Multiple sequence alignment - TraesCS2D01G224600

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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 TraesCS2D01G224600 chr2D 100.000 2411 0 0 1 2411 192183443 192185853 0.000000e+00 4453
1 TraesCS2D01G224600 chr2A 95.229 1006 40 4 896 1895 205914957 205913954 0.000000e+00 1585
2 TraesCS2D01G224600 chr2A 84.202 595 52 21 310 863 205915548 205914955 7.580000e-150 540
3 TraesCS2D01G224600 chr2A 91.756 279 14 5 1894 2167 205913870 205913596 1.750000e-101 379
4 TraesCS2D01G224600 chr2A 96.154 130 2 1 2282 2411 205911651 205911525 2.430000e-50 209
5 TraesCS2D01G224600 chr2A 94.286 105 5 1 2180 2283 205913409 205913305 2.480000e-35 159
6 TraesCS2D01G224600 chr2B 92.483 1051 42 13 665 1690 248139540 248138502 0.000000e+00 1469
7 TraesCS2D01G224600 chr2B 86.912 680 48 13 4 667 248140249 248139595 0.000000e+00 725
8 TraesCS2D01G224600 chr2B 81.534 639 35 22 1683 2267 248138404 248137795 1.310000e-122 449
9 TraesCS2D01G224600 chr2B 94.167 120 4 1 2292 2411 248137798 248137682 1.900000e-41 180
10 TraesCS2D01G224600 chr3D 82.346 912 116 27 644 1536 570839361 570840246 0.000000e+00 750
11 TraesCS2D01G224600 chr3A 87.994 633 71 4 911 1542 703844637 703844009 0.000000e+00 743
12 TraesCS2D01G224600 chr3B 87.048 332 36 5 911 1238 757930981 757931309 3.790000e-98 368


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 TraesCS2D01G224600 chr2D 192183443 192185853 2410 False 4453.00 4453 100.0000 1 2411 1 chr2D.!!$F1 2410
1 TraesCS2D01G224600 chr2A 205911525 205915548 4023 True 574.40 1585 92.3254 310 2411 5 chr2A.!!$R1 2101
2 TraesCS2D01G224600 chr2B 248137682 248140249 2567 True 705.75 1469 88.7740 4 2411 4 chr2B.!!$R1 2407
3 TraesCS2D01G224600 chr3D 570839361 570840246 885 False 750.00 750 82.3460 644 1536 1 chr3D.!!$F1 892
4 TraesCS2D01G224600 chr3A 703844009 703844637 628 True 743.00 743 87.9940 911 1542 1 chr3A.!!$R1 631

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
678 771 0.18135 CCCTAATCCCTGTCTGTGCC 59.819 60.0 0.0 0.0 0.0 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2136 2534 0.525761 CGTTTGCCCCTAATGGTGTG 59.474 55.0 0.0 0.0 0.0 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
36 37 2.564553 ATCTTCGCCGTCAGTCTGCC 62.565 60.000 0.00 0.00 0.00 4.85
63 64 4.200283 CCCTCGGCAGTCGCTCTC 62.200 72.222 0.00 0.00 39.05 3.20
64 65 4.544689 CCTCGGCAGTCGCTCTCG 62.545 72.222 0.00 0.00 39.05 4.04
