Multiple sequence alignment - TraesCS7A01G530500

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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 TraesCS7A01G530500 chr7A 100.000 2954 0 0 1 2954 709676846 709679799 0.000000e+00 5456.0
1 TraesCS7A01G530500 chr7A 80.037 536 83 14 2325 2849 709698576 709699098 2.780000e-100 375.0
2 TraesCS7A01G530500 chr7A 81.840 424 51 13 1006 1422 709990642 709990238 1.700000e-87 333.0
3 TraesCS7A01G530500 chr7A 92.683 41 2 1 2906 2945 709699086 709699126 1.140000e-04 58.4
4 TraesCS7A01G530500 chr7D 90.523 1530 113 13 443 1960 616928845 616930354 0.000000e+00 1993.0
5 TraesCS7A01G530500 chr7D 87.500 904 66 12 2060 2954 616930399 616931264 0.000000e+00 1000.0
6 TraesCS7A01G530500 chr7D 79.461 964 128 39 586 1515 616942913 616943840 1.160000e-173 619.0
7 TraesCS7A01G530500 chr7D 91.150 452 33 7 1 450 616925127 616925573 9.050000e-170 606.0
8 TraesCS7A01G530500 chr7D 84.198 424 43 15 1006 1422 617114564 617114158 9.930000e-105 390.0
9 TraesCS7A01G530500 chr7D 89.744 78 7 1 2323 2399 616943885 616943962 6.740000e-17 99.0
10 TraesCS7A01G530500 chr7D 94.340 53 3 0 2849 2901 104637907 104637959 6.790000e-12 82.4
11 TraesCS7A01G530500 chr7D 94.231 52 3 0 2854 2905 379845482 379845533 2.440000e-11 80.5
12 TraesCS7A01G530500 chr7D 85.714 56 8 0 540 595 586699783 586699838 3.180000e-05 60.2
13 TraesCS7A01G530500 chr7B 86.694 1706 176 30 2 1670 711004093 711005784 0.000000e+00 1845.0
14 TraesCS7A01G530500 chr7B 88.947 950 88 6 2012 2954 711031948 711032887 0.000000e+00 1157.0
15 TraesCS7A01G530500 chr7B 77.546 432 54 19 1101 1516 711482395 711481991 1.380000e-53 220.0
16 TraesCS7A01G530500 chr7B 91.304 92 8 0 1006 1097 711483027 711482936 3.090000e-25 126.0
17 TraesCS7A01G530500 chr7B 93.617 47 2 1 547 592 12955904 12955950 5.280000e-08 69.4
18 TraesCS7A01G530500 chrUn 92.857 56 2 2 2850 2905 119816194 119816141 2.440000e-11 80.5
19 TraesCS7A01G530500 chrUn 94.595 37 1 1 559 595 386260223 386260258 4.110000e-04 56.5
20 TraesCS7A01G530500 chr4D 92.857 56 3 1 2850 2905 441813640 441813586 2.440000e-11 80.5
21 TraesCS7A01G530500 chr1A 91.379 58 3 2 2848 2905 6160668 6160723 8.780000e-11 78.7
22 TraesCS7A01G530500 chr3A 91.379 58 2 2 2848 2905 319954130 319954076 3.160000e-10 76.8
23 TraesCS7A01G530500 chr2B 90.000 60 5 1 2846 2905 246954256 246954314 3.160000e-10 76.8
24 TraesCS7A01G530500 chr2B 94.595 37 1 1 559 595 714254231 714254196 4.110000e-04 56.5
25 TraesCS7A01G530500 chr2B 94.595 37 1 1 559 595 714254629 714254594 4.110000e-04 56.5
26 TraesCS7A01G530500 chr2B 94.595 37 1 1 559 595 714309625 714309590 4.110000e-04 56.5
27 TraesCS7A01G530500 chr2A 96.774 31 1 0 561 591 565074390 565074360 5.000000e-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 TraesCS7A01G530500 chr7A 709676846 709679799 2953 False 5456.000000 5456 100.000000 1 2954 1 chr7A.!!$F1 2953
