Multiple sequence alignment - TraesCS7A01G205300

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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 TraesCS7A01G205300 chr7A 100.000 9049 0 0 1 9049 167281317 167272269 0.000000e+00 16711
1 TraesCS7A01G205300 chr7D 97.830 7144 94 17 342 7443 165735977 165728853 0.000000e+00 12277
2 TraesCS7A01G205300 chr7D 92.207 1065 55 12 7480 8537 165728757 165727714 0.000000e+00 1482
3 TraesCS7A01G205300 chr7D 92.442 344 19 4 1 343 165736197 165735860 1.370000e-132 484
4 TraesCS7A01G205300 chr7D 84.713 314 30 9 8662 8971 165726699 165726400 1.910000e-76 298
5 TraesCS7A01G205300 chr7B 96.962 7176 162 23 342 7484 129662609 129655457 0.000000e+00 11993
6 TraesCS7A01G205300 chr7B 93.581 1075 47 13 7480 8537 129655405 129654336 0.000000e+00 1583
7 TraesCS7A01G205300 chr7B 89.646 396 30 7 8655 9049 129653467 129653082 2.270000e-135 494
8 TraesCS7A01G205300 chr7B 92.733 344 20 4 1 343 129662831 129662492 8.160000e-135 492
9 TraesCS7A01G205300 chr7B 89.406 387 30 5 8655 9040 129551101 129550725 2.290000e-130 477
10 TraesCS7A01G205300 chr7B 91.870 123 9 1 8533 8654 129653625 129653503 4.340000e-38 171
11 TraesCS7A01G205300 chr2A 80.876 251 46 2 7791 8040 155942143 155941894 7.170000e-46 196
12 TraesCS7A01G205300 chr2D 80.315 254 48 2 7788 8040 146308179 146308431 3.330000e-44 191
13 TraesCS7A01G205300 chr2B 79.921 254 49 2 7788 8040 206375935 206376187 1.550000e-42 185


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 TraesCS7A01G205300 chr7A 167272269 167281317 9048 True 16711.00 16711 100.0000 1 9049 1 chr7A.!!$R1 9048
1 TraesCS7A01G205300 chr7D 165726400 165736197 9797 True 3635.25 12277 91.7980 1 8971 4 chr7D.!!$R1 8970
2 TraesCS7A01G205300 chr7B 129653082 129662831 9749 True 2946.60 11993 92.9584 1 9049 5 chr7B.!!$R2 9048

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
222 223 1.216064 ACTGCCCAGCTCCATCATAA 58.784 50.000 0.00 0.00 0.00 1.90 F
223 224 1.779092 ACTGCCCAGCTCCATCATAAT 59.221 47.619 0.00 0.00 0.00 1.28 F
966 972 2.150014 TTGCTAGGTTTGGGCCTCCC 62.150 60.000 4.53 1.34 45.71 4.30 F
2253 2269 0.030638 AACGCATGGTGTCAAAGCAC 59.969 50.000 0.00 0.00 39.59 4.40 F
3484 3500 4.380867 CCAACAGATTTGCAATACCCTGAC 60.381 45.833 18.41 0.51 0.00 3.51 F
4841 4860 3.416156 ACAGTTTCAGCCCAAGAAGATC 58.584 45.455 0.00 0.00 0.00 2.75 F
5475 5498 2.744202 CCCATGTGAAGTACAGAGCAAC 59.256 50.000 0.00 0.00 43.80 4.17 F
7214 7279 1.662044 CCCTTTTCTGCCACTGTGC 59.338 57.895 1.29 0.00 0.00 4.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1182 1189 0.603707 ACCTCGACGAAGACGGTGTA 60.604 55.000 5.77 0.0 46.86 2.90 R
1207 1214 4.699522 GGAGAAACGCCGCCACCT 62.700 66.667 0.00 0.0 0.00 4.00 R
