Multiple sequence alignment - TraesCS1D01G290600

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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 TraesCS1D01G290600 chr1D 100.000 7369 0 0 1 7369 388644971 388637603 0.000000e+00 13609.0
1 TraesCS1D01G290600 chr1D 97.727 44 1 0 4480 4523 416580323 416580366 7.930000e-10 76.8
2 TraesCS1D01G290600 chr1B 93.724 7537 240 98 1 7369 522016907 522009436 0.000000e+00 11082.0
3 TraesCS1D01G290600 chr1A 92.061 4862 168 71 1 4740 487735205 487730440 0.000000e+00 6639.0
4 TraesCS1D01G290600 chr1A 95.819 1770 39 9 4739 6498 487730278 487728534 0.000000e+00 2826.0
5 TraesCS1D01G290600 chr1A 94.314 510 22 5 6570 7076 487728541 487728036 0.000000e+00 774.0
6 TraesCS1D01G290600 chr1A 94.361 266 15 0 7102 7367 487727780 487727515 6.880000e-110 409.0
7 TraesCS1D01G290600 chr5D 81.481 162 18 3 5706 5856 69103534 69103374 1.000000e-23 122.0
8 TraesCS1D01G290600 chr5A 96.610 59 2 0 4479 4537 482768101 482768159 1.690000e-16 99.0
9 TraesCS1D01G290600 chr5A 90.476 63 4 2 4479 4540 659340044 659339983 1.700000e-11 82.4
10 TraesCS1D01G290600 chr5A 90.476 63 4 2 4479 4540 709195651 709195712 1.700000e-11 82.4
11 TraesCS1D01G290600 chr3A 81.301 123 13 3 5737 5859 611709640 611709752 2.830000e-14 91.6
12 TraesCS1D01G290600 chr7A 87.179 78 9 1 5762 5838 252188913 252188990 3.660000e-13 87.9
13 TraesCS1D01G290600 chr7A 97.826 46 1 0 4479 4524 77709537 77709492 6.130000e-11 80.5
14 TraesCS1D01G290600 chr7A 77.181 149 23 4 5720 5867 73808247 73808109 7.930000e-10 76.8
15 TraesCS1D01G290600 chr4B 95.745 47 1 1 4477 4523 418517475 418517430 2.850000e-09 75.0
16 TraesCS1D01G290600 chr2A 95.652 46 2 0 4478 4523 699526830 699526785 2.850000e-09 75.0


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 TraesCS1D01G290600 chr1D 388637603 388644971 7368 True 13609 13609 100.00000 1 7369 1 chr1D.!!$R1 7368
1 TraesCS1D01G290600 chr1B 522009436 522016907 7471 True 11082 11082 93.72400 1 7369 1 chr1B.!!$R1 7368
2 TraesCS1D01G290600 chr1A 487727515 487735205 7690 True 2662 6639 94.13875 1 7367 4 chr1A.!!$R1 7366

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
825 937 0.389166 GTCGGATCGCTCCATCATCC 60.389 60.000 6.06 0.00 42.19 3.51 F
827 939 0.389556 CGGATCGCTCCATCATCCTG 60.390 60.000 6.06 0.00 42.19 3.86 F
1010 1163 0.389687 AGTGCTTTGCTCTCGCTCTC 60.390 55.000 0.00 0.00 36.97 3.20 F
1400 1563 0.389948 CCACGCCTTCAGGTACACTC 60.390 60.000 0.00 0.00 37.57 3.51 F