1 TraesCS7A01G530500 chr7A 709698576 709699126 550 False 216.700000 375 86.360000 2325 2945 2 chr7A.!!$F2 620
2 TraesCS7A01G530500 chr7D 616925127 616931264 6137 False 1199.666667 1993 89.724333 1 2954 3 chr7D.!!$F4 2953
3 TraesCS7A01G530500 chr7D 616942913 616943962 1049 False 359.000000 619 84.602500 586 2399 2 chr7D.!!$F5 1813
4 TraesCS7A01G530500 chr7B 711004093 711005784 1691 False 1845.000000 1845 86.694000 2 1670 1 chr7B.!!$F2 1668
5 TraesCS7A01G530500 chr7B 711031948 711032887 939 False 1157.000000 1157 88.947000 2012 2954 1 chr7B.!!$F3 942

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
889 4184 0.033228 GCCATAGCTCAGTCGCAGAT 59.967 55.0 0.0 0.0 35.33 2.9 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2376 5730 0.250124 TCCACGTCACCCACAACATC 60.25 55.0 0.0 0.0 0.0 3.06 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
106 107 3.491639 TGATTTTGTTGGTCACTCGTACG 59.508 43.478 9.53 9.53 0.00 3.67
111 112 2.287188 TGTTGGTCACTCGTACGAAGTC 60.287 50.000 20.00 11.91 43.93 3.01
117 118 0.443088 ACTCGTACGAAGTCTCAGCG 59.557 55.000 20.00 6.62 43.93 5.18
159 160 7.169140 AGTTTCAAAAACTCGGCAAAACATATC 59.831 33.333 0.00 0.00 0.00 1.63
187 188 2.216898 GATCTCATTTGAAGGCCCTCG 58.783 52.381 0.00 0.00 0.00 4.63
195 196 2.526873 AAGGCCCTCGTCACCAGT 60.527 61.111 0.00 0.00 0.00 4.00
220 221 4.981674 ACACGAATATGCAAACCAAACTTG 59.018 37.500 0.00 0.00 0.00 3.16
229 230 9.777297 ATATGCAAACCAAACTTGATTTAAACT 57.223 25.926 0.00 0.00 0.00 2.66
259 260 9.358872 GGTTCAAAGGATATGAAAGAATGAAAC 57.641 33.333 0.00 0.00 38.44 2.78
268 270 6.817765 ATGAAAGAATGAAACCGAAAGCTA 57.182 33.333 0.00 0.00 0.00 3.32
324 327 0.629058 TACAAATCCCTCCCCTTGGC 59.371 55.000 0.00 0.00 0.00 4.52
353 359 3.641437 TGCTGCCACTGAAACAATAAC 57.359 42.857 0.00 0.00 0.00 1.89
467 3754 3.701532 TTTGCCTTGTAAACGTTGAGG 57.298 42.857 0.00 8.63 0.00 3.86
474 3761 5.335661 GCCTTGTAAACGTTGAGGAATCAAT 60.336 40.000 18.78 0.00 31.79 2.57
484 3771 5.990386 CGTTGAGGAATCAATCTCAGATGAT 59.010 40.000 0.00 0.00 40.55 2.45
485 3772 6.482641 CGTTGAGGAATCAATCTCAGATGATT 59.517 38.462 10.42 10.42 46.15 2.57
486 3773 7.012138 CGTTGAGGAATCAATCTCAGATGATTT 59.988 37.037 11.41 1.17 44.15 2.17
487 3774 8.684520 GTTGAGGAATCAATCTCAGATGATTTT 58.315 33.333 11.41 6.00 44.15 1.82
488 3775 8.818622 TGAGGAATCAATCTCAGATGATTTTT 57.181 30.769 11.41 5.76 44.15 1.94
526 3813 4.867608 AGTTTAACACCATGTTTGTGCAAC 59.132 37.500 0.00 6.04 41.45 4.17
700 3992 7.840342 TTATTTTTCTTTCAAGCAGTTGCAA 57.160 28.000 6.90 0.00 45.16 4.08
718 4011 8.445493 CAGTTGCAAATTTTGTCTCTTTTTCTT 58.555 29.630 0.00 0.00 0.00 2.52
729 4022 7.502120 TGTCTCTTTTTCTTTCTCTTCCATG 57.498 36.000 0.00 0.00 0.00 3.66
752 4046 3.380320 ACCCACGAGGCTAAAAATTATGC 59.620 43.478 0.00 0.00 40.58 3.14