68 69 4.863925 GGCAGTCGCTCTCGCTCC 62.864 72.222 0.00 0.00 38.60 4.70
94 95 3.274383 ACTTCCTCCCCCTTTTGGATTA 58.726 45.455 0.00 0.00 44.07 1.75
97 98 1.411644 CCTCCCCCTTTTGGATTAGGC 60.412 57.143 0.00 0.00 44.07 3.93
124 125 3.728864 GCACTGCTGTACCGATGAAATTG 60.729 47.826 0.00 0.00 0.00 2.32
126 127 3.684788 ACTGCTGTACCGATGAAATTGAC 59.315 43.478 0.00 0.00 0.00 3.18
130 131 4.496341 GCTGTACCGATGAAATTGACCATG 60.496 45.833 0.00 0.00 0.00 3.66
135 136 3.489738 CCGATGAAATTGACCATGGAAGC 60.490 47.826 21.47 7.92 0.00 3.86
137 138 4.497006 CGATGAAATTGACCATGGAAGCTC 60.497 45.833 21.47 5.87 0.00 4.09
142 143 2.479566 TGACCATGGAAGCTCTGTTC 57.520 50.000 21.47 2.11 0.00 3.18
152 153 3.003793 GGAAGCTCTGTTCAAGTTTGGAC 59.996 47.826 0.00 0.00 37.19 4.02
163 164 5.319043 TCAAGTTTGGACTGTAGGGATTT 57.681 39.130 0.00 0.00 35.91 2.17
165 166 4.724279 AGTTTGGACTGTAGGGATTTGT 57.276 40.909 0.00 0.00 33.99 2.83
184 185 7.379529 GGATTTGTGTGTTCATTGAACTGTAAG 59.620 37.037 25.49 0.00 42.39 2.34
193 194 7.442969 TGTTCATTGAACTGTAAGACGGTTTAT 59.557 33.333 25.49 1.00 46.83 1.40
194 195 8.928733 GTTCATTGAACTGTAAGACGGTTTATA 58.071 33.333 19.90 0.00 46.83 0.98
195 196 8.697846 TCATTGAACTGTAAGACGGTTTATAG 57.302 34.615 5.34 0.00 46.83 1.31
196 197 8.525316 TCATTGAACTGTAAGACGGTTTATAGA 58.475 33.333 5.34 1.09 46.83 1.98
197 198 9.146984 CATTGAACTGTAAGACGGTTTATAGAA 57.853 33.333 5.34 0.00 46.83 2.10
198 199 9.715121 ATTGAACTGTAAGACGGTTTATAGAAA 57.285 29.630 5.34 4.62 46.83 2.52
199 200 8.752766 TGAACTGTAAGACGGTTTATAGAAAG 57.247 34.615 5.34 0.00 46.83 2.62
200 201 8.579006 TGAACTGTAAGACGGTTTATAGAAAGA 58.421 33.333 5.34 0.00 46.83 2.52
201 202 9.415544 GAACTGTAAGACGGTTTATAGAAAGAA 57.584 33.333 5.34 0.00 46.83 2.52
202 203 9.768662 AACTGTAAGACGGTTTATAGAAAGAAA 57.231 29.630 10.42 0.00 44.74 2.52
203 204 9.420551 ACTGTAAGACGGTTTATAGAAAGAAAG 57.579 33.333 10.42 0.00 32.95 2.62
204 205 9.635520 CTGTAAGACGGTTTATAGAAAGAAAGA 57.364 33.333 0.00 0.00 34.07 2.52
268 269 0.675837 GGGACCTAGGTTTTGGCGTC 60.676 60.000 17.53 0.00 0.00 5.19
270 271 1.271217 GGACCTAGGTTTTGGCGTCTT 60.271 52.381 17.53 0.00 0.00 3.01
271 272 2.027837 GGACCTAGGTTTTGGCGTCTTA 60.028 50.000 17.53 0.00 0.00 2.10
284 285 9.434559 GTTTTGGCGTCTTATACTATTTTGATC 57.565 33.333 0.00 0.00 0.00 2.92
287 288 7.375834 TGGCGTCTTATACTATTTTGATCGAT 58.624 34.615 0.00 0.00 0.00 3.59
289 290 9.517609 GGCGTCTTATACTATTTTGATCGATAT 57.482 33.333 0.00 0.00 0.00 1.63