2790 2992 0.446616 GATGAAGGTCCGAAAACGGC 59.553 55.000 3.67 0.00 0.00 5.68 F
2810 3012 2.539142 GCGATTGATCTTGCAAGCTCTG 60.539 50.000 25.89 15.97 32.32 3.35 F
4316 4521 1.198759 TGGTCCTGTTGGGGCTAGTC 61.199 60.000 0.00 0.00 40.18 2.59 F
4410 4619 3.307762 GCCCTTCACAAGTTGAGTAGGAT 60.308 47.826 21.96 0.00 35.02 3.24 F
5830 6208 0.527385 GCGCAAGGCAGTGACAAAAA 60.527 50.000 0.30 0.00 42.87 1.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2790 2992 2.676839 ACAGAGCTTGCAAGATCAATCG 59.323 45.455 37.79 26.51 43.60 3.34 R
2946 3148 1.975407 CAAAGCCAGTCCTGCAGGG 60.975 63.158 32.23 17.23 35.41 4.45 R
3035 3237 2.787249 CTGAATGCAGCGGAACCG 59.213 61.111 9.00 9.00 43.09 4.44 R
3485 3689 2.813908 GCCCGTAGCAACTCGGTG 60.814 66.667 0.00 0.00 44.51 4.94 R
4298 4503 0.910088 AGACTAGCCCCAACAGGACC 60.910 60.000 0.00 0.00 38.24 4.46 R
4871 5243 2.628696 CCCAACGCAAGCATCTGCA 61.629 57.895 4.79 0.00 42.77 4.41 R
5813 6191 1.211743 GCTTTTTGTCACTGCCTTGC 58.788 50.000 0.00 0.00 0.00 4.01 R
6043 6422 1.490490 TGGCTGTTGGTCTCTTTCTGT 59.510 47.619 0.00 0.00 0.00 3.41 R
6650 7034 0.107017 TTATCCTGCTTCTGCCCAGC 60.107 55.000 0.00 0.00 38.71 4.85 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
41 42 5.812642 GGTCGTCAATTAAGATCACATCTGT 59.187 40.000 0.00 0.00 40.13 3.41
97 100 1.710249 CAGCACGAACGCAATCTTTTG 59.290 47.619 0.00 0.00 35.85 2.44
114 117 4.689345 TCTTTTGCTTTTACGAGGTAGAGC 59.311 41.667 0.00 6.39 33.08 4.09
124 130 4.175787 ACGAGGTAGAGCACTAACTTTG 57.824 45.455 10.25 8.67 45.42 2.77
153 159 9.297586 CACTTTTCTTTTGTTTTTACCCTACTC 57.702 33.333 0.00 0.00 0.00 2.59
154 160 8.472413 ACTTTTCTTTTGTTTTTACCCTACTCC 58.528 33.333 0.00 0.00 0.00 3.85
155 161 6.964807 TTCTTTTGTTTTTACCCTACTCCC 57.035 37.500 0.00 0.00 0.00 4.30
156 162 6.015991 TCTTTTGTTTTTACCCTACTCCCA 57.984 37.500 0.00 0.00 0.00 4.37
158 164 7.757611 TCTTTTGTTTTTACCCTACTCCCATA 58.242 34.615 0.00 0.00 0.00 2.74
159 165 7.886446 TCTTTTGTTTTTACCCTACTCCCATAG 59.114 37.037 0.00 0.00 0.00 2.23
160 166 6.956102 TTGTTTTTACCCTACTCCCATAGA 57.044 37.500 0.00 0.00 0.00 1.98
161 167 7.519347 TTGTTTTTACCCTACTCCCATAGAT 57.481 36.000 0.00 0.00 0.00 1.98
162 168 8.626917 TTGTTTTTACCCTACTCCCATAGATA 57.373 34.615 0.00 0.00 0.00 1.98
163 169 8.258850 TGTTTTTACCCTACTCCCATAGATAG 57.741 38.462 0.00 0.00 0.00 2.08
164 170 7.847848 TGTTTTTACCCTACTCCCATAGATAGT 59.152 37.037 0.00 0.00 0.00 2.12
165 171 8.366401 GTTTTTACCCTACTCCCATAGATAGTC 58.634 40.741 0.00 0.00 0.00 2.59