847 4142 3.669122 GCGTCAGGAATATATGTCGTCAC 59.331 47.826 0.00 0.00 31.95 3.67
889 4184 0.033228 GCCATAGCTCAGTCGCAGAT 59.967 55.000 0.00 0.00 35.33 2.90
993 4297 3.951979 CAGGATGGACGATAGCAAAAC 57.048 47.619 0.00 0.00 42.67 2.43
1288 4602 3.436700 GCGGCAAGCTGGTAATTTATT 57.563 42.857 2.69 0.00 44.04 1.40
1297 4611 7.290118 CAAGCTGGTAATTTATTTTGTTGCAC 58.710 34.615 0.00 0.00 0.00 4.57
1300 4614 7.042119 AGCTGGTAATTTATTTTGTTGCACAAC 60.042 33.333 6.57 6.57 37.90 3.32
1302 4616 8.723942 TGGTAATTTATTTTGTTGCACAACTT 57.276 26.923 14.16 1.29 37.90 2.66
1308 4622 5.710613 ATTTTGTTGCACAACTTTTACCG 57.289 34.783 14.16 0.00 37.90 4.02
1319 4633 4.392754 ACAACTTTTACCGTTCGAAAGTGT 59.607 37.500 10.21 9.70 41.36 3.55
1327 4641 1.782023 CGTTCGAAAGTGTATGTGCGC 60.782 52.381 0.00 0.00 0.00 6.09
1333 4647 3.666638 CGAAAGTGTATGTGCGCATCAAA 60.667 43.478 17.64 0.00 36.58 2.69
1335 4649 4.439305 AAGTGTATGTGCGCATCAAAAT 57.561 36.364 17.64 5.55 36.58 1.82
1336 4650 5.559427 AAGTGTATGTGCGCATCAAAATA 57.441 34.783 17.64 4.52 36.58 1.40
1337 4651 5.756195 AGTGTATGTGCGCATCAAAATAT 57.244 34.783 17.64 2.66 36.58 1.28
1359 4673 2.897436 TCTCTTCTGACATTGGCATCG 58.103 47.619 0.00 0.00 0.00 3.84
1361 4675 2.606725 CTCTTCTGACATTGGCATCGAC 59.393 50.000 0.00 0.00 0.00 4.20
1539 4862 3.305335 CCCATCTGGCATAATTTTACGGC 60.305 47.826 0.00 0.00 0.00 5.68
1573 4897 9.553064 CAGTCATTTCTATAAGCCTTGTAATCT 57.447 33.333 0.00 0.00 0.00 2.40
1582 4906 9.922305 CTATAAGCCTTGTAATCTTTTTCTTCG 57.078 33.333 0.00 0.00 0.00 3.79
1588 4912 4.138290 TGTAATCTTTTTCTTCGCCACCA 58.862 39.130 0.00 0.00 0.00 4.17
1592 4916 2.116366 CTTTTTCTTCGCCACCAAACG 58.884 47.619 0.00 0.00 0.00 3.60
1593 4917 0.248702 TTTTCTTCGCCACCAAACGC 60.249 50.000 0.00 0.00 0.00 4.84
1648 4973 5.410439 TCTCCGAACTTAATGTTAGCAAACC 59.590 40.000 0.00 0.00 39.30 3.27
1659 4984 9.991388 TTAATGTTAGCAAACCGACATTATAAC 57.009 29.630 8.16 0.00 41.73 1.89
1672 4997 6.696148 CCGACATTATAACTTAGCTTCTTCGT 59.304 38.462 0.00 0.00 0.00 3.85
1700 5025 8.728337 ACGAGTTTACTTTTACCTTCTCTTTT 57.272 30.769 0.00 0.00 0.00 2.27
1775 5100 8.862325 TTGTGGTGAGTTAAGATTTATGTGAT 57.138 30.769 0.00 0.00 0.00 3.06
1787 5112 8.674263 AAGATTTATGTGATTTTTGTTTGCCA 57.326 26.923 0.00 0.00 0.00 4.92
1838 5163 3.764237 TTCGACTTCCTTTTGCCTACT 57.236 42.857 0.00 0.00 0.00 2.57
1884 5209 9.445786 AACATATTATTTATAAGCGCAACACAC 57.554 29.630 11.47 0.00 0.00 3.82
1923 5248 4.617200 CCCTTTGGGTTCTTGGCA 57.383 55.556 0.00 0.00 38.25 4.92
1960 5285 1.691434 CTCTAGGGAGGTGAGCATTCC 59.309 57.143 0.00 0.00 36.03 3.01
1961 5286 1.008327 TCTAGGGAGGTGAGCATTCCA 59.992 52.381 0.00 0.00 32.50 3.53
1962 5287 2.053244 CTAGGGAGGTGAGCATTCCAT 58.947 52.381 0.00 0.00 32.50 3.41
1964 5289 0.533755 GGGAGGTGAGCATTCCATCG 60.534 60.000 0.00 0.00 32.50 3.84
1965 5290 0.179000 GGAGGTGAGCATTCCATCGT 59.821 55.000 0.00 0.00 0.00 3.73
