 0.00 3.85
700 721 2.997315 CACCTGACCTGCCGGAGA 60.997 66.667 5.05 0.00 0.00 3.71
701 722 2.997897 ACCTGACCTGCCGGAGAC 60.998 66.667 5.05 0.00 0.00 3.36
702 723 3.775654 CCTGACCTGCCGGAGACC 61.776 72.222 5.05 0.00 0.00 3.85
994 1030 1.836383 CTACAGTGGACGATAACCGC 58.164 55.000 0.00 0.00 43.32 5.68
1035 1071 1.616628 TCCCTCTTTGCCTCTCCCC 60.617 63.158 0.00 0.00 0.00 4.81
1036 1072 1.617839 CCCTCTTTGCCTCTCCCCT 60.618 63.158 0.00 0.00 0.00 4.79
1037 1073 1.631071 CCCTCTTTGCCTCTCCCCTC 61.631 65.000 0.00 0.00 0.00 4.30
1038 1074 0.620121 CCTCTTTGCCTCTCCCCTCT 60.620 60.000 0.00 0.00 0.00 3.69
1039 1075 0.829990 CTCTTTGCCTCTCCCCTCTC 59.170 60.000 0.00 0.00 0.00 3.20
1040 1076 0.618968 TCTTTGCCTCTCCCCTCTCC 60.619 60.000 0.00 0.00 0.00 3.71
1041 1077 1.616628 TTTGCCTCTCCCCTCTCCC 60.617 63.158 0.00 0.00 0.00 4.30
1743 1799 1.070445 CGATGATGGAGTGGGAGGC 59.930 63.158 0.00 0.00 0.00 4.70
1783 1839 2.288025 GGAGAGGCCACCGTACCAA 61.288 63.158 5.01 0.00 36.34 3.67
1936 1995 8.662476 CAACAAGTGCTGTTAAGCTGTCTACG 62.662 46.154 0.00 0.00 46.91 3.51
1939 1998 1.269166 CTGTTAAGCTGTCTACGCCG 58.731 55.000 0.00 0.00 0.00 6.46
1942 2001 0.457853 TTAAGCTGTCTACGCCGCTG 60.458 55.000 0.00 0.00 32.22 5.18
1947 2006 0.249073 CTGTCTACGCCGCTGCTATT 60.249 55.000 0.00 0.00 34.43 1.73
2013 2072 1.340889 TGTGTGGCCAATTCTTGCTTC 59.659 47.619 7.24 0.00 0.00 3.86
2073 2132 4.479619 GTCTTGCACCATAAGCTTTCAAG 58.520 43.478 3.20 9.13 0.00 3.02
2088 2147 4.376615 GCTTTCAAGTCGTGTTGCGTATTA 60.377 41.667 0.00 0.00 42.13 0.98
2231 2330 8.571336 CCCTTCATGATTCAGGTGTTAATATTC 58.429 37.037 10.39 0.00 0.00 1.75
2448 2552 4.864334 GTCTGATGGGGCTGGGCG 62.864 72.222 0.00 0.00 0.00 6.13
2459 2563 2.046023 CTGGGCGATGAACTGGCA 60.046 61.111 0.00 0.00 0.00 4.92
2731 2851 7.690256 AGTCCATGTAACTGAAGAAATTAGGT 58.310 34.615 0.00 0.00 0.00 3.08
2785 2905 8.557864 CCAATTGTTCATCTGATATCTTGAGTC 58.442 37.037 4.43 3.76 0.00 3.36
2786 2906 9.327628 CAATTGTTCATCTGATATCTTGAGTCT 57.672 33.333 3.98 0.00 0.00 3.24
2878 3024 7.213252 GCATAATGTTGTGCACTAATTTCTG 57.787 36.000 19.41 14.66 43.66 3.02
2879 3025 6.808212 GCATAATGTTGTGCACTAATTTCTGT 59.192 34.615 19.41 0.00 43.66 3.41
2880 3026 7.967854 GCATAATGTTGTGCACTAATTTCTGTA 59.032 33.333 19.41 0.78 43.66 2.74