2322 2338 6.655078 ACCTGTTCAAGAATGCTGTTTATT 57.345 33.333 0.00 0.0 0.00 1.40 R
3865 3881 0.234106 CAGCACGAAGTCTGCAACAG 59.766 55.000 0.00 0.0 41.61 3.16 R
5429 5452 1.545428 GGACAATGTGGAGACCAGCAA 60.545 52.381 0.00 0.0 32.34 3.91 R
6829 6853 1.004745 AGGTTGGTGCACCCTAGAATG 59.995 52.381 32.62 0.0 37.58 2.67 R
7239 7304 0.031449 GATCTGGAGCGGAGTAGCAC 59.969 60.000 0.00 0.0 40.15 4.40 R
8372 8520 0.035056 CCAGCCAAGAAAGGGTCGAT 60.035 55.000 0.00 0.0 37.26 3.59 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
35 36 2.839486 ATGACGCTCAAGGTTTCTCA 57.161 45.000 0.00 0.00 0.00 3.27
90 91 1.877637 AACAGAGCACAACGCACATA 58.122 45.000 0.00 0.00 46.13 2.29
197 198 1.545582 CCGGATTTTGCTTCACCACAT 59.454 47.619 0.00 0.00 0.00 3.21
198 199 2.752354 CCGGATTTTGCTTCACCACATA 59.248 45.455 0.00 0.00 0.00 2.29
199 200 3.192422 CCGGATTTTGCTTCACCACATAA 59.808 43.478 0.00 0.00 0.00 1.90
201 202 4.320861 CGGATTTTGCTTCACCACATAACA 60.321 41.667 0.00 0.00 0.00 2.41
202 203 5.622007 CGGATTTTGCTTCACCACATAACAT 60.622 40.000 0.00 0.00 0.00 2.71
204 205 6.751888 GGATTTTGCTTCACCACATAACATAC 59.248 38.462 0.00 0.00 0.00 2.39
205 206 6.892658 TTTTGCTTCACCACATAACATACT 57.107 33.333 0.00 0.00 0.00 2.12
206 207 5.878332 TTGCTTCACCACATAACATACTG 57.122 39.130 0.00 0.00 0.00 2.74
207 208 3.689161 TGCTTCACCACATAACATACTGC 59.311 43.478 0.00 0.00 0.00 4.40
208 209 3.065371 GCTTCACCACATAACATACTGCC 59.935 47.826 0.00 0.00 0.00 4.85
209 210 3.275617 TCACCACATAACATACTGCCC 57.724 47.619 0.00 0.00 0.00 5.36
222 223 1.216064 ACTGCCCAGCTCCATCATAA 58.784 50.000 0.00 0.00 0.00 1.90
223 224 1.779092 ACTGCCCAGCTCCATCATAAT 59.221 47.619 0.00 0.00 0.00 1.28
255 256 9.612620 CATAAAAGGGAAGAAACGCAATATATC 57.387 33.333 0.00 0.00 0.00 1.63
345 346 9.411801 GACATAAGTCAAAAGAAAGGGAAATTC 57.588 33.333 0.00 0.00 44.34 2.17
346 347 8.923270 ACATAAGTCAAAAGAAAGGGAAATTCA 58.077 29.630 0.00 0.00 0.00 2.57
347 348 9.933723 CATAAGTCAAAAGAAAGGGAAATTCAT 57.066 29.630 0.00 0.00 0.00 2.57
362 363 9.476202 AGGGAAATTCATAAAAGAAAAGAAACG 57.524 29.630 0.00 0.00 0.00 3.60
363 364 8.221100 GGGAAATTCATAAAAGAAAAGAAACGC 58.779 33.333 0.00 0.00 0.00 4.84
364 365 8.760569 GGAAATTCATAAAAGAAAAGAAACGCA 58.239 29.630 0.00 0.00 0.00 5.24
410 411 9.807921 TTTTTCCTATCAAGAAATACAAGTCCT 57.192 29.630 0.00 0.00 33.45 3.85
475 477 8.427902 AGAAAGGCAAAAGGAAAGAAGATAAT 57.572 30.769 0.00 0.00 0.00 1.28
645 651 4.035102 GCACCTTCGCCTTCCCCT 62.035 66.667 0.00 0.00 0.00 4.79
648 654 2.269241 CCTTCGCCTTCCCCTCAC 59.731 66.667 0.00 0.00 0.00 3.51
732 738 3.730761 CGCAGCAGCCACTGAACC 61.731 66.667 7.73 0.00 40.25 3.62
966 972 2.150014 TTGCTAGGTTTGGGCCTCCC 62.150 60.000 4.53 1.34 45.71 4.30