1966 5291 1.576356 GAGGTGAGCATTCCATCGTC 58.424 55.000 0.00 0.00 0.00 4.20
1967 5292 0.179000 AGGTGAGCATTCCATCGTCC 59.821 55.000 0.00 0.00 0.00 4.79
1968 5293 1.154205 GGTGAGCATTCCATCGTCCG 61.154 60.000 0.00 0.00 0.00 4.79
1969 5294 0.179111 GTGAGCATTCCATCGTCCGA 60.179 55.000 0.00 0.00 0.00 4.55
1970 5295 0.179111 TGAGCATTCCATCGTCCGAC 60.179 55.000 0.00 0.00 0.00 4.79
1971 5296 1.209275 GAGCATTCCATCGTCCGACG 61.209 60.000 14.94 14.94 44.19 5.12
1972 5297 1.518572 GCATTCCATCGTCCGACGT 60.519 57.895 19.89 5.60 43.14 4.34
1973 5298 1.082117 GCATTCCATCGTCCGACGTT 61.082 55.000 19.89 9.68 43.14 3.99
1974 5299 0.645355 CATTCCATCGTCCGACGTTG 59.355 55.000 19.89 20.15 43.14 4.10
1975 5300 1.082117 ATTCCATCGTCCGACGTTGC 61.082 55.000 21.43 0.00 43.14 4.17
1976 5301 3.541831 CCATCGTCCGACGTTGCG 61.542 66.667 21.43 13.38 43.14 4.85
1988 5313 3.195698 GTTGCGGCGCCCTTCTAG 61.196 66.667 30.82 6.63 0.00 2.43
1998 5323 2.413765 CCTTCTAGCGAGGGCGAC 59.586 66.667 4.52 0.00 46.35 5.19
2002 5327 4.615834 CTAGCGAGGGCGACGAGC 62.616 72.222 0.00 0.00 46.35 5.03
2030 5355 1.271379 ACCTTTCGGTGATGGAACTGG 60.271 52.381 0.00 0.00 43.51 4.00
2031 5356 1.003118 CCTTTCGGTGATGGAACTGGA 59.997 52.381 0.00 0.00 0.00 3.86
2032 5357 2.356125 CCTTTCGGTGATGGAACTGGAT 60.356 50.000 0.00 0.00 0.00 3.41
2033 5358 2.401583 TTCGGTGATGGAACTGGATG 57.598 50.000 0.00 0.00 0.00 3.51
2034 5359 0.541392 TCGGTGATGGAACTGGATGG 59.459 55.000 0.00 0.00 0.00 3.51
2035 5360 1.097547 CGGTGATGGAACTGGATGGC 61.098 60.000 0.00 0.00 0.00 4.40
2036 5361 1.097547 GGTGATGGAACTGGATGGCG 61.098 60.000 0.00 0.00 0.00 5.69
2037 5362 1.451927 TGATGGAACTGGATGGCGC 60.452 57.895 0.00 0.00 0.00 6.53
2038 5363 1.153086 GATGGAACTGGATGGCGCT 60.153 57.895 7.64 0.00 0.00 5.92
2039 5364 1.442526 GATGGAACTGGATGGCGCTG 61.443 60.000 7.64 0.00 0.00 5.18
2040 5365 2.825836 GGAACTGGATGGCGCTGG 60.826 66.667 7.64 0.00 0.00 4.85
2041 5366 2.045926 GAACTGGATGGCGCTGGT 60.046 61.111 7.64 0.00 0.00 4.00
2042 5367 2.360350 AACTGGATGGCGCTGGTG 60.360 61.111 7.64 0.00 0.00 4.17
2081 5435 1.209261 TGGCGATGACATAGCTTCCAA 59.791 47.619 18.34 0.00 0.00 3.53
2093 5447 1.600636 CTTCCAAAGACGGCTGGCA 60.601 57.895 0.00 0.00 32.33 4.92
2099 5453 2.142292 AAAGACGGCTGGCATCCCTT 62.142 55.000 0.00 0.00 0.00 3.95
2124 5478 4.699522 GGCCTCCTTCGCGGTGTT 62.700 66.667 6.13 0.00 0.00 3.32
2136 5490 0.240945 GCGGTGTTGGTCCTTCAATG 59.759 55.000 0.00 0.00 0.00 2.82
2150 5504 3.119245 CCTTCAATGATGTTTGAGGGCTG 60.119 47.826 2.90 0.00 43.31 4.85
2153 5507 1.471119 ATGATGTTTGAGGGCTGCAG 58.529 50.000 10.11 10.11 0.00 4.41
2178 5532 5.650266 TGTCTAGTTGTCTTTGCTTTTTGGA 59.350 36.000 0.00 0.00 0.00 3.53
2214 5568 6.881067 TCCTGAGCTCCATTATATAATGCT 57.119 37.500 24.38 19.63 41.23 3.79
2321 5675 2.205911 GCGCCATCCTCTTTTCTAGAC 58.794 52.381 0.00 0.00 0.00 2.59