2885 3031 9.840427 ATGTTGTGCACTAATTTCTGTATTAAC 57.160 29.630 19.41 8.98 0.00 2.01
2886 3032 8.012809 TGTTGTGCACTAATTTCTGTATTAACG 58.987 33.333 19.41 0.00 0.00 3.18
2887 3033 7.661127 TGTGCACTAATTTCTGTATTAACGT 57.339 32.000 19.41 0.00 0.00 3.99
2888 3034 8.090250 TGTGCACTAATTTCTGTATTAACGTT 57.910 30.769 19.41 5.88 0.00 3.99
2889 3035 8.561212 TGTGCACTAATTTCTGTATTAACGTTT 58.439 29.630 19.41 0.00 0.00 3.60
2890 3036 9.389570 GTGCACTAATTTCTGTATTAACGTTTT 57.610 29.630 10.32 0.00 0.00 2.43
2891 3037 9.953697 TGCACTAATTTCTGTATTAACGTTTTT 57.046 25.926 5.91 0.00 0.00 1.94
2921 3067 8.778358 GGAATTCCTGTATTAACTTGATGCTAG 58.222 37.037 17.73 0.00 0.00 3.42
2972 3118 9.978044 ATAAGTTAATTACGCTAGTTTAGAGGG 57.022 33.333 0.00 0.00 0.00 4.30
2981 3127 4.443621 GCTAGTTTAGAGGGTTGATCACC 58.556 47.826 0.00 0.00 46.46 4.02
3031 3177 2.528127 TCGGCCCTTGGTCCTCAA 60.528 61.111 0.00 0.00 0.00 3.02
3039 3185 3.372025 GCCCTTGGTCCTCAATGTAGAAT 60.372 47.826 0.00 0.00 34.45 2.40
3058 3204 5.755849 AGAATGAATCTACCCGAAACCAAT 58.244 37.500 0.00 0.00 36.32 3.16
3206 3515 4.300803 TGTAGTAGTTTAACGTGTGCTGG 58.699 43.478 0.00 0.00 0.00 4.85
3219 3528 3.616560 CGTGTGCTGGTAGTCAAAGGTAT 60.617 47.826 0.00 0.00 0.00 2.73
3220 3529 3.933332 GTGTGCTGGTAGTCAAAGGTATC 59.067 47.826 0.00 0.00 0.00 2.24
3236 3545 2.230266 GGTATCTCTAGCTAGCCAGTGC 59.770 54.545 16.35 5.52 37.95 4.40
3351 3660 2.235891 CCAGTTTTGTTCCTGTACCCC 58.764 52.381 0.00 0.00 0.00 4.95
3371 3680 4.339247 CCCCGAGAAAATATGAACTTGCAT 59.661 41.667 0.00 0.00 0.00 3.96
3382 3691 9.632638 AAATATGAACTTGCATAATCCTAGTGT 57.367 29.630 0.00 0.00 34.67 3.55
3491 3800 8.439286 GCTGTTTCTGAAATAGACTTCTACTTG 58.561 37.037 25.13 1.74 34.43 3.16
3519 3829 4.832248 TCTTCACACATGTCCCATTCTAC 58.168 43.478 0.00 0.00 0.00 2.59
3520 3830 4.285775 TCTTCACACATGTCCCATTCTACA 59.714 41.667 0.00 0.00 0.00 2.74
3535 3846 5.335897 CCATTCTACAAGGACCATTGTGTTG 60.336 44.000 15.50 4.07 43.14 3.33
3536 3847 4.431416 TCTACAAGGACCATTGTGTTGT 57.569 40.909 15.50 8.93 43.14 3.32
3537 3848 5.554437 TCTACAAGGACCATTGTGTTGTA 57.446 39.130 15.50 9.48 43.14 2.41
3538 3849 5.302360 TCTACAAGGACCATTGTGTTGTAC 58.698 41.667 15.50 0.00 43.14 2.90