334 335 1.799933 TCCCCACTTTTGCCAAACAT 58.200 45.000 0.00 0.00 0.00 2.71
369 382 8.740906 TGATTGTTACTAACTAAGACTCTGAGG 58.259 37.037 9.85 0.00 0.00 3.86
378 391 2.137810 AGACTCTGAGGTAGGAGTGC 57.862 55.000 9.85 0.00 42.06 4.40
386 411 2.184579 GTAGGAGTGCTGCGTCCC 59.815 66.667 15.20 6.57 32.70 4.46
387 412 2.283604 TAGGAGTGCTGCGTCCCA 60.284 61.111 15.20 1.59 32.70 4.37
420 445 7.541162 TGATGCTGATGAAATAGGAACTTTTG 58.459 34.615 0.00 0.00 41.75 2.44
423 448 6.493115 TGCTGATGAAATAGGAACTTTTGGAA 59.507 34.615 0.00 0.00 41.75 3.53
427 452 7.865385 TGATGAAATAGGAACTTTTGGAAAACG 59.135 33.333 0.00 0.00 41.75 3.60
508 533 8.367156 TGATGAACGAATTATGATATGGAGTGA 58.633 33.333 0.00 0.00 0.00 3.41
524 549 7.726033 ATGGAGTGACTGTAGAATTTAGTCT 57.274 36.000 0.00 0.00 41.01 3.24
590 617 4.093011 CCTGCAGGATATAGAGCCTTAGT 58.907 47.826 29.88 0.00 38.81 2.24
591 618 4.530161 CCTGCAGGATATAGAGCCTTAGTT 59.470 45.833 29.88 0.00 38.81 2.24
592 619 5.717178 CCTGCAGGATATAGAGCCTTAGTTA 59.283 44.000 29.88 0.00 38.81 2.24
597 627 9.974980 GCAGGATATAGAGCCTTAGTTATTATC 57.025 37.037 0.00 0.00 38.81 1.75
658 694 7.444792 TCGTATTAGACAGAGGAAGGATAACTC 59.555 40.741 0.00 0.00 0.00 3.01
664 700 4.015541 ACAGAGGAAGGATAACTCCCCTAA 60.016 45.833 0.00 0.00 43.21 2.69
673 766 2.972153 AACTCCCCTAATCCCTGTCT 57.028 50.000 0.00 0.00 0.00 3.41
675 768 1.366435 ACTCCCCTAATCCCTGTCTGT 59.634 52.381 0.00 0.00 0.00 3.41
678 771 0.181350 CCCTAATCCCTGTCTGTGCC 59.819 60.000 0.00 0.00 0.00 5.01
691 784 1.704628 TCTGTGCCAAGGAAGAATGGA 59.295 47.619 0.00 0.00 39.12 3.41
721 814 8.228464 GGAATTTAGGACTACTTTCACTTTTCG 58.772 37.037 0.00 0.00 0.00 3.46
754 851 8.406172 TGTTTTGAAGTACTTTGATTTTGAGC 57.594 30.769 10.02 0.00 0.00 4.26
783 895 6.086785 TCAATCATTCAATCTGCAACAACA 57.913 33.333 0.00 0.00 0.00 3.33
861 979 7.984422 TGCAATCATGAGTTTCTTCTCTTTA 57.016 32.000 0.09 0.00 35.68 1.85
884 1002 9.542462 TTTACCTTGAACATGTACTCATATAGC 57.458 33.333 0.00 0.00 32.47 2.97
933 1054 6.924111 ACCTTTATTTTGTTGATGTAGCAGG 58.076 36.000 0.00 0.00 0.00 4.85
995 1117 7.165318 TGTTCGACGATATTAGACTTTGATTCG 59.835 37.037 0.00 0.00 0.00 3.34
1100 1222 2.505819 TGGTATCTGGAAAGGAAGAGGC 59.494 50.000 0.00 0.00 0.00 4.70
1134 1256 3.511540 GCTTAAAGAATGGTTTCCAGGCT 59.488 43.478 0.00 0.00 36.75 4.58
1418 1540 5.755375 ACATCGAGGATATGTAGCTTGTTTG 59.245 40.000 3.06 0.00 35.82 2.93
1473 1595 3.541632 TCTCAGTCACCACTTTGAAACC 58.458 45.455 0.00 0.00 0.00 3.27
