Multiple sequence alignment - TraesCS1A01G220900

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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 TraesCS1A01G220900 chr1A 100.000 5734 0 0 1 5734 389828935 389834668 0.000000e+00 10589.0
1 TraesCS1A01G220900 chr3A 96.113 4760 112 36 1 4722 128544703 128539979 0.000000e+00 7697.0
2 TraesCS1A01G220900 chr3A 91.111 1035 74 14 4714 5734 128539663 128538633 0.000000e+00 1386.0
3 TraesCS1A01G220900 chr3A 85.897 234 27 5 5204 5433 379841394 379841625 1.600000e-60 244.0
4 TraesCS1A01G220900 chr3A 85.621 153 17 4 5556 5705 66516024 66516174 7.690000e-34 156.0
5 TraesCS1A01G220900 chr1D 93.362 2320 92 34 2552 4837 309987260 309989551 0.000000e+00 3374.0
6 TraesCS1A01G220900 chr1D 91.760 2063 114 18 498 2520 309985214 309987260 0.000000e+00 2817.0
7 TraesCS1A01G220900 chr1D 89.646 734 62 9 5005 5734 310131455 310132178 0.000000e+00 922.0
8 TraesCS1A01G220900 chr1D 86.626 329 16 6 1 301 309982233 309982561 7.120000e-89 339.0
9 TraesCS1A01G220900 chr1D 86.900 229 27 2 5207 5433 100879404 100879631 2.650000e-63 254.0
10 TraesCS1A01G220900 chr1D 84.000 150 20 4 5552 5699 409423137 409422990 2.150000e-29 141.0
11 TraesCS1A01G220900 chr1D 78.286 175 15 16 339 504 309982559 309982719 2.200000e-14 91.6
12 TraesCS1A01G220900 chr1B 91.546 2283 114 38 2552 4765 419970949 419968677 0.000000e+00 3073.0
13 TraesCS1A01G220900 chr1B 88.404 2613 163 45 1 2520 419973514 419970949 0.000000e+00 3018.0
14 TraesCS1A01G220900 chr1B 87.391 230 25 4 5207 5433 109248882 109248654 1.580000e-65 261.0
15 TraesCS1A01G220900 chr1B 86.897 145 16 3 5557 5699 551120348 551120205 5.950000e-35 159.0
16 TraesCS1A01G220900 chr1B 91.429 70 6 0 4797 4866 419968119 419968050 4.730000e-16 97.1
17 TraesCS1A01G220900 chr1B 97.561 41 1 0 4960 5000 419967913 419967873 2.870000e-08 71.3
18 TraesCS1A01G220900 chrUn 94.661 693 28 3 4076 4765 440332670 440331984 0.000000e+00 1066.0
19 TraesCS1A01G220900 chr2A 94.661 693 28 3 4076 4765 35795384 35794698 0.000000e+00 1066.0
20 TraesCS1A01G220900 chr3D 87.336 229 25 3 5207 5433 79555099 79555325 5.700000e-65 259.0
21 TraesCS1A01G220900 chr3D 83.333 150 17 6 5559 5707 517492191 517492049 1.300000e-26 132.0
22 TraesCS1A01G220900 chr3D 95.082 61 3 0 5647 5707 386809592 386809652 4.730000e-16 97.1
23 TraesCS1A01G220900 chr6D 88.318 214 23 1 5222 5433 454889249 454889462 7.370000e-64 255.0