3661 3980 2.630098 TGTTTCTGACCTCTGACCTCTG 59.370 50.000 0.00 0.00 0.00 3.35
3867 4187 6.216801 TCATACAATACAGTGTGTAGGGTC 57.783 41.667 5.88 0.00 36.14 4.46
3949 4275 3.674997 TCACATTTGGAACACTAGGAGC 58.325 45.455 0.00 0.00 39.29 4.70
4110 4440 4.202151 GGAGTTGTTGGTTGCTTTCTTCAT 60.202 41.667 0.00 0.00 0.00 2.57
4238 4568 9.299465 AGCTACTCCCTCTGTAAACTAATATAC 57.701 37.037 0.00 0.00 0.00 1.47
4239 4569 9.299465 GCTACTCCCTCTGTAAACTAATATACT 57.701 37.037 0.00 0.00 0.00 2.12
4241 4571 8.709272 ACTCCCTCTGTAAACTAATATACTCC 57.291 38.462 0.00 0.00 0.00 3.85
4242 4572 8.287350 ACTCCCTCTGTAAACTAATATACTCCA 58.713 37.037 0.00 0.00 0.00 3.86
4243 4573 9.315363 CTCCCTCTGTAAACTAATATACTCCAT 57.685 37.037 0.00 0.00 0.00 3.41
4244 4574 9.670442 TCCCTCTGTAAACTAATATACTCCATT 57.330 33.333 0.00 0.00 0.00 3.16
4293 4623 9.837525 AAAGTAGTGATCTAGTAAACGTTAGTG 57.162 33.333 0.00 0.00 30.49 2.74
4294 4624 8.783833 AGTAGTGATCTAGTAAACGTTAGTGA 57.216 34.615 0.00 0.00 0.00 3.41
4295 4625 9.393512 AGTAGTGATCTAGTAAACGTTAGTGAT 57.606 33.333 0.00 1.66 0.00 3.06
4296 4626 9.649024 GTAGTGATCTAGTAAACGTTAGTGATC 57.351 37.037 0.00 11.09 0.00 2.92
4297 4627 8.508883 AGTGATCTAGTAAACGTTAGTGATCT 57.491 34.615 19.96 9.73 32.74 2.75
4359 4726 8.885494 AAACAAAGCATCTATAGCTCTAGAAG 57.115 34.615 12.36 9.49 42.53 2.85
4405 4772 3.076621 CAGTGCATTCAGCCAAGACTTA 58.923 45.455 0.00 0.00 44.83 2.24
4447 4816 8.040716 AGACTTCACGAATTATTCCGAAAAAT 57.959 30.769 0.00 0.00 0.00 1.82
4470 4839 8.526218 AATATAATCAGCACATACAGAAGACG 57.474 34.615 0.00 0.00 0.00 4.18
4516 4885 4.989279 TTCAGCAGAGCAAAAAGTTTCT 57.011 36.364 0.00 0.00 0.00 2.52
4652 5031 1.559682 ACATTAGGGCATCTCCAACGT 59.440 47.619 0.00 0.00 36.21 3.99
4685 5064 4.873129 CTCCGGCATCCGTCCGTG 62.873 72.222 0.00 0.00 46.80 4.94
4719 5098 2.213513 TCCACGGACACTGATGCCA 61.214 57.895 0.00 0.00 0.00 4.92
4720 5099 1.302431 CCACGGACACTGATGCCAA 60.302 57.895 0.00 0.00 0.00 4.52
4743 5123 2.100631 GTCCATCCAACGCTGTCCG 61.101 63.158 0.00 0.00 44.21 4.79
4778 5159 7.921745 CGACCCCAATTTGTTTTCTTTAAAGTA 59.078 33.333 14.74 2.61 0.00 2.24
4784 5165 6.777827 TTTGTTTTCTTTAAAGTACGCACG 57.222 33.333 14.74 0.00 0.00 5.34
4906 5287 2.359850 TTGACCGCCCACAGATGC 60.360 61.111 0.00 0.00 0.00 3.91