1565 1688 3.583086 CCACTGGGATAACGGAGGATATT 59.417 47.826 0.00 0.00 35.59 1.28
1589 1712 6.581171 TGGAGCACTGTATCTAGATGTATG 57.419 41.667 15.79 9.14 0.00 2.39
1592 1715 7.724061 TGGAGCACTGTATCTAGATGTATGTAA 59.276 37.037 15.79 0.00 0.00 2.41
1598 1721 9.290988 ACTGTATCTAGATGTATGTAACAGAGG 57.709 37.037 25.67 9.68 42.70 3.69
1721 1972 2.736721 CCGGTCGCATATATTTCCACTG 59.263 50.000 0.00 0.00 0.00 3.66
1745 1996 4.581868 CAGTTTCCCCTCGGTTTGTATAA 58.418 43.478 0.00 0.00 0.00 0.98
1760 2038 7.065324 CGGTTTGTATAATTTCCACTCTAAGCA 59.935 37.037 0.00 0.00 0.00 3.91
1761 2039 8.398665 GGTTTGTATAATTTCCACTCTAAGCAG 58.601 37.037 0.00 0.00 0.00 4.24
1762 2040 8.947115 GTTTGTATAATTTCCACTCTAAGCAGT 58.053 33.333 0.00 0.00 0.00 4.40
1763 2041 8.492673 TTGTATAATTTCCACTCTAAGCAGTG 57.507 34.615 0.00 0.00 43.13 3.66
1764 2042 7.847096 TGTATAATTTCCACTCTAAGCAGTGA 58.153 34.615 3.59 0.00 45.92 3.41
1765 2043 7.981789 TGTATAATTTCCACTCTAAGCAGTGAG 59.018 37.037 3.59 1.42 45.92 3.51
1766 2044 4.899352 ATTTCCACTCTAAGCAGTGAGT 57.101 40.909 3.59 2.03 45.92 3.41
1767 2045 6.360370 AATTTCCACTCTAAGCAGTGAGTA 57.640 37.500 3.59 0.00 45.92 2.59
1768 2046 5.801531 TTTCCACTCTAAGCAGTGAGTAA 57.198 39.130 3.59 0.00 45.92 2.24
1769 2047 6.360370 TTTCCACTCTAAGCAGTGAGTAAT 57.640 37.500 3.59 0.00 45.92 1.89
1770 2048 6.360370 TTCCACTCTAAGCAGTGAGTAATT 57.640 37.500 3.59 0.00 45.92 1.40
1771 2049 6.360370 TCCACTCTAAGCAGTGAGTAATTT 57.640 37.500 3.59 0.00 45.92 1.82
1772 2050 7.476540 TCCACTCTAAGCAGTGAGTAATTTA 57.523 36.000 3.59 0.00 45.92 1.40
1773 2051 7.548097 TCCACTCTAAGCAGTGAGTAATTTAG 58.452 38.462 3.59 0.00 45.92 1.85
1774 2052 6.758886 CCACTCTAAGCAGTGAGTAATTTAGG 59.241 42.308 3.59 0.00 45.92 2.69
1775 2053 7.324178 CACTCTAAGCAGTGAGTAATTTAGGT 58.676 38.462 0.00 0.00 45.92 3.08
1776 2054 7.276658 CACTCTAAGCAGTGAGTAATTTAGGTG 59.723 40.741 0.00 0.00 45.92 4.00
1777 2055 6.106673 TCTAAGCAGTGAGTAATTTAGGTGC 58.893 40.000 0.00 0.00 0.00 5.01
1778 2056 4.559862 AGCAGTGAGTAATTTAGGTGCT 57.440 40.909 0.00 0.00 35.22 4.40
1779 2057 5.677319 AGCAGTGAGTAATTTAGGTGCTA 57.323 39.130 0.00 0.00 38.23 3.49
1780 2058 6.240549 AGCAGTGAGTAATTTAGGTGCTAT 57.759 37.500 0.00 0.00 38.23 2.97
1781 2059 7.361457 AGCAGTGAGTAATTTAGGTGCTATA 57.639 36.000 0.00 0.00 38.23 1.31
1782 2060 7.967908 AGCAGTGAGTAATTTAGGTGCTATAT 58.032 34.615 0.00 0.00 38.23 0.86
1783 2061 7.875041 AGCAGTGAGTAATTTAGGTGCTATATG 59.125 37.037 0.00 0.00 38.23 1.78
1784 2062 7.360438 GCAGTGAGTAATTTAGGTGCTATATGC 60.360 40.741 0.00 0.00 43.25 3.14