1128 1135 4.776322 CGAGGTGCCGCCATGGAA 62.776 66.667 18.40 0.00 42.00 3.53
1158 1165 2.601299 GGGTTGGATGGGGCTACC 59.399 66.667 0.00 0.00 40.81 3.18
1207 1214 1.085091 GTCTTCGTCGAGGTCTGCTA 58.915 55.000 4.85 0.00 0.00 3.49
1606 1613 3.079578 CCATGGCTATGATGATGGTGAC 58.920 50.000 12.26 0.00 36.36 3.67
2253 2269 0.030638 AACGCATGGTGTCAAAGCAC 59.969 50.000 0.00 0.00 39.59 4.40
2322 2338 6.952773 AAGGTTACAAACAAACTAGCATCA 57.047 33.333 0.00 0.00 0.00 3.07
3308 3324 5.984725 TCGTGCCTCTAAATTTCCTTGATA 58.015 37.500 0.00 0.00 0.00 2.15
3484 3500 4.380867 CCAACAGATTTGCAATACCCTGAC 60.381 45.833 18.41 0.51 0.00 3.51
3812 3828 6.457355 CATTGTCATCCATTTTCCTGTTTGA 58.543 36.000 0.00 0.00 0.00 2.69
3865 3881 4.036262 TGCCTTATTAATGTGTTCCATCGC 59.964 41.667 0.00 0.00 31.75 4.58
4705 4724 7.312899 CCCCTTTTGACATATTTCTGTGTAAC 58.687 38.462 0.00 0.00 37.35 2.50
4841 4860 3.416156 ACAGTTTCAGCCCAAGAAGATC 58.584 45.455 0.00 0.00 0.00 2.75
5308 5331 9.515020 CACTAGAATATTCTCAGTCAAGTTCTC 57.485 37.037 21.17 0.00 38.70 2.87
5429 5452 3.071602 TCTGTTGAAGGCTCTGCTAGTTT 59.928 43.478 0.00 0.00 0.00 2.66
5475 5498 2.744202 CCCATGTGAAGTACAGAGCAAC 59.256 50.000 0.00 0.00 43.80 4.17
5532 5555 4.020662 ACATTGGAGAAGTCAGAGTCTTCC 60.021 45.833 0.00 0.00 41.27 3.46
5875 5898 7.384439 TCACAAAGTGTTTCAGATGTTGTTA 57.616 32.000 0.00 0.00 34.79 2.41
6099 6122 5.106908 GGTTTCTTTTGAGGATGAAGACTCG 60.107 44.000 0.00 0.00 36.53 4.18
6805 6829 5.236478 ACTTTACTCACTGTGTTGTGTATGC 59.764 40.000 7.79 0.00 38.90 3.14
6829 6853 6.526674 GCCTGTTGTTTACATGCTTGTAATAC 59.473 38.462 21.72 20.31 45.33 1.89
6845 6869 4.471747 TGTAATACATTCTAGGGTGCACCA 59.528 41.667 35.78 16.88 43.89 4.17
7214 7279 1.662044 CCCTTTTCTGCCACTGTGC 59.338 57.895 1.29 0.00 0.00 4.57
7219 7284 3.755526 TTCTGCCACTGTGCTGCGT 62.756 57.895 1.29 0.00 0.00 5.24
7239 7304 3.490759 GCGGTCACAGCATGGTCG 61.491 66.667 0.00 0.00 43.62 4.79
7248 7313 4.110493 GCATGGTCGTGCTACTCC 57.890 61.111 7.82 0.00 41.82 3.85
7250 7315 1.878522 CATGGTCGTGCTACTCCGC 60.879 63.158 0.00 0.00 0.00 5.54
7333 7402 1.228306 CACACGGGCCCCTTGTTTA 60.228 57.895 18.66 0.00 33.65 2.01
7395 7464 3.075148 GTTTCCTACCTTCCTGTTGCTC 58.925 50.000 0.00 0.00 0.00 4.26
7511 7655 8.503196 GTTTTCTGTTTCCAAAAGTTGAAACAT 58.497 29.630 16.12 0.00 43.60 2.71
7512 7656 8.614469 TTTCTGTTTCCAAAAGTTGAAACATT 57.386 26.923 16.12 0.00 43.60 2.71
7513 7657 8.614469 TTCTGTTTCCAAAAGTTGAAACATTT 57.386 26.923 16.12 0.00 43.60 2.32
7514 7658 8.614469 TCTGTTTCCAAAAGTTGAAACATTTT 57.386 26.923 16.12 1.92 43.60 1.82
7547 7691 1.622811 TGGTGGATGATTTTGGTTGGC 59.377 47.619 0.00 0.00 0.00 4.52
7584 7728 9.953697 ACTATCAGTCGAGTTATTAGTTCATTC 57.046 33.333 0.00 0.00 0.00 2.67