4917 5298 3.139850 CCCACAGATGCTCAATCAGATC 58.860 50.000 0.00 0.00 37.81 2.75
4924 5305 4.903049 AGATGCTCAATCAGATCTTCCTCT 59.097 41.667 0.00 0.00 37.81 3.69
4973 5354 6.293618 CGAATTTGTTGATGCATTTGAACAG 58.706 36.000 15.34 5.21 30.37 3.16
4990 5371 5.427378 TGAACAGACTCTTCAAATGTGACA 58.573 37.500 0.00 0.00 31.90 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 2.212652 CCTTTTTGCTGGGTCAAAAGC 58.787 47.619 2.58 0.00 43.95 3.51
8 9 0.467804 GCCCTTTTTGCTGGGTCAAA 59.532 50.000 0.00 0.00 45.06 2.69
73 74 2.008242 TGGACTTGGGAATTTGGTGG 57.992 50.000 0.00 0.00 0.00 4.61
74 75 3.494223 GGTTTGGACTTGGGAATTTGGTG 60.494 47.826 0.00 0.00 0.00 4.17
75 76 2.703536 GGTTTGGACTTGGGAATTTGGT 59.296 45.455 0.00 0.00 0.00 3.67
154 155 0.963355 AAACGTTGCAGGTGTGGTGT 60.963 50.000 0.00 0.00 0.00 4.16
159 160 0.375803 GACGAAAACGTTGCAGGTGT 59.624 50.000 0.00 0.00 0.00 4.16
700 721 3.402681 CCTGACCATGGCTCCGGT 61.403 66.667 13.04 0.00 38.56 5.28
701 722 3.083349 TCCTGACCATGGCTCCGG 61.083 66.667 13.04 14.00 0.00 5.14
702 723 2.187946 GTCCTGACCATGGCTCCG 59.812 66.667 13.04 5.30 0.00 4.63
703 724 2.187946 CGTCCTGACCATGGCTCC 59.812 66.667 13.04 1.64 0.00 4.70
704 725 2.187946 CCGTCCTGACCATGGCTC 59.812 66.667 13.04 9.46 0.00 4.70
705 726 4.101448 GCCGTCCTGACCATGGCT 62.101 66.667 13.04 0.00 42.44 4.75
707 728 4.838152 CCGCCGTCCTGACCATGG 62.838 72.222 11.19 11.19 0.00 3.66
930 966 4.547367 ATAAGCTCCCCGCACCGC 62.547 66.667 0.00 0.00 42.61 5.68
931 967 0.179067 TAAATAAGCTCCCCGCACCG 60.179 55.000 0.00 0.00 42.61 4.94
932 968 2.047002 TTAAATAAGCTCCCCGCACC 57.953 50.000 0.00 0.00 42.61 5.01
970 1006 1.033202 TATCGTCCACTGTAGCGCCA 61.033 55.000 2.29 0.00 0.00 5.69
994 1030 1.732683 GAATGTTTGTTGCCGCGGG 60.733 57.895 29.38 8.95 0.00 6.13
1401 1457 2.358247 ACGCCGTGTTGACCATCC 60.358 61.111 0.00 0.00 0.00 3.51
1743 1799 0.763652 CCTCATGGGGATGACCTGAG 59.236 60.000 5.34 0.00 40.03 3.35
1890 1949 3.181504 TGCAGCATTGTCAGAAATCATCG 60.182 43.478 0.00 0.00 0.00 3.84
1894 1953 3.904571 TGTTGCAGCATTGTCAGAAATC 58.095 40.909 0.00 0.00 0.00 2.17
1923 1982 0.457853 CAGCGGCGTAGACAGCTTAA 60.458 55.000 9.37 0.00 42.12 1.85
1939 1998 2.195922 CCCAAATTTCGCAATAGCAGC 58.804 47.619 0.00 0.00 42.27 5.25