167 173 3.656751 ACCCTACTCCCATAGATAGTCGT 59.343 47.826 0.00 0.00 0.00 4.34
221 227 1.723003 GCGACGTCGTTTTTACTGGAT 59.277 47.619 35.48 0.00 42.22 3.41
243 249 1.674962 GTACGCCTAACCAGACGAGAT 59.325 52.381 0.00 0.00 0.00 2.75
273 287 1.402787 AGCAGGTTTTTCAGGTGGTG 58.597 50.000 0.00 0.00 0.00 4.17
280 297 4.284746 AGGTTTTTCAGGTGGTGAACAAAA 59.715 37.500 0.00 0.00 45.23 2.44
352 410 0.533085 TCGATCGCACAAAACCCACA 60.533 50.000 11.09 0.00 0.00 4.17
374 435 3.774528 CCACTGCGAGCTAGCCCA 61.775 66.667 16.65 5.63 36.02 5.36
552 642 4.312052 GCAGGTGCGGTTCCAATA 57.688 55.556 0.00 0.00 0.00 1.90
566 656 3.239253 AATAGTAGGGCCGCGGGG 61.239 66.667 29.38 15.40 0.00 5.73
594 692 4.388499 GTGCGAAGGGAAGGCCGA 62.388 66.667 0.00 0.00 33.83 5.54
654 762 1.064296 CGCTGGACGCTGGTAGTAG 59.936 63.158 0.00 0.00 36.13 2.57
816 928 3.518998 CCTCCACGTCGGATCGCT 61.519 66.667 7.11 0.00 45.19 4.93
817 929 2.024871 CTCCACGTCGGATCGCTC 59.975 66.667 7.11 0.00 45.19 5.03
818 930 3.471244 CTCCACGTCGGATCGCTCC 62.471 68.421 7.11 0.00 45.19 4.70
819 931 3.822192 CCACGTCGGATCGCTCCA 61.822 66.667 6.06 0.00 42.19 3.86
820 932 2.413351 CACGTCGGATCGCTCCAT 59.587 61.111 6.06 0.00 42.19 3.41
821 933 1.658717 CACGTCGGATCGCTCCATC 60.659 63.158 6.06 0.00 42.19 3.51
822 934 2.119029 ACGTCGGATCGCTCCATCA 61.119 57.895 6.06 0.00 42.19 3.07
823 935 1.287191 CGTCGGATCGCTCCATCAT 59.713 57.895 6.06 0.00 42.19 2.45
824 936 0.730834 CGTCGGATCGCTCCATCATC 60.731 60.000 6.06 0.00 42.19 2.92
825 937 0.389166 GTCGGATCGCTCCATCATCC 60.389 60.000 6.06 0.00 42.19 3.51
826 938 0.540597 TCGGATCGCTCCATCATCCT 60.541 55.000 6.06 0.00 42.19 3.24
827 939 0.389556 CGGATCGCTCCATCATCCTG 60.390 60.000 6.06 0.00 42.19 3.86
828 940 0.673022 GGATCGCTCCATCATCCTGC 60.673 60.000 0.00 0.00 41.64 4.85
829 941 0.673022 GATCGCTCCATCATCCTGCC 60.673 60.000 0.00 0.00 0.00 4.85
830 942 2.446142 ATCGCTCCATCATCCTGCCG 62.446 60.000 0.00 0.00 0.00 5.69
831 943 2.976903 GCTCCATCATCCTGCCGC 60.977 66.667 0.00 0.00 0.00 6.53
832 944 2.664185 CTCCATCATCCTGCCGCG 60.664 66.667 0.00 0.00 0.00 6.46
997 1150 3.068691 TCGCTCCCGCTAGTGCTT 61.069 61.111 0.00 0.00 36.97 3.91
999 1152 2.456119 CGCTCCCGCTAGTGCTTTG 61.456 63.158 0.00 0.00 36.97 2.77
1001 1154 1.078848 CTCCCGCTAGTGCTTTGCT 60.079 57.895 0.00 0.00 36.97 3.91
1002 1155 1.079127 TCCCGCTAGTGCTTTGCTC 60.079 57.895 0.00 0.00 36.97 4.26
1005 1158 1.416813 CCGCTAGTGCTTTGCTCTCG 61.417 60.000 0.00 0.00 34.22 4.04
1009 1162 0.891373 TAGTGCTTTGCTCTCGCTCT 59.109 50.000 0.00 0.00 34.22 4.09