24 TraesCS1A01G220900 chr6D 79.730 222 44 1 2595 2815 10424240 10424461 5.950000e-35 159.0
25 TraesCS1A01G220900 chr4B 86.580 231 25 5 5207 5433 15617673 15617445 3.430000e-62 250.0
26 TraesCS1A01G220900 chr7D 86.325 234 24 7 5202 5433 620720082 620719855 1.230000e-61 248.0
27 TraesCS1A01G220900 chr3B 81.410 156 28 1 5553 5707 503341591 503341746 6.030000e-25 126.0


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 TraesCS1A01G220900 chr1A 389828935 389834668 5733 False 10589.00 10589 100.0000 1 5734 1 chr1A.!!$F1 5733
1 TraesCS1A01G220900 chr3A 128538633 128544703 6070 True 4541.50 7697 93.6120 1 5734 2 chr3A.!!$R1 5733
2 TraesCS1A01G220900 chr1D 309982233 309989551 7318 False 1655.40 3374 87.5085 1 4837 4 chr1D.!!$F3 4836
3 TraesCS1A01G220900 chr1D 310131455 310132178 723 False 922.00 922 89.6460 5005 5734 1 chr1D.!!$F2 729
4 TraesCS1A01G220900 chr1B 419967873 419973514 5641 True 1564.85 3073 92.2350 1 5000 4 chr1B.!!$R3 4999
5 TraesCS1A01G220900 chrUn 440331984 440332670 686 True 1066.00 1066 94.6610 4076 4765 1 chrUn.!!$R1 689
6 TraesCS1A01G220900 chr2A 35794698 35795384 686 True 1066.00 1066 94.6610 4076 4765 1 chr2A.!!$R1 689

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
208 220 0.248949 GCACGTAGTACTAGGCCAGC 60.249 60.000 19.89 17.16 41.61 4.85 F
251 288 1.516603 GCTGCCGAGGTTCGTCTAC 60.517 63.158 0.00 0.00 38.40 2.59 F
1456 4058 0.974383 ACGGATGGTTCTTCGGTTCT 59.026 50.000 0.00 0.00 0.00 3.01 F
1655 4262 2.125229 CAGGTCTCGCAGCTGCAT 60.125 61.111 36.03 12.94 43.58 3.96 F
3824 6471 0.176910 GAGGGCTGCTCTAACTGGTC 59.823 60.000 0.00 0.00 0.00 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1288 3881 1.926511 GAAGCGTTGCTCCATGGTGG 61.927 60.000 12.58 7.36 38.25 4.61 R
2899 5528 4.228567 TGGTGACTCCGTGCGCAA 62.229 61.111 14.00 0.00 39.52 4.85 R
3179 5809 0.031178 AAGCTCAAAGCAAAGCCACG 59.969 50.000 1.29 0.00 45.56 4.94 R
4187 6891 1.446966 GACCAGCTGCTTCTCGTCC 60.447 63.158 8.66 0.00 0.00 4.79 R
5149 8798 0.095245 CATGACCGCATCGAACACAC 59.905 55.000 0.00 0.00 30.68 3.82 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
160 172 1.746615 CTCAGGTCAATGCCGTGGG 60.747 63.158 0.00 0.00 0.00 4.61
192 204 2.110420 GCATACCGGTAGGGGCAC 59.890 66.667 26.25 7.11 43.47 5.01
194 206 2.042639 ATACCGGTAGGGGCACGT 60.043 61.111 20.91 0.00 43.47 4.49
195 207 1.108727 CATACCGGTAGGGGCACGTA 61.109 60.000 20.91 0.00 43.47 3.57