1942 2001 3.733443 ATCCCCAAATTTCGCAATAGC 57.267 42.857 0.00 0.00 37.42 2.97
1947 2006 3.397482 CAAACAATCCCCAAATTTCGCA 58.603 40.909 0.00 0.00 0.00 5.10
1957 2016 5.047377 TGTTCTATTTGAGCAAACAATCCCC 60.047 40.000 0.00 0.00 32.96 4.81
2013 2072 6.882610 TCAGCAATAATTACTGGGCTATTG 57.117 37.500 0.00 0.00 35.68 1.90
2088 2147 3.204831 AGGGATCGTCCTCTAAAGTACCT 59.795 47.826 4.41 0.00 36.57 3.08
2231 2330 5.604758 TGATCAGTCCTCTAATGAACCAG 57.395 43.478 0.00 0.00 0.00 4.00
2448 2552 3.044059 GCCGCTGTGCCAGTTCATC 62.044 63.158 4.45 0.00 33.43 2.92
2534 2638 1.374758 CAGGTCGGTGAGCAGAACC 60.375 63.158 0.00 0.00 31.89 3.62
2755 2875 9.678941 CAAGATATCAGATGAACAATTGGATTG 57.321 33.333 10.83 0.00 45.59 2.67
2785 2905 5.991933 ATCAGATGCTACCTATACACCAG 57.008 43.478 0.00 0.00 0.00 4.00
2786 2906 8.435931 AAATATCAGATGCTACCTATACACCA 57.564 34.615 0.00 0.00 0.00 4.17
2891 3037 9.627123 CATCAAGTTAATACAGGAATTCCCTAA 57.373 33.333 21.22 6.79 45.60 2.69
2892 3038 7.719633 GCATCAAGTTAATACAGGAATTCCCTA 59.280 37.037 21.22 11.07 45.60 3.53
2894 3040 6.547510 AGCATCAAGTTAATACAGGAATTCCC 59.452 38.462 21.22 2.94 36.42 3.97
2895 3041 7.573968 AGCATCAAGTTAATACAGGAATTCC 57.426 36.000 17.31 17.31 0.00 3.01
2896 3042 9.547753 TCTAGCATCAAGTTAATACAGGAATTC 57.452 33.333 0.00 0.00 0.00 2.17
2972 3118 2.723124 AACAAATGCGGGTGATCAAC 57.277 45.000 0.73 0.73 0.00 3.18
2981 3127 6.850317 CCAACTAAATTCAAAAACAAATGCGG 59.150 34.615 0.00 0.00 0.00 5.69
3039 3185 4.295141 ACATTGGTTTCGGGTAGATTCA 57.705 40.909 0.00 0.00 0.00 2.57
3058 3204 8.472007 ACATGGGAAAACTGAAATACTTAACA 57.528 30.769 0.00 0.00 0.00 2.41
3206 3515 6.072342 GGCTAGCTAGAGATACCTTTGACTAC 60.072 46.154 25.15 0.00 0.00 2.73
3219 3528 1.107114 GTGCACTGGCTAGCTAGAGA 58.893 55.000 32.14 13.58 41.91 3.10
3220 3529 0.820226 TGTGCACTGGCTAGCTAGAG 59.180 55.000 32.14 25.35 41.91 2.43
3236 3545 9.554724 AGCATTTTATTTACGTCTGTTTATGTG 57.445 29.630 0.00 0.00 0.00 3.21
3351 3660 8.562892 AGGATTATGCAAGTTCATATTTTCTCG 58.437 33.333 0.00 0.00 0.00 4.04
3491 3800 4.323417 TGGGACATGTGTGAAGATAACAC 58.677 43.478 1.15 0.00 46.55 3.32
3519 3829 2.875933 ACGTACAACACAATGGTCCTTG 59.124 45.455 0.00 0.00 0.00 3.61
3520 3830 3.202829 ACGTACAACACAATGGTCCTT 57.797 42.857 0.00 0.00 0.00 3.36