7586 7730 5.742453 TCAGTCGAGTTATTAGTTCATTCGC 59.258 40.000 0.00 0.00 0.00 4.70
7602 7746 1.112916 TCGCCTATTCGGATCTGGCA 61.113 55.000 17.51 5.48 43.38 4.92
7701 7846 9.254133 CGATCTGAATGATTAGTATTGTTGAGT 57.746 33.333 0.00 0.00 35.14 3.41
7736 7881 6.763135 TGAAGTGAATATTGTATGTCTCCAGC 59.237 38.462 0.00 0.00 0.00 4.85
7758 7906 1.269621 GCTCTTTGGCATGCATGATCC 60.270 52.381 30.64 21.79 0.00 3.36
7768 7916 4.486090 GCATGCATGATCCATTCTCATTC 58.514 43.478 30.64 3.15 31.00 2.67
7770 7918 2.551032 TGCATGATCCATTCTCATTCGC 59.449 45.455 0.00 0.00 31.00 4.70
7796 7944 1.939934 CTGTTTCCTTGTTCGCAGTCA 59.060 47.619 0.00 0.00 0.00 3.41
7821 7969 1.757699 GTGTGATGGACTACTCCCTCC 59.242 57.143 0.00 0.00 35.34 4.30
7847 7995 1.535015 GGCATCGACGAGGAGAAGAAG 60.535 57.143 14.58 0.00 0.00 2.85
7880 8028 2.234908 GGGGATCATTGACTATCTCCGG 59.765 54.545 0.00 0.00 33.16 5.14
7889 8037 2.022195 GACTATCTCCGGCAGTACACA 58.978 52.381 0.00 0.00 0.00 3.72
8021 8169 3.844211 AGGCCATGTCAAAGTACTTCCTA 59.156 43.478 8.95 0.00 0.00 2.94
8106 8254 1.386533 GAGTGCAAGATGGGGTGATG 58.613 55.000 0.00 0.00 0.00 3.07
8109 8257 2.484062 GCAAGATGGGGTGATGGCG 61.484 63.158 0.00 0.00 0.00 5.69
8140 8288 7.361799 GGAAGCGGTACATTGTTTTCTTTCTAT 60.362 37.037 0.00 0.00 0.00 1.98
8365 8513 5.705609 AATGCGTGAGTTTCCTTACAAAT 57.294 34.783 0.00 0.00 0.00 2.32
8372 8520 4.576873 TGAGTTTCCTTACAAATGCAACGA 59.423 37.500 0.00 0.00 0.00 3.85
8377 8525 3.369756 TCCTTACAAATGCAACGATCGAC 59.630 43.478 24.34 11.22 0.00 4.20
8433 8582 9.433153 ACTTACTAGTTAATTCCCTCGAAAAAG 57.567 33.333 0.00 0.00 0.00 2.27
8435 8584 9.649167 TTACTAGTTAATTCCCTCGAAAAAGAG 57.351 33.333 0.00 0.00 37.97 2.85
8439 8588 8.459911 AGTTAATTCCCTCGAAAAAGAGAAAA 57.540 30.769 0.00 0.00 40.57 2.29
8476 8630 3.670625 TGCGTTACTACTGCCTTCATTT 58.329 40.909 0.00 0.00 0.00 2.32
8487 8641 8.220559 ACTACTGCCTTCATTTCATAATATGGT 58.779 33.333 0.00 0.00 0.00 3.55
8489 8643 8.310122 ACTGCCTTCATTTCATAATATGGTTT 57.690 30.769 0.00 0.00 0.00 3.27
8554 9718 6.464222 TGTTGATTCAGATCGTTAGGAAACT 58.536 36.000 0.00 0.00 38.74 2.66
8590 9754 1.302511 GCGTGTTGTGAGGTGGGAT 60.303 57.895 0.00 0.00 0.00 3.85
8607 9771 2.572104 GGGATAATTCCGCCATAGGTCT 59.428 50.000 0.00 0.00 43.63 3.85
8635 9800 1.942657 CTTCAAGCCATCCATGTACGG 59.057 52.381 0.00 0.00 0.00 4.02
8646 9812 1.069090 ATGTACGGCGCTATGGGTG 59.931 57.895 6.90 0.00 0.00 4.61
8673 9887 3.282157 CCCATCCATTGCGCGGAG 61.282 66.667 8.83 0.00 35.56 4.63
8701 9915 2.063979 TGGCGGGGATAGGTGTCAG 61.064 63.158 0.00 0.00 0.00 3.51
8723 9937 2.632377 TGTCCATCTTGCTCGATTTCC 58.368 47.619 0.00 0.00 0.00 3.13
8724 9938 1.594862 GTCCATCTTGCTCGATTTCCG 59.405 52.381 0.00 0.00 40.25 4.30