1853 2134 3.629398 CAGCATATTGTCCAACCCTCTTC 59.371 47.826 0.00 0.00 0.00 2.87
1886 2167 4.650754 ATTCTCCAAGCTGATTTCATGC 57.349 40.909 0.00 0.00 0.00 4.06
1894 2175 3.960571 AGCTGATTTCATGCCTTGTACT 58.039 40.909 0.00 0.00 0.00 2.73
1895 2176 3.693085 AGCTGATTTCATGCCTTGTACTG 59.307 43.478 0.00 0.00 0.00 2.74
1915 2283 9.197306 TGTACTGTATAAGGCATCTTCTAAGAA 57.803 33.333 0.00 0.00 38.77 2.52
1952 2320 5.408604 GGGCTATTTATAACATGACTCACCG 59.591 44.000 0.00 0.00 0.00 4.94
1982 2350 4.085619 CGTTTTCTTTTGCCGTCATTCAAG 60.086 41.667 0.00 0.00 0.00 3.02
2069 2466 4.005650 TGCTGGATTGAGATCAAACTCAC 58.994 43.478 0.00 0.00 44.94 3.51
2124 2522 7.315142 CCAATTGTTATGTTGTTACAGCAGAT 58.685 34.615 8.04 0.00 37.77 2.90
2132 2530 9.836864 TTATGTTGTTACAGCAGATAATCTCAT 57.163 29.630 8.04 0.00 37.77 2.90
2133 2531 7.543947 TGTTGTTACAGCAGATAATCTCATG 57.456 36.000 0.00 0.00 0.00 3.07
2134 2532 7.105588 TGTTGTTACAGCAGATAATCTCATGT 58.894 34.615 0.00 0.00 0.00 3.21
2135 2533 8.257306 TGTTGTTACAGCAGATAATCTCATGTA 58.743 33.333 0.00 0.00 0.00 2.29
2136 2534 8.543774 GTTGTTACAGCAGATAATCTCATGTAC 58.456 37.037 0.00 0.00 29.34 2.90
2164 2563 0.402504 AGGGGCAAACGGTATTCACA 59.597 50.000 0.00 0.00 0.00 3.58
2168 2655 3.492829 GGGGCAAACGGTATTCACAAAAA 60.493 43.478 0.00 0.00 0.00 1.94
2198 2771 8.035394 CACAGAAGGTAGAAATACATACACAGT 58.965 37.037 0.00 0.00 0.00 3.55
2202 2775 9.865321 GAAGGTAGAAATACATACACAGTGTAA 57.135 33.333 17.43 1.71 36.31 2.41
2204 2777 7.980099 AGGTAGAAATACATACACAGTGTAAGC 59.020 37.037 17.43 7.31 36.31 3.09
2276 2849 5.537674 CCAGCCCTGATTCTAGCATTATTTT 59.462 40.000 0.00 0.00 0.00 1.82
2277 2850 6.716628 CCAGCCCTGATTCTAGCATTATTTTA 59.283 38.462 0.00 0.00 0.00 1.52
2278 2851 7.395489 CCAGCCCTGATTCTAGCATTATTTTAT 59.605 37.037 0.00 0.00 0.00 1.40
2279 2852 9.453572 CAGCCCTGATTCTAGCATTATTTTATA 57.546 33.333 0.00 0.00 0.00 0.98
2280 2853 9.678260 AGCCCTGATTCTAGCATTATTTTATAG 57.322 33.333 0.00 0.00 0.00 1.31
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.106566 AGATCAGAGAAGCATCGTGGT 58.893 47.619 0.00 0.00 0.00 4.16
1 2 2.886862 AGATCAGAGAAGCATCGTGG 57.113 50.000 0.00 0.00 0.00 4.94
2 3 2.788233 CGAAGATCAGAGAAGCATCGTG 59.212 50.000 0.00 0.00 0.00 4.35
8 9 0.179124 ACGGCGAAGATCAGAGAAGC 60.179 55.000 16.62 0.00 0.00 3.86
62 63 1.076192 GAGGAAGTAGGGGGAGCGA 60.076 63.158 0.00 0.00 0.00 4.93
63 64 2.134933 GGAGGAAGTAGGGGGAGCG 61.135 68.421 0.00 0.00 0.00 5.03