2376 5730 1.227380 GGTGGCGGCTCACTCATAG 60.227 63.158 11.43 0.00 37.75 2.23
2423 5778 3.390967 TCATGAACACCAAGAACCTCTCA 59.609 43.478 0.00 0.00 0.00 3.27
2426 5782 1.428869 ACACCAAGAACCTCTCAGCT 58.571 50.000 0.00 0.00 0.00 4.24
2472 5828 5.620206 TCTTGTATATAGGGTGCATTGGTG 58.380 41.667 0.00 0.00 0.00 4.17
2473 5829 4.365514 TGTATATAGGGTGCATTGGTGG 57.634 45.455 0.00 0.00 0.00 4.61
2512 5868 4.709397 ACACATCTCAGAACCAAAACCAAA 59.291 37.500 0.00 0.00 0.00 3.28
2598 5955 5.157940 AGCACTTGTGATCTCTGTTATGT 57.842 39.130 4.79 0.00 0.00 2.29
2626 5984 4.386312 GGGTTGGGAACTTGATGGATGATA 60.386 45.833 0.00 0.00 0.00 2.15
2696 6054 0.323178 AGCAGCTGAAACCTGATGGG 60.323 55.000 20.43 0.00 41.89 4.00
2703 6061 3.976701 AAACCTGATGGGGCGAGCG 62.977 63.158 0.00 0.00 40.03 5.03
2735 6093 5.395435 CGATGGATGATGGATAGAGCAAGAT 60.395 44.000 0.00 0.00 0.00 2.40
2757 6115 6.943146 AGATATTAACATAGAGCTGGACGAGA 59.057 38.462 0.00 0.00 0.00 4.04
2804 6169 6.391227 AAATGTTGTGTTTAGAGGGTTCAG 57.609 37.500 0.00 0.00 0.00 3.02
2809 6174 3.075148 GTGTTTAGAGGGTTCAGAAGGC 58.925 50.000 0.00 0.00 0.00 4.35
2817 6182 1.408822 GGGTTCAGAAGGCCATGTAGG 60.409 57.143 5.01 0.00 41.84 3.18
2818 6183 1.282157 GGTTCAGAAGGCCATGTAGGT 59.718 52.381 5.01 0.00 40.61 3.08
2830 6195 4.506625 GGCCATGTAGGTATGCCAGATTAA 60.507 45.833 1.54 0.00 40.61 1.40
2839 6204 7.618019 AGGTATGCCAGATTAACATAGAAGA 57.382 36.000 1.54 0.00 37.19 2.87
2902 6268 2.223876 GCGAAGATACCGATTACACCCA 60.224 50.000 0.00 0.00 0.00 4.51
2907 6273 3.199071 AGATACCGATTACACCCAGCAAA 59.801 43.478 0.00 0.00 0.00 3.68
2945 6311 5.035784 CGAGAGGAATGGAAAGTTGAAAC 57.964 43.478 0.00 0.00 0.00 2.78
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 9.673454 AAATGACCAAGAAAATCGTAAGTTTAC 57.327 29.630 0.00 0.00 39.48 2.01
14 15 9.672086 CAAATGACCAAGAAAATCGTAAGTTTA 57.328 29.630 0.00 0.00 39.48 2.01
21 22 6.391227 AGAACAAATGACCAAGAAAATCGT 57.609 33.333 0.00 0.00 0.00 3.73
66 67 9.545105 ACAAAATCATAAGTTTCAGAAATTGCA 57.455 25.926 0.00 0.00 0.00 4.08
106 107 2.608268 GGTTTCTACCGCTGAGACTTC 58.392 52.381 0.00 0.00 34.01 3.01
117 118 6.849588 TTGAAACTTCGTTAGGTTTCTACC 57.150 37.500 16.02 0.00 46.43 3.18
187 188 3.930229 TGCATATTCGTGTTACTGGTGAC 59.070 43.478 0.00 0.00 0.00 3.67
195 196 6.320494 AGTTTGGTTTGCATATTCGTGTTA 57.680 33.333 0.00 0.00 0.00 2.41
229 230 9.709495 CATTCTTTCATATCCTTTGAACCAAAA 57.291 29.630 0.00 0.00 32.75 2.44
241 242 6.693113 GCTTTCGGTTTCATTCTTTCATATCC 59.307 38.462 0.00 0.00 0.00 2.59
259 260 4.038763 ACCCCTTTTTCTTTTAGCTTTCGG 59.961 41.667 0.00 0.00 0.00 4.30
268 270 2.899976 CACGCAACCCCTTTTTCTTTT 58.100 42.857 0.00 0.00 0.00 2.27
295 298 0.392461 GGGATTTGTAGCACGCAGGA 60.392 55.000 0.00 0.00 0.00 3.86
327 330 1.771073 TTTCAGTGGCAGCAACGACG 61.771 55.000 0.00 0.00 0.00 5.12
335 338 7.224362 TGAAAAATGTTATTGTTTCAGTGGCAG 59.776 33.333 0.00 0.00 35.60 4.85