8725 9939 1.207089 TCCATCTTGCTCGATTTCCGT 59.793 47.619 0.00 0.00 39.75 4.69
8726 9940 2.009774 CCATCTTGCTCGATTTCCGTT 58.990 47.619 0.00 0.00 39.75 4.44
8727 9941 2.030946 CCATCTTGCTCGATTTCCGTTC 59.969 50.000 0.00 0.00 39.75 3.95
8811 10028 2.611518 ACTAAATGCAGCTCAGACGAC 58.388 47.619 0.00 0.00 0.00 4.34
8812 10029 1.585668 CTAAATGCAGCTCAGACGACG 59.414 52.381 0.00 0.00 0.00 5.12
8813 10030 0.038251 AAATGCAGCTCAGACGACGA 60.038 50.000 0.00 0.00 0.00 4.20
8819 10036 0.382515 AGCTCAGACGACGATTAGCC 59.617 55.000 0.00 0.00 0.00 3.93
8875 10093 2.293399 CCTGGACTTTAAACGCTTGCTT 59.707 45.455 0.00 0.00 0.00 3.91
8879 10097 3.308530 GACTTTAAACGCTTGCTTGCAT 58.691 40.909 0.00 0.00 0.00 3.96
8960 10178 3.945981 TCGACTACCACAAAGCACATA 57.054 42.857 0.00 0.00 0.00 2.29
8973 10191 3.895232 AGCACATAGGATGACTTCGTT 57.105 42.857 0.00 0.00 0.00 3.85
8982 10200 8.021973 ACATAGGATGACTTCGTTAATATCGTC 58.978 37.037 0.00 0.00 0.00 4.20
9008 10226 2.307098 AGGCTGCTCCTGTATTTCTTGT 59.693 45.455 0.00 0.00 45.54 3.16
9015 10233 7.659390 GCTGCTCCTGTATTTCTTGTATCTATT 59.341 37.037 0.00 0.00 0.00 1.73
9016 10234 9.553064 CTGCTCCTGTATTTCTTGTATCTATTT 57.447 33.333 0.00 0.00 0.00 1.40
9018 10236 8.704234 GCTCCTGTATTTCTTGTATCTATTTCG 58.296 37.037 0.00 0.00 0.00 3.46
9034 10252 8.798748 ATCTATTTCGTTTTGTATAGACGAGG 57.201 34.615 0.00 0.00 45.18 4.63
9040 10258 4.435121 CGTTTTGTATAGACGAGGCCAAAC 60.435 45.833 5.01 0.87 38.99 2.93
9042 10260 3.795623 TGTATAGACGAGGCCAAACTC 57.204 47.619 5.01 0.00 0.00 3.01
9043 10261 3.093814 TGTATAGACGAGGCCAAACTCA 58.906 45.455 5.01 0.00 37.34 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 1.940613 GTGTTGAGAAACCTTGAGCGT 59.059 47.619 0.00 0.00 0.00 5.07
35 36 5.299279 AGGTCTTTGATGTCATTTTCGTGTT 59.701 36.000 0.00 0.00 0.00 3.32
90 91 5.183904 GTGTTCCCTATTGAGACTTTGCAAT 59.816 40.000 0.00 0.00 38.24 3.56
169 170 1.185315 AGCAAAATCCGGATTGTGGG 58.815 50.000 37.02 24.07 36.70 4.61
197 198 1.578897 TGGAGCTGGGCAGTATGTTA 58.421 50.000 0.00 0.00 39.31 2.41
198 199 0.921896 ATGGAGCTGGGCAGTATGTT 59.078 50.000 0.00 0.00 39.31 2.71
199 200 0.471617 GATGGAGCTGGGCAGTATGT 59.528 55.000 0.00 0.00 39.31 2.29
201 202 1.442773 ATGATGGAGCTGGGCAGTAT 58.557 50.000 0.00 0.00 0.00 2.12
202 203 2.101640 TATGATGGAGCTGGGCAGTA 57.898 50.000 0.00 0.00 0.00 2.74
204 205 2.581216 ATTATGATGGAGCTGGGCAG 57.419 50.000 0.00 0.00 0.00 4.85
205 206 4.451891 TTAATTATGATGGAGCTGGGCA 57.548 40.909 0.00 0.00 0.00 5.36
206 207 5.477984 TGAATTAATTATGATGGAGCTGGGC 59.522 40.000 0.00 0.00 0.00 5.36
207 208 7.713734 ATGAATTAATTATGATGGAGCTGGG 57.286 36.000 0.00 0.00 0.00 4.45
222 223 8.527810 TGCGTTTCTTCCCTTTTATGAATTAAT 58.472 29.630 0.00 0.00 0.00 1.40