64 65 1.766864 GGGAGGAAGTAGGGGGAGC 60.767 68.421 0.00 0.00 0.00 4.70
65 66 1.074395 GGGGAGGAAGTAGGGGGAG 60.074 68.421 0.00 0.00 0.00 4.30
66 67 2.654204 GGGGGAGGAAGTAGGGGGA 61.654 68.421 0.00 0.00 0.00 4.81
67 68 2.039724 GGGGGAGGAAGTAGGGGG 60.040 72.222 0.00 0.00 0.00 5.40
68 69 0.253677 AAAGGGGGAGGAAGTAGGGG 60.254 60.000 0.00 0.00 0.00 4.79
94 95 2.632544 TACAGCAGTGCGTACGCCT 61.633 57.895 35.11 27.30 41.09 5.52
97 98 2.150218 CGGTACAGCAGTGCGTACG 61.150 63.158 27.78 22.41 38.42 3.67
124 125 2.479566 TGAACAGAGCTTCCATGGTC 57.520 50.000 12.58 1.25 34.96 4.02
126 127 2.787994 ACTTGAACAGAGCTTCCATGG 58.212 47.619 4.97 4.97 0.00 3.66
130 131 3.003793 GTCCAAACTTGAACAGAGCTTCC 59.996 47.826 0.00 0.00 0.00 3.46
135 136 4.752101 CCTACAGTCCAAACTTGAACAGAG 59.248 45.833 0.00 0.00 31.71 3.35
137 138 3.815401 CCCTACAGTCCAAACTTGAACAG 59.185 47.826 0.00 0.00 31.71 3.16
142 143 4.827284 ACAAATCCCTACAGTCCAAACTTG 59.173 41.667 0.00 0.00 31.71 3.16
152 153 5.473162 TCAATGAACACACAAATCCCTACAG 59.527 40.000 0.00 0.00 0.00 2.74
163 164 5.006261 CGTCTTACAGTTCAATGAACACACA 59.994 40.000 25.63 8.10 44.11 3.72
165 166 4.509970 CCGTCTTACAGTTCAATGAACACA 59.490 41.667 25.63 9.15 44.11 3.72
194 195 8.927411 TCCTCCAAATTGATTTTCTTTCTTTCT 58.073 29.630 0.00 0.00 0.00 2.52
195 196 9.546428 TTCCTCCAAATTGATTTTCTTTCTTTC 57.454 29.630 0.00 0.00 0.00 2.62
196 197 9.904198 TTTCCTCCAAATTGATTTTCTTTCTTT 57.096 25.926 0.00 0.00 0.00 2.52
198 199 9.716531 GATTTCCTCCAAATTGATTTTCTTTCT 57.283 29.630 0.00 0.00 34.60 2.52
199 200 8.939929 GGATTTCCTCCAAATTGATTTTCTTTC 58.060 33.333 0.00 0.00 44.26 2.62
200 201 8.663167 AGGATTTCCTCCAAATTGATTTTCTTT 58.337 29.630 0.00 0.00 44.77 2.52
201 202 8.211030 AGGATTTCCTCCAAATTGATTTTCTT 57.789 30.769 0.00 0.00 44.77 2.52
202 203 7.803487 AGGATTTCCTCCAAATTGATTTTCT 57.197 32.000 0.00 0.00 44.77 2.52
241 242 4.017867 CCAAAACCTAGGTCCCCAATCTTA 60.018 45.833 16.64 0.00 0.00 2.10
242 243 3.245622 CCAAAACCTAGGTCCCCAATCTT 60.246 47.826 16.64 0.00 0.00 2.40
287 288 9.515226 GCCCATAATCAAAATCTGGTTACTATA 57.485 33.333 0.00 0.00 33.35 1.31
289 290 7.350382 TGCCCATAATCAAAATCTGGTTACTA 58.650 34.615 0.00 0.00 33.35 1.82
350 359 7.402650 ACTCCTACCTCAGAGTCTTAGTTAGTA 59.597 40.741 5.50 0.00 39.08 1.82
354 367 5.258051 CACTCCTACCTCAGAGTCTTAGTT 58.742 45.833 0.79 0.00 41.38 2.24
359 372 1.638589 AGCACTCCTACCTCAGAGTCT 59.361 52.381 0.00 0.00 41.38 3.24
369 382 2.167398 TTGGGACGCAGCACTCCTAC 62.167 60.000 6.15 0.00 0.00 3.18