353 359 7.223193 TCACTCAGAGCAATTGTTTGAAAAATG 59.777 33.333 7.40 5.51 34.60 2.32
373 379 7.703058 AAAAGGAGAGAAAGTTTTTCACTCA 57.297 32.000 21.78 0.00 37.71 3.41
413 420 3.463944 ACGTCAGGTTGAGAAATCGTTT 58.536 40.909 0.00 0.00 0.00 3.60
415 422 2.814280 ACGTCAGGTTGAGAAATCGT 57.186 45.000 0.00 0.00 0.00 3.73
526 3813 9.640963 AGTACAAAGTTATACTAGAGTGCAAAG 57.359 33.333 0.00 0.00 29.70 2.77
700 3992 9.809096 GGAAGAGAAAGAAAAAGAGACAAAATT 57.191 29.630 0.00 0.00 0.00 1.82
718 4011 1.550524 CTCGTGGGTCATGGAAGAGAA 59.449 52.381 0.00 0.00 0.00 2.87
729 4022 4.497507 GCATAATTTTTAGCCTCGTGGGTC 60.498 45.833 12.12 0.00 43.94 4.46
752 4046 8.286191 ACTCTTCTATTTTCTTATTGGCCAAG 57.714 34.615 24.94 10.72 0.00 3.61
889 4184 0.390340 GACAACATCGCCTGCTCTGA 60.390 55.000 0.00 0.00 0.00 3.27
985 4289 5.565509 TGTCACCATGGATTAGTTTTGCTA 58.434 37.500 21.47 0.00 0.00 3.49
993 4297 2.715749 TGCCTGTCACCATGGATTAG 57.284 50.000 21.47 10.59 0.00 1.73
1258 4572 2.736995 CTTGCCGCCGTCGAGAAA 60.737 61.111 0.00 0.00 38.10 2.52
1297 4611 4.900664 ACACTTTCGAACGGTAAAAGTTG 58.099 39.130 10.00 8.78 40.32 3.16
1300 4614 6.068931 CACATACACTTTCGAACGGTAAAAG 58.931 40.000 6.60 6.32 36.35 2.27
1302 4616 4.084433 GCACATACACTTTCGAACGGTAAA 60.084 41.667 6.60 0.00 0.00 2.01
1306 4620 1.201769 CGCACATACACTTTCGAACGG 60.202 52.381 6.60 1.39 0.00 4.44
1308 4622 1.193650 TGCGCACATACACTTTCGAAC 59.806 47.619 5.66 0.00 0.00 3.95
1319 4633 8.552083 AAGAGATATATTTTGATGCGCACATA 57.448 30.769 14.90 5.60 36.35 2.29
1333 4647 7.548427 CGATGCCAATGTCAGAAGAGATATATT 59.452 37.037 0.00 0.00 0.00 1.28
1335 4649 6.209391 TCGATGCCAATGTCAGAAGAGATATA 59.791 38.462 0.00 0.00 0.00 0.86
1336 4650 5.011431 TCGATGCCAATGTCAGAAGAGATAT 59.989 40.000 0.00 0.00 0.00 1.63
1337 4651 4.342092 TCGATGCCAATGTCAGAAGAGATA 59.658 41.667 0.00 0.00 0.00 1.98
1539 4862 9.566432 AGGCTTATAGAAATGACTGGATTTTAG 57.434 33.333 0.00 0.00 0.00 1.85
1573 4897 1.799548 GCGTTTGGTGGCGAAGAAAAA 60.800 47.619 0.00 0.00 0.00 1.94
1576 4900 3.027292 GCGTTTGGTGGCGAAGAA 58.973 55.556 0.00 0.00 0.00 2.52
1582 4906 1.613270 CTAATTTCGCGTTTGGTGGC 58.387 50.000 5.77 0.00 0.00 5.01
1588 4912 4.693566 TCTCAATCACCTAATTTCGCGTTT 59.306 37.500 5.77 1.21 0.00 3.60
1592 4916 6.701841 TGTAGATCTCAATCACCTAATTTCGC 59.298 38.462 0.00 0.00 34.07 4.70
1593 4917 8.648557 TTGTAGATCTCAATCACCTAATTTCG 57.351 34.615 0.00 0.00 34.07 3.46
1648 4973 7.356557 CGACGAAGAAGCTAAGTTATAATGTCG 60.357 40.741 0.00 0.00 36.47 4.35
1659 4984 2.522372 TCGTCGACGAAGAAGCTAAG 57.478 50.000 36.25 5.24 46.30 2.18
1672 4997 6.016777 AGAGAAGGTAAAAGTAAACTCGTCGA 60.017 38.462 0.00 0.00 0.00 4.20
1717 5042 6.476378 GCAGCCTAAATTATTCCCTAGATCA 58.524 40.000 0.00 0.00 0.00 2.92
1719 5044 5.013183 ACGCAGCCTAAATTATTCCCTAGAT 59.987 40.000 0.00 0.00 0.00 1.98
1749 5074 8.862325 TCACATAAATCTTAACTCACCACAAT 57.138 30.769 0.00 0.00 0.00 2.71