223 224 7.887381 TGCGTTTCTTCCCTTTTATGAATTAA 58.113 30.769 0.00 0.00 0.00 1.40
238 239 9.643652 CTGAGAAAAGATATATTGCGTTTCTTC 57.356 33.333 13.04 9.11 40.92 2.87
314 315 8.977412 TCCCTTTCTTTTGACTTATGTCTTTTT 58.023 29.630 9.87 0.00 43.29 1.94
315 316 8.533569 TCCCTTTCTTTTGACTTATGTCTTTT 57.466 30.769 9.87 0.00 43.29 2.27
316 317 8.533569 TTCCCTTTCTTTTGACTTATGTCTTT 57.466 30.769 9.87 0.00 43.29 2.52
317 318 8.533569 TTTCCCTTTCTTTTGACTTATGTCTT 57.466 30.769 9.87 0.00 43.29 3.01
318 319 8.712228 ATTTCCCTTTCTTTTGACTTATGTCT 57.288 30.769 9.87 0.00 43.29 3.41
319 320 9.411801 GAATTTCCCTTTCTTTTGACTTATGTC 57.588 33.333 1.85 1.85 43.20 3.06
320 321 8.923270 TGAATTTCCCTTTCTTTTGACTTATGT 58.077 29.630 0.00 0.00 0.00 2.29
321 322 9.933723 ATGAATTTCCCTTTCTTTTGACTTATG 57.066 29.630 0.00 0.00 0.00 1.90
336 337 9.476202 CGTTTCTTTTCTTTTATGAATTTCCCT 57.524 29.630 0.00 0.00 0.00 4.20
337 338 8.221100 GCGTTTCTTTTCTTTTATGAATTTCCC 58.779 33.333 0.00 0.00 0.00 3.97
338 339 8.760569 TGCGTTTCTTTTCTTTTATGAATTTCC 58.239 29.630 0.00 0.00 0.00 3.13
384 385 9.807921 AGGACTTGTATTTCTTGATAGGAAAAA 57.192 29.630 0.00 0.00 36.47 1.94
475 477 8.740123 TGTATTTCCTGCCTTTTATAATTCGA 57.260 30.769 0.00 0.00 0.00 3.71
483 485 8.871125 TGGTTTTATTGTATTTCCTGCCTTTTA 58.129 29.630 0.00 0.00 0.00 1.52
486 488 6.926630 TGGTTTTATTGTATTTCCTGCCTT 57.073 33.333 0.00 0.00 0.00 4.35
487 489 6.926630 TTGGTTTTATTGTATTTCCTGCCT 57.073 33.333 0.00 0.00 0.00 4.75
497 499 5.048507 GCCGTTGGTTTTGGTTTTATTGTA 58.951 37.500 0.00 0.00 0.00 2.41
640 646 4.075793 CGGAGGAGGGTGAGGGGA 62.076 72.222 0.00 0.00 0.00 4.81
645 651 4.779733 GGAGGCGGAGGAGGGTGA 62.780 72.222 0.00 0.00 0.00 4.02
729 735 4.070552 GCTCGAGGCTCCACGGTT 62.071 66.667 15.58 0.00 38.06 4.44
732 738 3.893763 ATCGCTCGAGGCTCCACG 61.894 66.667 15.58 10.34 39.13 4.94
966 972 0.529555 CCACAAAAACCAACTGCCGG 60.530 55.000 0.00 0.00 0.00 6.13
1158 1165 4.838152 CGCTCCGGTGGGGACATG 62.838 72.222 12.42 0.00 46.14 3.21
1182 1189 0.603707 ACCTCGACGAAGACGGTGTA 60.604 55.000 5.77 0.00 46.86 2.90
1207 1214 4.699522 GGAGAAACGCCGCCACCT 62.700 66.667 0.00 0.00 0.00 4.00
1606 1613 5.916883 GCAATTCGGTGAATCCATCAAATAG 59.083 40.000 0.00 0.00 40.50 1.73
2322 2338 6.655078 ACCTGTTCAAGAATGCTGTTTATT 57.345 33.333 0.00 0.00 0.00 1.40
3019 3035 0.031414 TGCCCCTTAGGAGGACCTAC 60.031 60.000 0.00 0.00 46.97 3.18
3172 3188 1.149148 GCTTCTCAAGTGGACGAACC 58.851 55.000 0.00 0.00 39.54 3.62
3460 3476 3.763360 CAGGGTATTGCAAATCTGTTGGA 59.237 43.478 1.71 0.00 0.00 3.53
3484 3500 2.739293 TCTCATCTCGATGAACGTCG 57.261 50.000 10.50 9.72 46.10 5.12
3788 3804 6.457355 TCAAACAGGAAAATGGATGACAATG 58.543 36.000 0.00 0.00 0.00 2.82
3812 3828 4.503991 GCCTACTAGGTATCTGCTTGCAAT 60.504 45.833 0.00 0.00 37.80 3.56