1010 1163 0.389687 AGTGCTTTGCTCTCGCTCTC 60.390 55.000 0.00 0.00 36.97 3.20
1011 1164 1.445066 TGCTTTGCTCTCGCTCTCG 60.445 57.895 0.00 0.00 36.97 4.04
1013 1166 1.214062 CTTTGCTCTCGCTCTCGGT 59.786 57.895 0.00 0.00 36.97 4.69
1014 1167 0.800300 CTTTGCTCTCGCTCTCGGTC 60.800 60.000 0.00 0.00 36.97 4.79
1017 1175 1.817941 GCTCTCGCTCTCGGTCTCT 60.818 63.158 0.00 0.00 36.13 3.10
1031 1189 0.800012 GTCTCTCTCTCGTCGCAGTT 59.200 55.000 0.00 0.00 0.00 3.16
1400 1563 0.389948 CCACGCCTTCAGGTACACTC 60.390 60.000 0.00 0.00 37.57 3.51
1402 1565 1.218316 CGCCTTCAGGTACACTCCC 59.782 63.158 0.00 0.00 37.57 4.30
1403 1566 1.218316 GCCTTCAGGTACACTCCCG 59.782 63.158 0.00 0.00 37.57 5.14
1409 1588 0.976073 CAGGTACACTCCCGGTCCAT 60.976 60.000 0.00 0.00 0.00 3.41
1422 1604 1.741145 CGGTCCATTAGTTTTTCCCCG 59.259 52.381 0.00 0.00 0.00 5.73
1442 1624 1.150536 TGTGTTGAACCCTCCTGGC 59.849 57.895 0.00 0.00 37.83 4.85
1495 1677 2.100631 CGGGGCGTGTGATTGACTC 61.101 63.158 0.00 0.00 0.00 3.36
1524 1706 2.020720 ACGCTGTGAATCTCGATCTCT 58.979 47.619 0.00 0.00 0.00 3.10
1609 1798 4.041723 CCGAATTTTGTCGCTTCTGTTTT 58.958 39.130 0.00 0.00 39.74 2.43
1867 2062 2.507102 AGATTGGCGACGACAGCG 60.507 61.111 2.40 0.00 44.79 5.18
2049 2244 2.780643 CTTGATGAGTGCGGTGCG 59.219 61.111 0.00 0.00 0.00 5.34
2263 2458 3.548770 TCCTCAGGATCATTTGTCATGC 58.451 45.455 0.00 0.00 0.00 4.06
2270 2472 3.547613 GGATCATTTGTCATGCTTCGCTC 60.548 47.826 0.00 0.00 0.00 5.03
2282 2484 1.129437 GCTTCGCTCTAACAAGCTTGG 59.871 52.381 29.18 12.70 39.61 3.61
2405 2607 4.739716 CGAACCCAGAACAAACTTGAATTG 59.260 41.667 0.00 0.00 0.00 2.32
2494 2696 4.561735 TTCCAAAATTCGTTGTCCTCAC 57.438 40.909 0.00 0.00 0.00 3.51
2605 2807 7.953158 TGACTTCAGAGTAAAAGATGAACTG 57.047 36.000 0.00 0.00 35.88 3.16
2606 2808 6.931281 TGACTTCAGAGTAAAAGATGAACTGG 59.069 38.462 0.00 0.00 35.88 4.00
2790 2992 0.446616 GATGAAGGTCCGAAAACGGC 59.553 55.000 3.67 0.00 0.00 5.68
2810 3012 2.539142 GCGATTGATCTTGCAAGCTCTG 60.539 50.000 25.89 15.97 32.32 3.35
2945 3147 7.285566 ACTTGTATGCTCATGTGATAGGATTT 58.714 34.615 0.00 0.00 0.00 2.17
2946 3148 7.443575 ACTTGTATGCTCATGTGATAGGATTTC 59.556 37.037 0.00 0.00 0.00 2.17
3035 3237 7.434897 GGAAGATATCGCATCACTGAATATCTC 59.565 40.741 9.81 5.90 37.85 2.75
3417 3621 8.150296 GCCTGTTAAATATTAATCCCAGCATTT 58.850 33.333 0.00 0.00 0.00 2.32
3485 3689 6.738114 TCAACAGGAACATCTTTTCATTGTC 58.262 36.000 0.00 0.00 29.56 3.18