196 208 0.825010 ATACCGGTAGGGGCACGTAG 60.825 60.000 20.91 0.00 43.47 3.51
197 209 2.210144 TACCGGTAGGGGCACGTAGT 62.210 60.000 11.16 0.00 42.93 2.73
198 210 1.453745 CCGGTAGGGGCACGTAGTA 60.454 63.158 0.00 0.00 41.61 1.82
199 211 1.728490 CCGGTAGGGGCACGTAGTAC 61.728 65.000 0.00 0.00 41.61 2.73
200 212 0.749454 CGGTAGGGGCACGTAGTACT 60.749 60.000 0.00 0.00 41.61 2.73
201 213 1.475034 CGGTAGGGGCACGTAGTACTA 60.475 57.143 0.00 0.00 41.61 1.82
202 214 2.225467 GGTAGGGGCACGTAGTACTAG 58.775 57.143 1.87 0.53 41.61 2.57
203 215 2.225467 GTAGGGGCACGTAGTACTAGG 58.775 57.143 18.68 18.68 41.61 3.02
204 216 0.754587 AGGGGCACGTAGTACTAGGC 60.755 60.000 19.89 15.17 41.61 3.93
208 220 0.248949 GCACGTAGTACTAGGCCAGC 60.249 60.000 19.89 17.16 41.61 4.85
251 288 1.516603 GCTGCCGAGGTTCGTCTAC 60.517 63.158 0.00 0.00 38.40 2.59
504 3063 3.982576 ACAGTAAAAACTTTGGAGCGG 57.017 42.857 0.00 0.00 0.00 5.52
574 3133 2.024871 GAGACATCGCGGAGTCGG 59.975 66.667 20.50 0.00 39.67 4.79
602 3162 2.034879 ACGGCATGGCGAGTTCTTG 61.035 57.895 43.12 16.13 0.00 3.02
603 3163 2.486966 GGCATGGCGAGTTCTTGC 59.513 61.111 2.41 3.64 35.42 4.01
604 3164 2.334946 GGCATGGCGAGTTCTTGCA 61.335 57.895 2.41 0.00 37.12 4.08
605 3165 1.660560 GGCATGGCGAGTTCTTGCAT 61.661 55.000 2.41 3.62 37.12 3.96
688 3249 3.081993 GCTTCCGCGCAGTTACTC 58.918 61.111 8.75 0.00 0.00 2.59
893 3486 2.821366 CGCGGGATGCTCTTTGCT 60.821 61.111 0.00 0.00 43.27 3.91
1052 3645 3.777925 CGTGAACGGAGCGCAAGG 61.778 66.667 11.47 0.00 35.37 3.61
1456 4058 0.974383 ACGGATGGTTCTTCGGTTCT 59.026 50.000 0.00 0.00 0.00 3.01
1655 4262 2.125229 CAGGTCTCGCAGCTGCAT 60.125 61.111 36.03 12.94 43.58 3.96
2899 5528 4.747931 GCATGGCCTCCATATACTGTCTTT 60.748 45.833 3.32 0.00 43.15 2.52
3038 5667 8.542497 AGTAACAAAAGCATTGTCGAAGTATA 57.458 30.769 8.16 0.00 0.00 1.47
3120 5749 7.961351 ACAGGTTTGTTGGAAAAATGATGATA 58.039 30.769 0.00 0.00 32.28 2.15
3132 5761 8.958043 GGAAAAATGATGATAATCGTGCTTTAC 58.042 33.333 0.00 0.00 0.00 2.01
3184 5814 7.589574 AATTGTATAACAAAAATTCCGTGGC 57.410 32.000 0.00 0.00 41.96 5.01
3185 5815 5.968528 TGTATAACAAAAATTCCGTGGCT 57.031 34.783 0.00 0.00 0.00 4.75
3341 5971 5.567138 ACACTGGTTTCTCTGTTTTCTTG 57.433 39.130 0.00 0.00 0.00 3.02
3386 6017 1.000394 CAGTGTGTCATCCCACGTGTA 60.000 52.381 15.65 2.16 38.20 2.90
3519 6156 6.604171 TGGAGTTCATAATGATGTGGCTAAT 58.396 36.000 0.00 0.00 34.41 1.73