1820 5145 3.058914 CACAAGTAGGCAAAAGGAAGTCG 60.059 47.826 0.00 0.00 0.00 4.18
1838 5163 6.701145 TGTTTTGTAGAATTAGCCACACAA 57.299 33.333 0.00 0.00 0.00 3.33
1874 5199 1.871789 GTGTTGTGGTGTGTTGCGC 60.872 57.895 0.00 0.00 0.00 6.09
1875 5200 0.523125 CTGTGTTGTGGTGTGTTGCG 60.523 55.000 0.00 0.00 0.00 4.85
1876 5201 0.525761 ACTGTGTTGTGGTGTGTTGC 59.474 50.000 0.00 0.00 0.00 4.17
1877 5202 2.227626 TGAACTGTGTTGTGGTGTGTTG 59.772 45.455 0.00 0.00 0.00 3.33
1878 5203 2.509569 TGAACTGTGTTGTGGTGTGTT 58.490 42.857 0.00 0.00 0.00 3.32
1879 5204 2.192664 TGAACTGTGTTGTGGTGTGT 57.807 45.000 0.00 0.00 0.00 3.72
1880 5205 2.487762 AGTTGAACTGTGTTGTGGTGTG 59.512 45.455 0.00 0.00 0.00 3.82
1881 5206 2.487762 CAGTTGAACTGTGTTGTGGTGT 59.512 45.455 16.84 0.00 41.19 4.16
1882 5207 2.746904 TCAGTTGAACTGTGTTGTGGTG 59.253 45.455 23.17 0.00 46.03 4.17
1883 5208 2.747446 GTCAGTTGAACTGTGTTGTGGT 59.253 45.455 23.17 0.00 46.03 4.16
1884 5209 2.097466 GGTCAGTTGAACTGTGTTGTGG 59.903 50.000 23.17 0.00 46.03 4.17
1922 5247 2.479198 CGCAGCTGCACACTGATG 59.521 61.111 36.03 15.08 42.21 3.07
1956 5281 1.082117 GCAACGTCGGACGATGGAAT 61.082 55.000 34.40 10.34 46.05 3.01
1958 5283 2.126228 GCAACGTCGGACGATGGA 60.126 61.111 34.40 0.00 46.05 3.41
1959 5284 3.541831 CGCAACGTCGGACGATGG 61.542 66.667 34.40 21.67 46.05 3.51
1971 5296 3.195698 CTAGAAGGGCGCCGCAAC 61.196 66.667 22.54 11.79 0.00 4.17
1980 5305 2.833582 TCGCCCTCGCTAGAAGGG 60.834 66.667 21.08 21.08 45.43 3.95
1981 5306 2.413765 GTCGCCCTCGCTAGAAGG 59.586 66.667 0.00 0.00 35.26 3.46
1982 5307 2.024871 CGTCGCCCTCGCTAGAAG 59.975 66.667 0.00 0.00 35.26 2.85
1983 5308 2.437180 TCGTCGCCCTCGCTAGAA 60.437 61.111 0.00 0.00 35.26 2.10
1984 5309 2.895865 CTCGTCGCCCTCGCTAGA 60.896 66.667 0.00 0.00 35.26 2.43
1985 5310 4.615834 GCTCGTCGCCCTCGCTAG 62.616 72.222 0.00 0.00 35.26 3.42
1998 5323 4.351054 AAAGGTGGCCCCTGCTCG 62.351 66.667 12.97 0.00 45.47 5.03
2019 5344 1.451927 GCGCCATCCAGTTCCATCA 60.452 57.895 0.00 0.00 0.00 3.07
2040 5365 4.374702 CTTGCACGTCTGGCGCAC 62.375 66.667 10.83 0.00 46.11 5.34
2044 5369 3.121030 ATCGCTTGCACGTCTGGC 61.121 61.111 0.00 0.00 0.00 4.85
2045 5370 2.743752 CCATCGCTTGCACGTCTGG 61.744 63.158 0.00 0.00 33.21 3.86
2046 5371 2.780643 CCATCGCTTGCACGTCTG 59.219 61.111 0.00 0.00 0.00 3.51
2047 5372 3.121030 GCCATCGCTTGCACGTCT 61.121 61.111 0.00 0.00 0.00 4.18
2048 5373 4.505217 CGCCATCGCTTGCACGTC 62.505 66.667 0.00 0.00 0.00 4.34
2050 5375 3.566853 ATCGCCATCGCTTGCACG 61.567 61.111 0.00 0.00 35.26 5.34
2051 5376 2.023741 CATCGCCATCGCTTGCAC 59.976 61.111 0.00 0.00 35.26 4.57
2052 5377 2.125188 TCATCGCCATCGCTTGCA 60.125 55.556 0.00 0.00 35.26 4.08
2053 5378 1.779025 ATGTCATCGCCATCGCTTGC 61.779 55.000 0.00 0.00 35.26 4.01
2054 5379 1.458445 CTATGTCATCGCCATCGCTTG 59.542 52.381 0.00 0.00 35.26 4.01