3491 3695 5.362556 AACATCTTTTCATTGTCACCGAG 57.637 39.130 0.00 0.00 0.00 4.63
3545 3749 4.024670 AGTATAACCAGGAGTCCAGTGAC 58.975 47.826 12.86 7.83 42.09 3.67
4103 4308 9.125026 GACATTTGGTCTCTTGGATGTATATTT 57.875 33.333 0.00 0.00 43.46 1.40
4179 4384 5.781210 TTCTGTTTGGTTTGCATGACATA 57.219 34.783 0.00 0.00 0.00 2.29
4212 4417 7.531871 GCGCATCAACATACATTTTATCTACTG 59.468 37.037 0.30 0.00 0.00 2.74
4316 4521 1.198759 TGGTCCTGTTGGGGCTAGTC 61.199 60.000 0.00 0.00 40.18 2.59
4410 4619 3.307762 GCCCTTCACAAGTTGAGTAGGAT 60.308 47.826 21.96 0.00 35.02 3.24
4454 4663 5.009010 TGAACAGGAGAGTGAATTCAAAAGC 59.991 40.000 10.35 0.00 0.00 3.51
4524 4733 9.674824 AAATATAAGACCGTTTAGATCACTACG 57.325 33.333 0.00 0.94 0.00 3.51
4985 5357 4.370364 TTTCAGTTTGTGCCTGTCTTTC 57.630 40.909 0.00 0.00 0.00 2.62
5142 5519 6.035866 TGCACACTTAAGTTGAAGCAAAATTG 59.964 34.615 5.07 0.00 0.00 2.32
5813 6191 1.065401 TGCACTTTGGTCAGAAAAGCG 59.935 47.619 0.00 0.00 38.03 4.68
5830 6208 0.527385 GCGCAAGGCAGTGACAAAAA 60.527 50.000 0.30 0.00 42.87 1.94
5833 6211 1.480205 CAAGGCAGTGACAAAAAGCG 58.520 50.000 0.00 0.00 0.00 4.68
5880 6258 3.627577 ACTTTGATCACCACACAAGTGTC 59.372 43.478 2.28 0.00 44.39 3.67
5898 6277 5.872635 AGTGTCATTTAGAACATGCATTCG 58.127 37.500 0.00 0.00 33.57 3.34
6043 6422 1.667151 GCCTGCTGCAAATCAACCA 59.333 52.632 3.02 0.00 40.77 3.67
6204 6585 1.703411 TCTTCCTTTTGCAACTGGGG 58.297 50.000 14.66 8.05 0.00 4.96
6219 6600 0.818296 TGGGGTTTTTGTTCGTGTGG 59.182 50.000 0.00 0.00 0.00 4.17
6462 6845 1.409661 GGATTGGGGGTATGTGTGTCC 60.410 57.143 0.00 0.00 0.00 4.02
6527 6910 6.612863 AGCAAAAGCTCCAAAAATATATCCCT 59.387 34.615 0.00 0.00 0.00 4.20
6528 6911 7.126268 AGCAAAAGCTCCAAAAATATATCCCTT 59.874 33.333 0.00 0.00 0.00 3.95
6532 6915 9.881773 AAAGCTCCAAAAATATATCCCTTATCA 57.118 29.630 0.00 0.00 0.00 2.15
6628 7012 3.038788 TGCTACTGATTCTTTGTCGCA 57.961 42.857 0.00 0.00 31.59 5.10
6794 7178 2.031157 GCATTGTAACTTCACCAAGCGT 60.031 45.455 0.00 0.00 32.09 5.07
6807 7191 0.792640 CAAGCGTCTTTCGTCAGCAT 59.207 50.000 0.00 0.00 42.13 3.79
6826 7212 5.801947 CAGCATCCAAAAAGTGCTATACAAC 59.198 40.000 0.00 0.00 46.67 3.32
6857 7243 5.965033 AATCACTGATGTAGAACCCTGAT 57.035 39.130 0.00 0.00 0.00 2.90
6871 7257 2.307768 CCCTGATCATGCTTTGCAGAT 58.692 47.619 0.00 2.04 43.65 2.90
6916 7302 2.082231 CCATCAGCAAGGTTGTCTGAG 58.918 52.381 16.52 11.18 41.23 3.35
7084 7479 9.359653 ACGAATATAACTGTACAAGTATACCCT 57.640 33.333 0.00 0.00 38.56 4.34
7090 7485 5.586877 ACTGTACAAGTATACCCTCCAGAA 58.413 41.667 0.00 0.00 37.36 3.02