3667 6304 7.342541 TGATCTCATGCCAAATCCTGAATTTAA 59.657 33.333 0.00 0.00 35.77 1.52
3772 6409 3.442273 TCGCTGAAACAAACCAAAGAAGT 59.558 39.130 0.00 0.00 0.00 3.01
3773 6410 4.636648 TCGCTGAAACAAACCAAAGAAGTA 59.363 37.500 0.00 0.00 0.00 2.24
3774 6411 5.298276 TCGCTGAAACAAACCAAAGAAGTAT 59.702 36.000 0.00 0.00 0.00 2.12
3777 6414 7.112984 CGCTGAAACAAACCAAAGAAGTATAAC 59.887 37.037 0.00 0.00 0.00 1.89
3779 6416 9.233232 CTGAAACAAACCAAAGAAGTATAACAC 57.767 33.333 0.00 0.00 0.00 3.32
3781 6418 6.644248 ACAAACCAAAGAAGTATAACACCC 57.356 37.500 0.00 0.00 0.00 4.61
3782 6419 6.370453 ACAAACCAAAGAAGTATAACACCCT 58.630 36.000 0.00 0.00 0.00 4.34
3819 6464 1.520342 CGCTGAGGGCTGCTCTAAC 60.520 63.158 0.00 0.00 39.13 2.34
3824 6471 0.176910 GAGGGCTGCTCTAACTGGTC 59.823 60.000 0.00 0.00 0.00 4.02
3835 6482 4.394300 GCTCTAACTGGTCTAAGTACGACA 59.606 45.833 0.00 0.00 33.11 4.35
3839 6486 4.715527 ACTGGTCTAAGTACGACATTCC 57.284 45.455 0.00 0.00 33.11 3.01
3902 6550 6.073327 TGTAATGTAGACGGCTTCAGATAG 57.927 41.667 0.00 0.00 0.00 2.08
4006 6677 4.126520 TCTGAACCAAGGCCCTAAATTT 57.873 40.909 0.00 0.00 0.00 1.82
4011 6682 5.479027 TGAACCAAGGCCCTAAATTTAGTTC 59.521 40.000 20.99 16.13 0.00 3.01
4012 6683 4.350245 ACCAAGGCCCTAAATTTAGTTCC 58.650 43.478 20.99 19.47 0.00 3.62
4030 6702 6.241207 AGTTCCGTAACTGTTCATGAATTG 57.759 37.500 12.12 9.93 44.40 2.32
4033 6705 5.789521 TCCGTAACTGTTCATGAATTGAGA 58.210 37.500 12.12 0.00 35.27 3.27
4034 6706 6.227522 TCCGTAACTGTTCATGAATTGAGAA 58.772 36.000 12.12 0.82 35.27 2.87
4119 6823 5.511386 AACCTGATTTCTGGAGAAGTGAT 57.489 39.130 10.13 0.00 38.22 3.06
4128 6832 4.347607 TCTGGAGAAGTGATGTCTGATCA 58.652 43.478 0.00 0.00 0.00 2.92
4154 6858 0.179004 ACCCGCAGTGGTTTGAATCA 60.179 50.000 0.00 0.00 33.91 2.57
4315 7019 2.421314 CCTGACGCCGCCATCATA 59.579 61.111 0.00 0.00 0.00 2.15
4316 7020 1.956170 CCTGACGCCGCCATCATAC 60.956 63.158 0.00 0.00 0.00 2.39
4318 7022 0.530650 CTGACGCCGCCATCATACTT 60.531 55.000 0.00 0.00 0.00 2.24
4319 7023 0.747852 TGACGCCGCCATCATACTTA 59.252 50.000 0.00 0.00 0.00 2.24
4338 7044 0.467290 AGACTGATCTCCTCGAGGCC 60.467 60.000 27.39 15.06 34.44 5.19
4339 7045 0.467290 GACTGATCTCCTCGAGGCCT 60.467 60.000 27.39 3.86 34.44 5.19
4340 7046 0.754957 ACTGATCTCCTCGAGGCCTG 60.755 60.000 27.39 18.01 34.44 4.85
4341 7047 1.456518 TGATCTCCTCGAGGCCTGG 60.457 63.158 27.39 10.16 34.44 4.45
4342 7048 2.123077 ATCTCCTCGAGGCCTGGG 60.123 66.667 27.39 10.12 34.44 4.45