378 391 3.365666 GCATCATGATTATTGGGACGCAG 60.366 47.826 5.16 0.00 0.00 5.18
386 411 9.788960 CCTATTTCATCAGCATCATGATTATTG 57.211 33.333 5.16 5.08 37.84 1.90
387 412 9.749340 TCCTATTTCATCAGCATCATGATTATT 57.251 29.630 5.16 0.00 37.84 1.40
420 445 4.785025 GCCTCAAAACAAAATGCGTTTTCC 60.785 41.667 13.72 0.00 43.00 3.13
423 448 2.611751 GGCCTCAAAACAAAATGCGTTT 59.388 40.909 0.00 0.00 38.19 3.60
427 452 7.608308 TTTATATGGCCTCAAAACAAAATGC 57.392 32.000 3.32 0.00 0.00 3.56
508 533 8.451908 AAACAGCAAAGACTAAATTCTACAGT 57.548 30.769 0.00 0.00 0.00 3.55
518 543 7.223777 GCCACAAATAAAAACAGCAAAGACTAA 59.776 33.333 0.00 0.00 0.00 2.24
524 549 3.879892 GGGCCACAAATAAAAACAGCAAA 59.120 39.130 4.39 0.00 0.00 3.68
560 585 5.357314 GCTCTATATCCTGCAGGTTATACGA 59.643 44.000 31.58 26.44 33.44 3.43
597 627 8.653338 CAAAGAGATGCATTTTATTTGGTTCTG 58.347 33.333 17.58 0.93 0.00 3.02
603 633 8.523523 TGACACAAAGAGATGCATTTTATTTG 57.476 30.769 21.06 21.06 33.53 2.32
614 644 6.712241 ATACGACTTTGACACAAAGAGATG 57.288 37.500 24.48 14.99 0.00 2.90
658 694 0.181350 GCACAGACAGGGATTAGGGG 59.819 60.000 0.00 0.00 0.00 4.79
664 700 0.842030 TCCTTGGCACAGACAGGGAT 60.842 55.000 0.00 0.00 42.06 3.85
673 766 1.704628 TCTCCATTCTTCCTTGGCACA 59.295 47.619 0.00 0.00 32.80 4.57
675 768 2.357465 CCATCTCCATTCTTCCTTGGCA 60.357 50.000 0.00 0.00 32.80 4.92
678 771 6.786967 AAATTCCATCTCCATTCTTCCTTG 57.213 37.500 0.00 0.00 0.00 3.61
691 784 8.152023 AGTGAAAGTAGTCCTAAATTCCATCT 57.848 34.615 0.00 0.00 0.00 2.90
721 814 9.730420 ATCAAAGTACTTCAAAACATTACACAC 57.270 29.630 8.95 0.00 0.00 3.82
754 851 9.361315 TGTTGCAGATTGAATGATTGATTAAAG 57.639 29.630 0.00 0.00 0.00 1.85
861 979 7.366847 AGCTATATGAGTACATGTTCAAGGT 57.633 36.000 2.30 0.20 37.87 3.50
884 1002 6.971602 TGCAGCAGTAAGTAGCTATAAGTAG 58.028 40.000 0.00 0.00 39.50 2.57
890 1008 3.452627 AGGTTGCAGCAGTAAGTAGCTAT 59.547 43.478 2.05 0.00 39.50 2.97
891 1009 2.832129 AGGTTGCAGCAGTAAGTAGCTA 59.168 45.455 2.05 0.00 39.50 3.32
892 1010 1.625818 AGGTTGCAGCAGTAAGTAGCT 59.374 47.619 2.05 0.00 42.94 3.32
933 1054 7.370383 TGCAGAAAGATGTAATTCCAAGAAAC 58.630 34.615 0.00 0.00 0.00 2.78
995 1117 5.975693 TGGTTCAAGAAAATCCATGGTAC 57.024 39.130 12.58 0.25 0.00 3.34
1100 1222 2.238521 TCTTTAAGCCAACCTGCCTTG 58.761 47.619 0.00 0.00 0.00 3.61
1134 1256 0.984230 AGAATCCCAGTTCTTCGCCA 59.016 50.000 0.00 0.00 34.92 5.69
1418 1540 4.335594 CACAAGGGACCTTTCGATAATTCC 59.664 45.833 0.00 0.00 33.42 3.01