7098 7496 2.024176 TACCCTCCAGAAGAACAGCA 57.976 50.000 0.00 0.00 0.00 4.41
7183 7809 1.102978 GGTCAATTTGTGGGATCCCG 58.897 55.000 26.03 9.74 39.42 5.14
7322 7948 9.781834 TTTCGAACATAATTGGATCAATAACAC 57.218 29.630 0.00 0.00 32.43 3.32
7327 7953 9.425248 AACATAATTGGATCAATAACACTGGAT 57.575 29.630 0.00 0.00 32.43 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
41 42 2.741759 TTGCTTACAGCGAGTCATCA 57.258 45.000 0.00 0.00 46.26 3.07
97 100 3.233684 AGTGCTCTACCTCGTAAAAGC 57.766 47.619 0.00 0.00 0.00 3.51
114 117 7.542130 ACAAAAGAAAAGTGCTCAAAGTTAGTG 59.458 33.333 0.00 0.00 0.00 2.74
124 130 6.816640 AGGGTAAAAACAAAAGAAAAGTGCTC 59.183 34.615 0.00 0.00 0.00 4.26
165 171 0.533491 TCATGGTAGTTCGGGGAACG 59.467 55.000 3.12 0.00 45.96 3.95
167 173 1.646912 TGTCATGGTAGTTCGGGGAA 58.353 50.000 0.00 0.00 0.00 3.97
221 227 1.885157 CGTCTGGTTAGGCGTACCA 59.115 57.895 12.22 12.22 46.47 3.25
252 258 2.031870 ACCACCTGAAAAACCTGCTTC 58.968 47.619 0.00 0.00 0.00 3.86
253 259 1.756538 CACCACCTGAAAAACCTGCTT 59.243 47.619 0.00 0.00 0.00 3.91
255 261 1.398692 TCACCACCTGAAAAACCTGC 58.601 50.000 0.00 0.00 0.00 4.85
258 272 3.878160 TTGTTCACCACCTGAAAAACC 57.122 42.857 0.00 0.00 40.73 3.27
273 287 2.363220 CGTCTGCGACTTGTTTTGTTC 58.637 47.619 7.03 0.00 41.33 3.18
326 384 3.226347 GTTTTGTGCGATCGAAGAAAGG 58.774 45.455 21.57 0.00 43.58 3.11
374 435 4.161565 TCTGGTTTGGTAGATGAGCGTTAT 59.838 41.667 0.00 0.00 0.00 1.89
551 641 4.783501 AACCCCGCGGCCCTACTA 62.784 66.667 22.85 0.00 0.00 1.82
566 656 1.574702 CCTTCGCACCTTTCCCGAAC 61.575 60.000 0.00 0.00 36.23 3.95
654 762 3.659183 TCTACCACTCCTACCAGGTAC 57.341 52.381 0.00 0.00 36.53 3.34
816 928 4.916293 GCGCGGCAGGATGATGGA 62.916 66.667 8.83 0.00 39.69 3.41
921 1056 4.821589 CCTTCTCGGGGCTGACGC 62.822 72.222 0.00 0.00 0.00 5.19
957 1104 2.686816 GCACGGGATCCAACCAACG 61.687 63.158 15.23 9.21 0.00 4.10
1001 1154 0.179094 GAGAGAGACCGAGAGCGAGA 60.179 60.000 0.00 0.00 40.82 4.04
1002 1155 0.179084 AGAGAGAGACCGAGAGCGAG 60.179 60.000 0.00 0.00 40.82 5.03
1005 1158 0.461339 ACGAGAGAGAGACCGAGAGC 60.461 60.000 0.00 0.00 0.00 4.09
1009 1162 1.810441 GCGACGAGAGAGAGACCGA 60.810 63.158 0.00 0.00 0.00 4.69
1010 1163 2.031044 CTGCGACGAGAGAGAGACCG 62.031 65.000 0.00 0.00 0.00 4.79
1011 1164 1.022451 ACTGCGACGAGAGAGAGACC 61.022 60.000 0.00 0.00 0.00 3.85
1013 1166 0.799393 CAACTGCGACGAGAGAGAGA 59.201 55.000 0.00 0.00 0.00 3.10
1014 1167 0.796491 GCAACTGCGACGAGAGAGAG 60.796 60.000 0.00 0.00 0.00 3.20