4668 7374 1.079336 GAGTGGCTCCCGTACAACC 60.079 63.158 0.00 0.00 0.00 3.77
4782 7831 8.234136 TGGCTGCTACTGGTATATGTATATAC 57.766 38.462 5.89 5.89 42.66 1.47
4837 8393 5.113502 ACTCAAACTAGCAATCAAAGCAC 57.886 39.130 0.00 0.00 0.00 4.40
4897 8546 1.871039 AGATTTTGTGCTGCGTACGTT 59.129 42.857 17.90 0.00 0.00 3.99
5000 8649 2.456119 CCCACGATCGAGCTTGTGC 61.456 63.158 24.34 0.00 40.05 4.57
5118 8767 2.030562 ACCGTGCCCTTCTCAACG 59.969 61.111 0.00 0.00 0.00 4.10
5149 8798 2.737932 GAAGTGGCAGCGCTTGTTGG 62.738 60.000 7.50 0.00 0.00 3.77
5156 8805 0.592247 CAGCGCTTGTTGGTGTGTTC 60.592 55.000 7.50 0.00 0.00 3.18
5158 8807 2.010670 CGCTTGTTGGTGTGTTCGA 58.989 52.632 0.00 0.00 0.00 3.71
5247 8896 5.402568 CAGATGTAAGCGCTCATATAAACGT 59.597 40.000 12.06 2.00 0.00 3.99
5248 8897 6.581166 CAGATGTAAGCGCTCATATAAACGTA 59.419 38.462 12.06 0.00 0.00 3.57
5252 8901 5.576337 AAGCGCTCATATAAACGTACATG 57.424 39.130 12.06 0.00 0.00 3.21
5277 8926 2.040947 TCACCCCTATGAATGCACACAA 59.959 45.455 0.00 0.00 0.00 3.33
5288 8939 2.120909 GCACACAAGCACACCACCT 61.121 57.895 0.00 0.00 0.00 4.00
5321 8972 1.699656 CGAGAAACTGAGCCGGCATG 61.700 60.000 31.54 19.90 0.00 4.06
5328 8979 0.879400 CTGAGCCGGCATGTCATCTC 60.879 60.000 31.54 15.36 0.00 2.75
5442 9093 2.423538 AGGATAAATGCGGACTTGTTGC 59.576 45.455 0.00 0.00 0.00 4.17
5459 9110 2.744202 GTTGCCGATGAAGAGTGTCATT 59.256 45.455 0.00 0.00 38.38 2.57
5467 9118 1.630878 GAAGAGTGTCATTGGGGAGGT 59.369 52.381 0.00 0.00 0.00 3.85
5480 9131 1.187087 GGGAGGTGTCTCGATTCAGT 58.813 55.000 0.00 0.00 40.85 3.41
5482 9133 2.359531 GGGAGGTGTCTCGATTCAGTAG 59.640 54.545 0.00 0.00 40.85 2.57
5488 9139 5.596361 AGGTGTCTCGATTCAGTAGATCATT 59.404 40.000 0.00 0.00 0.00 2.57
5514 9165 2.561209 TGAGCCAACCAGATACCCTA 57.439 50.000 0.00 0.00 0.00 3.53
5521 9172 0.397254 ACCAGATACCCTAGCACGCT 60.397 55.000 0.00 0.00 0.00 5.07
5524 9175 1.301009 GATACCCTAGCACGCTGCC 60.301 63.158 0.72 0.00 46.52 4.85
5525 9176 2.028125 GATACCCTAGCACGCTGCCA 62.028 60.000 0.72 0.00 46.52 4.92
5554 9205 2.031069 CGCAGTATACTACACCTCGCAT 60.031 50.000 4.74 0.00 0.00 4.73
5609 9260 2.702478 CTGCCCACTCATCATAAGAGGA 59.298 50.000 0.00 0.00 37.43 3.71
5622 9273 8.713971 TCATCATAAGAGGAGCCATTAACTTTA 58.286 33.333 0.00 0.00 29.97 1.85
5714 9366 8.045176 ACTTAGCATTCAAAGAGTATTCAACC 57.955 34.615 0.00 0.00 0.00 3.77
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