3865 3881 0.234106 CAGCACGAAGTCTGCAACAG 59.766 55.000 0.00 0.00 41.61 3.16
3999 4015 3.603532 CCACATCCATATCTTCCCATCG 58.396 50.000 0.00 0.00 0.00 3.84
4841 4860 3.207669 GCCCGCCTTCATGCTCAG 61.208 66.667 0.00 0.00 0.00 3.35
5429 5452 1.545428 GGACAATGTGGAGACCAGCAA 60.545 52.381 0.00 0.00 32.34 3.91
5475 5498 3.266686 TTCATCAGCCACCACCCCG 62.267 63.158 0.00 0.00 0.00 5.73
5532 5555 9.128404 TCAATTCTATCAGAAAGATTTGATGGG 57.872 33.333 6.40 0.00 37.82 4.00
5875 5898 4.649692 GGCTCATCATCATACACTGGAAT 58.350 43.478 0.00 0.00 0.00 3.01
6099 6122 4.846779 TTTTGCCTTATCCACAGAACAC 57.153 40.909 0.00 0.00 0.00 3.32
6829 6853 1.004745 AGGTTGGTGCACCCTAGAATG 59.995 52.381 32.62 0.00 37.58 2.67
6845 6869 5.141910 GAGGCCTTCTAGACATACTAGGTT 58.858 45.833 6.77 0.00 46.08 3.50
7021 7045 6.002704 AGGCTCCAAGATTCATAGCTATTTG 58.997 40.000 2.64 5.84 33.67 2.32
7214 7279 3.108289 CTGTGACCGCAGACGCAG 61.108 66.667 4.67 0.00 38.70 5.18
7219 7284 2.046988 CCATGCTGTGACCGCAGA 60.047 61.111 14.10 0.92 41.22 4.26
7239 7304 0.031449 GATCTGGAGCGGAGTAGCAC 59.969 60.000 0.00 0.00 40.15 4.40
7248 7313 1.117749 TCAGATGGGGATCTGGAGCG 61.118 60.000 11.24 0.00 46.02 5.03
7250 7315 3.249752 AGAATCAGATGGGGATCTGGAG 58.750 50.000 11.24 0.00 46.02 3.86
7275 7340 7.604549 ACATGCAAAATTAAGTCATGTCATGA 58.395 30.769 11.62 11.62 42.63 3.07
7436 7508 4.836825 TCAATCCTTTAGCTTCTCACCAG 58.163 43.478 0.00 0.00 0.00 4.00
7482 7626 6.516718 TCAACTTTTGGAAACAGAAAACACA 58.483 32.000 0.00 0.00 44.54 3.72
7547 7691 2.352651 CGACTGATAGTTGCCACATTGG 59.647 50.000 0.00 0.00 41.55 3.16
7551 7695 1.893137 ACTCGACTGATAGTTGCCACA 59.107 47.619 0.00 0.00 29.55 4.17
7552 7696 2.656560 ACTCGACTGATAGTTGCCAC 57.343 50.000 0.00 0.00 29.55 5.01
7584 7728 4.268687 GCCAGATCCGAATAGGCG 57.731 61.111 0.00 0.00 40.77 5.52
7586 7730 1.349026 ACCATGCCAGATCCGAATAGG 59.651 52.381 0.00 0.00 42.97 2.57
7602 7746 0.889186 GTGGCCGTTGACTTGACCAT 60.889 55.000 0.00 0.00 0.00 3.55
7654 7798 4.390603 TCGATTTTGTCAAACAGATACGGG 59.609 41.667 0.00 0.00 0.00 5.28
7758 7906 1.010350 GGCAGCGCGAATGAGAATG 60.010 57.895 12.10 0.00 0.00 2.67
7768 7916 3.357079 AAGGAAACAGGCAGCGCG 61.357 61.111 0.00 0.00 0.00 6.86
7770 7918 0.040067 GAACAAGGAAACAGGCAGCG 60.040 55.000 0.00 0.00 0.00 5.18
7796 7944 2.180276 GAGTAGTCCATCACACCCACT 58.820 52.381 0.00 0.00 0.00 4.00
7821 7969 1.811266 CCTCGTCGATGCCAACCAG 60.811 63.158 0.00 0.00 0.00 4.00
7847 7995 1.348008 TGATCCCCATCACCAGCTCC 61.348 60.000 0.00 0.00 33.80 4.70
7880 8028 2.226330 TGTTTGTCCCATGTGTACTGC 58.774 47.619 0.00 0.00 0.00 4.40
7889 8037 1.067295 TCTCCAGCTGTTTGTCCCAT 58.933 50.000 13.81 0.00 0.00 4.00