1400 1563 2.097036 GGGAAAAACTAATGGACCGGG 58.903 52.381 6.32 0.00 0.00 5.73
1402 1565 1.741145 CGGGGAAAAACTAATGGACCG 59.259 52.381 0.00 0.00 0.00 4.79
1403 1566 2.097036 CCGGGGAAAAACTAATGGACC 58.903 52.381 0.00 0.00 0.00 4.46
1409 1588 2.688958 CAACACACCGGGGAAAAACTAA 59.311 45.455 12.96 0.00 0.00 2.24
1422 1604 0.537371 CCAGGAGGGTTCAACACACC 60.537 60.000 0.00 0.00 0.00 4.16
1476 1658 3.124921 GTCAATCACACGCCCCGG 61.125 66.667 0.00 0.00 0.00 5.73
1495 1677 1.723542 GATTCACAGCGTCAGTCAGTG 59.276 52.381 0.00 0.00 0.00 3.66
1499 1681 1.135660 TCGAGATTCACAGCGTCAGTC 60.136 52.381 0.00 0.00 0.00 3.51
1500 1682 0.881796 TCGAGATTCACAGCGTCAGT 59.118 50.000 0.00 0.00 0.00 3.41
1504 1686 2.020720 AGAGATCGAGATTCACAGCGT 58.979 47.619 0.00 0.00 0.00 5.07
1524 1706 2.428569 GTCTCTCGTTGACGCGCA 60.429 61.111 5.73 1.71 39.60 6.09
1609 1798 0.028770 CAAGCGAAACAGCCAAACGA 59.971 50.000 0.00 0.00 38.01 3.85
1881 2076 4.807039 GCATTGCCCTTGCTGCGG 62.807 66.667 0.00 0.00 37.14 5.69
2049 2244 3.414700 CTGAACTGGTGCGCGTCC 61.415 66.667 8.43 11.81 0.00 4.79
2134 2329 2.693069 CGCACTGAGATCAAACTCCTT 58.307 47.619 0.00 0.00 36.22 3.36
2270 2472 4.452455 AGTGAATCGTTCCAAGCTTGTTAG 59.548 41.667 24.35 10.08 0.00 2.34
2282 2484 4.245660 TCCAATCACAGAGTGAATCGTTC 58.754 43.478 3.74 0.00 45.96 3.95
2405 2607 6.529125 CAGATCAACCAGCAAAATTACATCAC 59.471 38.462 0.00 0.00 0.00 3.06
2605 2807 9.778741 TTGTCATCTGTTATAAGGTCAATATCC 57.221 33.333 0.00 0.00 0.00 2.59
2790 2992 2.676839 ACAGAGCTTGCAAGATCAATCG 59.323 45.455 37.79 26.51 43.60 3.34
2945 3147 2.156098 AAAGCCAGTCCTGCAGGGA 61.156 57.895 32.23 16.32 42.77 4.20
2946 3148 1.975407 CAAAGCCAGTCCTGCAGGG 60.975 63.158 32.23 17.23 35.41 4.45
3035 3237 2.787249 CTGAATGCAGCGGAACCG 59.213 61.111 9.00 9.00 43.09 4.44
3485 3689 2.813908 GCCCGTAGCAACTCGGTG 60.814 66.667 0.00 0.00 44.51 4.94
3545 3749 2.678336 GGGCAATGAAAAGTAGACCTCG 59.322 50.000 0.00 0.00 0.00 4.63
3683 3888 7.735917 AGATATGGTGCTACTAATTGCAAGTA 58.264 34.615 4.94 5.76 41.10 2.24
4013 4218 1.001048 CGGTAAGAACGTGACTGGACA 60.001 52.381 0.00 0.00 0.00 4.02
4103 4308 2.316108 TCACCAGAGTACAGTTCAGCA 58.684 47.619 0.00 0.00 0.00 4.41
4179 4384 1.942657 GTATGTTGATGCGCCTCACAT 59.057 47.619 23.04 23.04 0.00 3.21
4212 4417 1.732405 GCTGTGATTGGCTTAAACCGC 60.732 52.381 0.00 0.00 0.00 5.68
4298 4503 0.910088 AGACTAGCCCCAACAGGACC 60.910 60.000 0.00 0.00 38.24 4.46
4428 4637 7.587037 TTTTGAATTCACTCTCCTGTTCAAT 57.413 32.000 7.89 0.00 36.03 2.57