3535 3846 6.987992 TCCTCAAAACCCAATATCATACGTAC 59.012 38.462 0.00 0.00 0.00 3.67
3536 3847 7.127012 TCCTCAAAACCCAATATCATACGTA 57.873 36.000 0.00 0.00 0.00 3.57
3537 3848 5.996644 TCCTCAAAACCCAATATCATACGT 58.003 37.500 0.00 0.00 0.00 3.57
3538 3849 6.935741 TTCCTCAAAACCCAATATCATACG 57.064 37.500 0.00 0.00 0.00 3.06
3661 3980 4.459089 GCCCTGGAGCCGAGTGAC 62.459 72.222 0.00 0.00 0.00 3.67
3867 4187 4.798882 ACTGGGTGACTATTCTAGAGGAG 58.201 47.826 0.00 0.00 0.00 3.69
3949 4275 1.533731 ACACCAAACAAATAGCGTCGG 59.466 47.619 0.00 0.00 0.00 4.79
4110 4440 3.580022 TCTGGAAGTGAGAAAGATGCTGA 59.420 43.478 0.00 0.00 33.76 4.26
4359 4726 8.677300 TGCTAAAATAGAATTGTGATTCACTCC 58.323 33.333 17.26 4.70 43.35 3.85
4405 4772 6.486993 GTGAAGTCTAAGTCCCTGTTCAAAAT 59.513 38.462 0.00 0.00 0.00 1.82
4447 4816 5.920840 GCGTCTTCTGTATGTGCTGATTATA 59.079 40.000 0.00 0.00 0.00 0.98
4451 4820 2.094026 TGCGTCTTCTGTATGTGCTGAT 60.094 45.455 0.00 0.00 0.00 2.90
4470 4839 7.703298 ATGTTTACACATTATGCAATCATGC 57.297 32.000 0.00 0.00 46.32 4.06
4516 4885 1.581934 CGTTTCTGCAGTGTCCTTCA 58.418 50.000 14.67 0.00 0.00 3.02
4696 5075 2.172483 ATCAGTGTCCGTGGACTGGC 62.172 60.000 19.17 9.89 44.80 4.85
4700 5079 1.741770 GGCATCAGTGTCCGTGGAC 60.742 63.158 12.17 12.17 44.77 4.02
4719 5098 3.981308 CGTTGGATGGACGCCTTT 58.019 55.556 0.00 0.00 33.42 3.11
4726 5105 2.264480 CGGACAGCGTTGGATGGA 59.736 61.111 3.74 0.00 32.67 3.41
4740 5120 2.504274 GGGGTCGGATGTATGCGGA 61.504 63.158 5.95 0.00 42.14 5.54
4743 5123 1.981256 AATTGGGGTCGGATGTATGC 58.019 50.000 0.00 0.00 0.00 3.14
4778 5159 1.785321 CGGCTATTTGAACGTGCGT 59.215 52.632 0.00 0.00 0.00 5.24
4784 5165 9.582431 TTAGACTATATATGCGGCTATTTGAAC 57.418 33.333 0.00 0.00 0.00 3.18
4875 5256 1.003812 CGGTCAAGGGGGACAACAATA 59.996 52.381 0.00 0.00 39.59 1.90
4906 5287 5.984926 GCAACTAGAGGAAGATCTGATTGAG 59.015 44.000 0.00 0.00 31.81 3.02
4917 5298 4.264460 ACTCACAAGCAACTAGAGGAAG 57.736 45.455 0.00 0.00 0.00 3.46
4924 5305 2.135139 CGAGCAACTCACAAGCAACTA 58.865 47.619 0.00 0.00 0.00 2.24
4973 5354 6.566197 AAATCCTGTCACATTTGAAGAGTC 57.434 37.500 0.00 0.00 31.90 3.36


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

AutoCloner maintained by Alex Coulton.