160 172 1.112113 TATGCGTGTTCTCTCCTCCC 58.888 55.000 0.00 0.00 0.00 4.30
192 204 0.030908 GCTGCTGGCCTAGTACTACG 59.969 60.000 3.32 0.00 34.27 3.51
203 215 4.864334 ATGGCTACGGCTGCTGGC 62.864 66.667 13.87 7.12 38.73 4.85
204 216 2.874648 TTCATGGCTACGGCTGCTGG 62.875 60.000 13.87 1.43 38.73 4.85
208 220 0.811616 GACCTTCATGGCTACGGCTG 60.812 60.000 0.00 0.00 40.22 4.85
251 288 1.163420 TGTTGCCGGTGCTACAGTTG 61.163 55.000 1.90 0.00 45.97 3.16
602 3162 0.734889 AGTAAATGGCACGAGCATGC 59.265 50.000 10.51 10.51 44.61 4.06
603 3163 1.331756 GGAGTAAATGGCACGAGCATG 59.668 52.381 7.26 0.00 44.61 4.06
604 3164 1.668419 GGAGTAAATGGCACGAGCAT 58.332 50.000 7.26 0.00 44.61 3.79
605 3165 0.739462 CGGAGTAAATGGCACGAGCA 60.739 55.000 7.26 0.00 44.61 4.26
686 3247 1.690985 GGGGAAGTGGGAGGAGGAG 60.691 68.421 0.00 0.00 0.00 3.69
687 3248 2.454941 GGGGAAGTGGGAGGAGGA 59.545 66.667 0.00 0.00 0.00 3.71
688 3249 2.692741 GGGGGAAGTGGGAGGAGG 60.693 72.222 0.00 0.00 0.00 4.30
720 3281 0.899019 GACAGGGAGAGTTGGAGACC 59.101 60.000 0.00 0.00 0.00 3.85
728 3289 1.379309 GGAGAGCGACAGGGAGAGT 60.379 63.158 0.00 0.00 0.00 3.24
1288 3881 1.926511 GAAGCGTTGCTCCATGGTGG 61.927 60.000 12.58 7.36 38.25 4.61
2899 5528 4.228567 TGGTGACTCCGTGCGCAA 62.229 61.111 14.00 0.00 39.52 4.85
3038 5667 7.388776 TCTGATTCTTTTCGACTGTGATTGAAT 59.611 33.333 0.00 0.00 0.00 2.57
3120 5749 3.197766 TCTCCAGGATGTAAAGCACGATT 59.802 43.478 0.00 0.00 0.00 3.34
3132 5761 8.752005 TGGAAAATAAATTACTCTCCAGGATG 57.248 34.615 0.00 0.00 0.00 3.51
3174 5804 1.686052 TCAAAGCAAAGCCACGGAATT 59.314 42.857 0.00 0.00 0.00 2.17
3175 5805 1.270550 CTCAAAGCAAAGCCACGGAAT 59.729 47.619 0.00 0.00 0.00 3.01
3177 5807 1.795170 GCTCAAAGCAAAGCCACGGA 61.795 55.000 0.00 0.00 41.89 4.69
3178 5808 1.372128 GCTCAAAGCAAAGCCACGG 60.372 57.895 0.00 0.00 41.89 4.94
3179 5809 0.031178 AAGCTCAAAGCAAAGCCACG 59.969 50.000 1.29 0.00 45.56 4.94
3181 5811 1.888512 CCTAAGCTCAAAGCAAAGCCA 59.111 47.619 1.29 0.00 45.56 4.75
3182 5812 1.889170 ACCTAAGCTCAAAGCAAAGCC 59.111 47.619 1.29 0.00 45.56 4.35
3184 5814 3.005155 AGCAACCTAAGCTCAAAGCAAAG 59.995 43.478 1.29 0.00 45.56 2.77
3185 5815 2.958355 AGCAACCTAAGCTCAAAGCAAA 59.042 40.909 1.29 0.00 45.56 3.68
3386 6017 4.261909 GCTAGATATGCCTGCAAAGCAATT 60.262 41.667 14.44 5.80 44.83 2.32
3519 6156 6.238731 GCAGCCTGCAATATGTGAGTTATTTA 60.239 38.462 12.82 0.00 44.26 1.40