4454 4663 2.799978 TGCAGAAATATACGGTCATGCG 59.200 45.455 0.00 0.00 35.23 4.73
4524 4733 3.906720 TGCTTACATTGTACTCCCTCC 57.093 47.619 0.00 0.00 0.00 4.30
4871 5243 2.628696 CCCAACGCAAGCATCTGCA 61.629 57.895 4.79 0.00 42.77 4.41
4968 5340 2.435372 TGGAAAGACAGGCACAAACT 57.565 45.000 0.00 0.00 0.00 2.66
4985 5357 7.285172 TGTGTGATGGGAACTTATGATATTTGG 59.715 37.037 0.00 0.00 0.00 3.28
5142 5519 4.929211 GGATTACAATGAAAAACAGCACCC 59.071 41.667 0.00 0.00 0.00 4.61
5349 5727 4.389374 CAACTCAAGATGTTGTACAGGGT 58.611 43.478 2.11 0.00 39.69 4.34
5699 6077 6.988622 TTTTTAACTATGGTGGTGATACCG 57.011 37.500 0.00 0.00 42.58 4.02
5796 6174 1.388547 TGCGCTTTTCTGACCAAAGT 58.611 45.000 9.73 0.00 34.27 2.66
5813 6191 1.211743 GCTTTTTGTCACTGCCTTGC 58.788 50.000 0.00 0.00 0.00 4.01
5880 6258 7.116090 TGGAAAAACGAATGCATGTTCTAAATG 59.884 33.333 0.00 0.00 0.00 2.32
5898 6277 6.040955 AGGAAGAGAAATGGAGTTGGAAAAAC 59.959 38.462 0.00 0.00 0.00 2.43
6043 6422 1.490490 TGGCTGTTGGTCTCTTTCTGT 59.510 47.619 0.00 0.00 0.00 3.41
6080 6459 4.435518 CGATACTTGTGTGAAAACCATCGG 60.436 45.833 0.00 0.00 31.58 4.18
6204 6585 4.655440 AAAAAGCCACACGAACAAAAAC 57.345 36.364 0.00 0.00 0.00 2.43
6387 6770 3.634910 GGACTGCCTAAACCAAACTTGAA 59.365 43.478 0.00 0.00 0.00 2.69
6462 6845 7.885297 TGAACTGAATATCAAAACCTTCCAAG 58.115 34.615 0.00 0.00 0.00 3.61
6628 7012 1.544825 TTCAGGAGCTTAGCGGCACT 61.545 55.000 1.45 0.00 34.17 4.40
6650 7034 0.107017 TTATCCTGCTTCTGCCCAGC 60.107 55.000 0.00 0.00 38.71 4.85
6794 7178 3.882888 ACTTTTTGGATGCTGACGAAAGA 59.117 39.130 0.00 0.00 0.00 2.52
6807 7191 7.908827 TTATCGTTGTATAGCACTTTTTGGA 57.091 32.000 0.00 0.00 0.00 3.53
6857 7243 4.637534 GGAGTAAAGATCTGCAAAGCATGA 59.362 41.667 0.00 0.00 38.13 3.07
6871 7257 2.783135 ACGTGTACGAGGGAGTAAAGA 58.217 47.619 11.79 0.00 43.02 2.52
6989 7376 5.601662 CCCGCAGAGAAGAAAGATGTAATA 58.398 41.667 0.00 0.00 0.00 0.98
6990 7377 4.446371 CCCGCAGAGAAGAAAGATGTAAT 58.554 43.478 0.00 0.00 0.00 1.89
7084 7479 2.645838 AAGCTTGCTGTTCTTCTGGA 57.354 45.000 0.00 0.00 0.00 3.86
7090 7485 2.789491 GCTCAAAAGCTTGCTGTTCT 57.211 45.000 0.00 0.00 45.55 3.01
7117 7742 6.006449 ACTCTGCAACTGAATTGGATTAGTT 58.994 36.000 0.00 0.00 38.08 2.24
7163 7789 1.102978 GGGATCCCACAAATTGACCG 58.897 55.000 26.95 0.00 35.81 4.79
7183 7809 2.034685 GCCAGAGTGGTTCCAAAGAAAC 59.965 50.000 0.00 0.00 40.46 2.78


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

AutoCloner maintained by Alex Coulton.