8021 8169 1.378762 CCATTGGTCGGGGACAGTT 59.621 57.895 0.00 0.00 33.68 3.16
8106 8254 3.766691 TACCGCTTCCCAGTCGCC 61.767 66.667 0.00 0.00 0.00 5.54
8109 8257 1.338769 ACAATGTACCGCTTCCCAGTC 60.339 52.381 0.00 0.00 0.00 3.51
8365 8513 0.320374 AGAAAGGGTCGATCGTTGCA 59.680 50.000 15.94 0.00 0.00 4.08
8372 8520 0.035056 CCAGCCAAGAAAGGGTCGAT 60.035 55.000 0.00 0.00 37.26 3.59
8377 8525 1.228675 AGCACCAGCCAAGAAAGGG 60.229 57.895 0.00 0.00 43.56 3.95
8531 8695 6.590292 TCAGTTTCCTAACGATCTGAATCAAC 59.410 38.462 0.00 0.00 39.31 3.18
8533 8697 6.280855 TCAGTTTCCTAACGATCTGAATCA 57.719 37.500 0.00 0.00 39.31 2.57
8534 8698 7.778470 AATCAGTTTCCTAACGATCTGAATC 57.222 36.000 0.00 0.00 39.31 2.52
8535 8699 9.838339 ATAAATCAGTTTCCTAACGATCTGAAT 57.162 29.630 0.00 0.00 39.31 2.57
8536 8700 9.667107 AATAAATCAGTTTCCTAACGATCTGAA 57.333 29.630 0.00 0.00 39.31 3.02
8554 9718 2.942376 ACGCGAGCCAATGAATAAATCA 59.058 40.909 15.93 0.00 43.67 2.57
8584 9748 2.039879 ACCTATGGCGGAATTATCCCAC 59.960 50.000 0.00 0.00 43.37 4.61
8590 9754 1.616865 CCGAGACCTATGGCGGAATTA 59.383 52.381 0.00 0.00 46.29 1.40
8607 9771 2.819984 GATGGCTTGAAGCACCCCGA 62.820 60.000 19.89 0.00 44.75 5.14
8646 9812 2.434428 CAATGGATGGGCTCAGCTATC 58.566 52.381 0.00 0.99 29.16 2.08
8651 9817 3.428797 CGCAATGGATGGGCTCAG 58.571 61.111 0.00 0.00 34.98 3.35
8701 9915 3.181506 GGAAATCGAGCAAGATGGACAAC 60.182 47.826 0.00 0.00 0.00 3.32
8724 9938 5.579511 TGCCTAAATTACAGCTACGAAGAAC 59.420 40.000 0.00 0.00 0.00 3.01
8725 9939 5.726397 TGCCTAAATTACAGCTACGAAGAA 58.274 37.500 0.00 0.00 0.00 2.52
8726 9940 5.333299 TGCCTAAATTACAGCTACGAAGA 57.667 39.130 0.00 0.00 0.00 2.87
8727 9941 5.986135 AGATGCCTAAATTACAGCTACGAAG 59.014 40.000 0.00 0.00 0.00 3.79
8811 10028 6.616947 TGTTTTCACCATAAAAGGCTAATCG 58.383 36.000 0.00 0.00 0.00 3.34
8812 10029 9.087424 GAATGTTTTCACCATAAAAGGCTAATC 57.913 33.333 0.00 0.00 0.00 1.75
8813 10030 8.815912 AGAATGTTTTCACCATAAAAGGCTAAT 58.184 29.630 0.00 0.00 34.08 1.73
8948 10166 4.201753 CGAAGTCATCCTATGTGCTTTGTG 60.202 45.833 0.00 0.00 31.08 3.33
8960 10178 5.301045 TGGACGATATTAACGAAGTCATCCT 59.699 40.000 0.00 0.00 45.00 3.24
8973 10191 4.081642 GGAGCAGCCTTATGGACGATATTA 60.082 45.833 0.00 0.00 34.57 0.98
9008 10226 9.888878 CCTCGTCTATACAAAACGAAATAGATA 57.111 33.333 0.00 0.00 43.96 1.98
9015 10233 3.056678 TGGCCTCGTCTATACAAAACGAA 60.057 43.478 3.32 0.00 43.96 3.85
9016 10234 2.492881 TGGCCTCGTCTATACAAAACGA 59.507 45.455 3.32 0.00 42.59 3.85
9018 10236 4.694037 AGTTTGGCCTCGTCTATACAAAAC 59.306 41.667 3.32 1.27 30.73 2.43
9026 10244 5.353394 AATAATGAGTTTGGCCTCGTCTA 57.647 39.130 3.32 0.00 34.04 2.59


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

AutoCloner maintained by Alex Coulton.