3667 6304 8.025445 GTCAGCTTTACATGAACAATCTGAATT 58.975 33.333 0.00 0.00 31.03 2.17
3710 6347 9.643735 TTTACCAAACTGAATTTTAGGGTCTTA 57.356 29.630 0.00 0.00 29.36 2.10
3777 6414 7.360101 GCGTGCTAATTTGATTACTATAGGGTG 60.360 40.741 4.43 0.00 0.00 4.61
3779 6416 6.874134 AGCGTGCTAATTTGATTACTATAGGG 59.126 38.462 4.43 0.00 0.00 3.53
3781 6418 8.520835 TCAGCGTGCTAATTTGATTACTATAG 57.479 34.615 0.00 0.00 0.00 1.31
3782 6419 7.598869 CCTCAGCGTGCTAATTTGATTACTATA 59.401 37.037 0.00 0.00 0.00 1.31
3819 6464 4.713824 TGGAATGTCGTACTTAGACCAG 57.286 45.455 0.00 0.00 37.80 4.00
3824 6471 5.403766 GCATGAGATGGAATGTCGTACTTAG 59.596 44.000 0.00 0.00 39.95 2.18
3835 6482 5.759059 TCAAACTTAGGCATGAGATGGAAT 58.241 37.500 0.00 0.00 0.00 3.01
3887 6535 3.701542 TGATGTTCTATCTGAAGCCGTCT 59.298 43.478 0.00 0.00 35.01 4.18
4006 6677 7.156000 TCAATTCATGAACAGTTACGGAACTA 58.844 34.615 13.94 0.00 38.33 2.24
4011 6682 6.480524 TTCTCAATTCATGAACAGTTACGG 57.519 37.500 11.07 0.00 37.67 4.02
4012 6683 8.781067 TTTTTCTCAATTCATGAACAGTTACG 57.219 30.769 11.07 0.00 37.67 3.18
4119 6823 4.075682 TGCGGGTAAAATTTGATCAGACA 58.924 39.130 0.00 0.00 0.00 3.41
4128 6832 3.385111 TCAAACCACTGCGGGTAAAATTT 59.615 39.130 0.00 0.00 41.32 1.82
4187 6891 1.446966 GACCAGCTGCTTCTCGTCC 60.447 63.158 8.66 0.00 0.00 4.79
4310 7014 6.774673 TCGAGGAGATCAGTCTAAGTATGAT 58.225 40.000 0.00 0.00 33.97 2.45
4311 7015 6.176014 TCGAGGAGATCAGTCTAAGTATGA 57.824 41.667 0.00 0.00 33.97 2.15
4315 7019 3.815809 CCTCGAGGAGATCAGTCTAAGT 58.184 50.000 28.21 0.00 37.39 2.24
4316 7020 2.552315 GCCTCGAGGAGATCAGTCTAAG 59.448 54.545 35.69 3.29 37.39 2.18
4318 7022 1.202830 GGCCTCGAGGAGATCAGTCTA 60.203 57.143 35.69 0.00 37.39 2.59
4319 7023 0.467290 GGCCTCGAGGAGATCAGTCT 60.467 60.000 35.69 0.00 37.39 3.24
4727 7757 1.810030 GGCGAGAACAACCTAGGCG 60.810 63.158 9.30 2.47 0.00 5.52
4734 7764 0.714439 GCTACGAAGGCGAGAACAAC 59.286 55.000 0.00 0.00 41.64 3.32
4782 7831 6.964807 TCATCTCAATCCCAAAACCATATG 57.035 37.500 0.00 0.00 0.00 1.78
4837 8393 3.056107 TGAGACCCAGTAAACTTCATCCG 60.056 47.826 0.00 0.00 0.00 4.18
4897 8546 3.434637 GAGAAAGAACAAAAACGCTGCA 58.565 40.909 0.00 0.00 0.00 4.41
5000 8649 1.812571 ACGCAGCCAAATAAAGTCCTG 59.187 47.619 0.00 0.00 0.00 3.86
5118 8767 0.242017 GCCACTTCATCCACAACTGC 59.758 55.000 0.00 0.00 0.00 4.40
5149 8798 0.095245 CATGACCGCATCGAACACAC 59.905 55.000 0.00 0.00 30.68 3.82
5156 8805 2.202919 TGCTCCATGACCGCATCG 60.203 61.111 0.00 0.00 30.68 3.84