2055 5380 1.788258 CTATGTCATCGCCATCGCTT 58.212 50.000 0.00 0.00 35.26 4.68
2056 5381 0.668706 GCTATGTCATCGCCATCGCT 60.669 55.000 0.00 0.00 35.26 4.93
2057 5382 0.668706 AGCTATGTCATCGCCATCGC 60.669 55.000 5.75 0.00 32.77 4.58
2058 5383 1.723542 GAAGCTATGTCATCGCCATCG 59.276 52.381 5.75 0.00 0.00 3.84
2081 5435 2.606587 AAGGGATGCCAGCCGTCTT 61.607 57.895 5.86 0.00 0.00 3.01
2121 5475 4.892345 TCAAACATCATTGAAGGACCAACA 59.108 37.500 0.00 0.00 36.42 3.33
2124 5478 4.081406 CCTCAAACATCATTGAAGGACCA 58.919 43.478 0.00 0.00 38.75 4.02
2136 5490 0.524862 CACTGCAGCCCTCAAACATC 59.475 55.000 15.27 0.00 0.00 3.06
2150 5504 3.134458 AGCAAAGACAACTAGACACTGC 58.866 45.455 0.00 0.00 0.00 4.40
2153 5507 5.743872 CCAAAAAGCAAAGACAACTAGACAC 59.256 40.000 0.00 0.00 0.00 3.67
2178 5532 1.531423 CTCAGGAGCAGCAACAATGT 58.469 50.000 0.00 0.00 0.00 2.71
2214 5568 9.840427 CACAAGAAAAACAAAGAGAAAACTCTA 57.160 29.630 0.00 0.00 32.66 2.43
2236 5590 4.517075 TCAACACAACACTGAAAGACACAA 59.483 37.500 0.00 0.00 37.43 3.33
2321 5675 5.235186 CAGGACGAAATAGTAAGGCTCAATG 59.765 44.000 0.00 0.00 0.00 2.82
2376 5730 0.250124 TCCACGTCACCCACAACATC 60.250 55.000 0.00 0.00 0.00 3.06
2423 5778 3.442273 GCTACATAGCCTCTATCGAAGCT 59.558 47.826 0.00 0.00 43.39 3.74
2443 5799 5.342017 TGCACCCTATATACAAGATAGGCT 58.658 41.667 2.65 0.00 43.23 4.58
2472 5828 7.979537 TGAGATGTGTCTGTACAAATGTATACC 59.020 37.037 0.00 0.00 33.45 2.73
2473 5829 8.926715 TGAGATGTGTCTGTACAAATGTATAC 57.073 34.615 0.00 0.00 33.45 1.47
2512 5868 0.842467 AGCAGGACCCCTACAGCTTT 60.842 55.000 0.00 0.00 27.89 3.51
2598 5955 1.217916 TCAAGTTCCCAACCCAGTCA 58.782 50.000 0.00 0.00 0.00 3.41
2626 5984 5.755375 GTGTCCACGAACATAGATGATCATT 59.245 40.000 10.14 2.85 30.86 2.57
2703 6061 1.607509 CCATCATCCATCGCTCCTCAC 60.608 57.143 0.00 0.00 0.00 3.51
2735 6093 6.954487 TTCTCGTCCAGCTCTATGTTAATA 57.046 37.500 0.00 0.00 0.00 0.98
2757 6115 3.796111 TCTCCTTCCTCTCCAGACAATT 58.204 45.455 0.00 0.00 0.00 2.32
2784 6142 4.764050 TCTGAACCCTCTAAACACAACA 57.236 40.909 0.00 0.00 0.00 3.33
2785 6143 4.515567 CCTTCTGAACCCTCTAAACACAAC 59.484 45.833 0.00 0.00 0.00 3.32
2804 6169 1.897560 GGCATACCTACATGGCCTTC 58.102 55.000 3.32 0.00 43.70 3.46
2809 6174 5.620206 TGTTAATCTGGCATACCTACATGG 58.380 41.667 0.00 0.00 42.93 3.66
2817 6182 9.364989 GATCTCTTCTATGTTAATCTGGCATAC 57.635 37.037 0.00 0.00 0.00 2.39
2818 6183 8.246871 CGATCTCTTCTATGTTAATCTGGCATA 58.753 37.037 0.00 0.00 0.00 3.14
2830 6195 9.883142 AAAAGAAAATCTCGATCTCTTCTATGT 57.117 29.630 0.00 0.00 0.00 2.29
2892 6258 2.614057 CGATCCTTTGCTGGGTGTAATC 59.386 50.000 0.00 0.00 0.00 1.75
2902 6268 2.224402 GGCCTTATCTCGATCCTTTGCT 60.224 50.000 0.00 0.00 0.00 3.91
2907 6273 1.074084 TCTCGGCCTTATCTCGATCCT 59.926 52.381 0.00 0.00 32.32 3.24


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

AutoCloner maintained by Alex Coulton.