5158 8807 0.105593 CTAGTGCTCCATGACCGCAT 59.894 55.000 0.00 0.00 35.93 4.73
5211 8860 4.178540 GCTTACATCTGTAGCCGTGTTTA 58.821 43.478 0.00 0.00 0.00 2.01
5212 8861 3.000727 GCTTACATCTGTAGCCGTGTTT 58.999 45.455 0.00 0.00 0.00 2.83
5213 8862 2.618053 GCTTACATCTGTAGCCGTGTT 58.382 47.619 0.00 0.00 0.00 3.32
5215 8864 1.200483 CGCTTACATCTGTAGCCGTG 58.800 55.000 0.00 0.00 0.00 4.94
5216 8865 0.527817 GCGCTTACATCTGTAGCCGT 60.528 55.000 0.00 0.00 32.37 5.68
5217 8866 0.249073 AGCGCTTACATCTGTAGCCG 60.249 55.000 2.64 7.11 0.00 5.52
5218 8867 1.202417 TGAGCGCTTACATCTGTAGCC 60.202 52.381 13.26 0.00 0.00 3.93
5219 8868 2.209838 TGAGCGCTTACATCTGTAGC 57.790 50.000 13.26 0.00 0.00 3.58
5220 8869 7.201274 CGTTTATATGAGCGCTTACATCTGTAG 60.201 40.741 13.26 0.00 0.00 2.74
5229 8878 5.118050 GCATGTACGTTTATATGAGCGCTTA 59.882 40.000 13.26 8.30 30.23 3.09
5247 8896 2.758130 TCATAGGGGTGAGTGCATGTA 58.242 47.619 0.00 0.00 0.00 2.29
5248 8897 1.583556 TCATAGGGGTGAGTGCATGT 58.416 50.000 0.00 0.00 0.00 3.21
5277 8926 0.539051 GCTCATAGAGGTGGTGTGCT 59.461 55.000 0.00 0.00 31.67 4.40
5288 8939 2.427453 GTTTCTCGGAGGTGCTCATAGA 59.573 50.000 4.96 0.00 31.08 1.98
5321 8972 6.028368 TGACTTCGTAAAATCTCGAGATGAC 58.972 40.000 27.93 22.38 37.38 3.06
5431 9082 0.443869 CTTCATCGGCAACAAGTCCG 59.556 55.000 0.00 0.00 46.52 4.79
5442 9093 2.283298 CCCAATGACACTCTTCATCGG 58.717 52.381 0.00 0.00 35.02 4.18
5459 9110 0.252057 TGAATCGAGACACCTCCCCA 60.252 55.000 0.00 0.00 36.04 4.96
5467 9118 6.543831 TCTCAATGATCTACTGAATCGAGACA 59.456 38.462 0.00 0.00 0.00 3.41
5480 9131 5.221601 GGTTGGCTCATCTCTCAATGATCTA 60.222 44.000 0.00 0.00 35.21 1.98
5482 9133 3.814283 GGTTGGCTCATCTCTCAATGATC 59.186 47.826 0.00 0.00 35.21 2.92
5488 9139 1.942776 TCTGGTTGGCTCATCTCTCA 58.057 50.000 0.00 0.00 0.00 3.27
5524 9175 2.030412 TATACTGCGGCGGCCATG 59.970 61.111 20.71 10.41 38.85 3.66
5525 9176 1.183030 TAGTATACTGCGGCGGCCAT 61.183 55.000 20.71 6.93 38.85 4.40
5554 9205 7.857404 CTAGGGAGGAAATTACCTTAGATGA 57.143 40.000 0.00 0.00 40.73 2.92
5590 9241 2.549778 GCTCCTCTTATGATGAGTGGGC 60.550 54.545 5.63 4.80 37.31 5.36
5609 9260 8.579850 TTGATGATGAAGTAAAGTTAATGGCT 57.420 30.769 0.00 0.00 0.00 4.75
5622 9273 8.799367 TGAAGATGTTGAATTTGATGATGAAGT 58.201 29.630 0.00 0.00 0.00 3.01


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

AutoCloner maintained by Alex Coulton.