1448 1570 6.202226 GTTTCAAAGTGGTGACTGAGATTTC 58.798 40.000 0.00 0.00 30.61 2.17
1473 1595 7.495934 AGGAAACTCTATTGACACCAAATATCG 59.504 37.037 0.00 0.00 32.90 2.92
1565 1688 6.551227 ACATACATCTAGATACAGTGCTCCAA 59.449 38.462 4.54 0.00 0.00 3.53
1589 1712 5.689383 TGACTGCAAAAATCCTCTGTTAC 57.311 39.130 0.00 0.00 0.00 2.50
1592 1715 4.147321 ACATGACTGCAAAAATCCTCTGT 58.853 39.130 0.00 0.00 0.00 3.41
1721 1972 1.228459 AAACCGAGGGGAAACTGCC 60.228 57.895 0.00 0.00 36.97 4.85
1745 1996 4.899352 ACTCACTGCTTAGAGTGGAAAT 57.101 40.909 10.33 0.00 43.09 2.17
1776 2054 6.259608 AGTCATTTGTCAAGTCAGCATATAGC 59.740 38.462 0.00 0.00 46.19 2.97
1777 2055 7.493645 TCAGTCATTTGTCAAGTCAGCATATAG 59.506 37.037 0.00 0.00 0.00 1.31
1778 2056 7.330262 TCAGTCATTTGTCAAGTCAGCATATA 58.670 34.615 0.00 0.00 0.00 0.86
1779 2057 6.175471 TCAGTCATTTGTCAAGTCAGCATAT 58.825 36.000 0.00 0.00 0.00 1.78
1780 2058 5.550290 TCAGTCATTTGTCAAGTCAGCATA 58.450 37.500 0.00 0.00 0.00 3.14
1781 2059 4.392047 TCAGTCATTTGTCAAGTCAGCAT 58.608 39.130 0.00 0.00 0.00 3.79
1782 2060 3.807553 TCAGTCATTTGTCAAGTCAGCA 58.192 40.909 0.00 0.00 0.00 4.41
1783 2061 5.368256 AATCAGTCATTTGTCAAGTCAGC 57.632 39.130 0.00 0.00 0.00 4.26
1784 2062 7.516481 CACTAATCAGTCATTTGTCAAGTCAG 58.484 38.462 0.00 0.00 29.03 3.51
1853 2134 2.376695 TGGAGAATAGGGTCCCTACG 57.623 55.000 20.58 0.00 39.10 3.51
1886 2167 6.821388 AGAAGATGCCTTATACAGTACAAGG 58.179 40.000 12.77 12.77 41.53 3.61
1952 2320 1.858458 GGCAAAAGAAAACGAAGTGCC 59.142 47.619 0.00 0.00 45.00 5.01
1982 2350 6.620678 TGGTTTTGCTGAATAATACTCAAGC 58.379 36.000 0.00 0.00 0.00 4.01
2069 2466 7.493645 TCATGTTAGCAACTCTTCATCATGTAG 59.506 37.037 0.00 0.00 34.02 2.74
2124 2522 6.183361 CCCCTAATGGTGTGTACATGAGATTA 60.183 42.308 0.00 0.15 29.70 1.75
2132 2530 1.363246 TGCCCCTAATGGTGTGTACA 58.637 50.000 0.00 0.00 0.00 2.90
2133 2531 2.490509 GTTTGCCCCTAATGGTGTGTAC 59.509 50.000 0.00 0.00 0.00 2.90
2134 2532 2.797786 GTTTGCCCCTAATGGTGTGTA 58.202 47.619 0.00 0.00 0.00 2.90
2135 2533 1.627864 GTTTGCCCCTAATGGTGTGT 58.372 50.000 0.00 0.00 0.00 3.72
2136 2534 0.525761 CGTTTGCCCCTAATGGTGTG 59.474 55.000 0.00 0.00 0.00 3.82
2169 2656 9.601217 GTGTATGTATTTCTACCTTCTGTGAAT 57.399 33.333 0.00 0.00 0.00 2.57
2171 2658 8.129496 TGTGTATGTATTTCTACCTTCTGTGA 57.871 34.615 0.00 0.00 0.00 3.58
2172 2659 8.035394 ACTGTGTATGTATTTCTACCTTCTGTG 58.965 37.037 0.00 0.00 0.00 3.66
2204 2777 6.203530 CCTGTACCAATAACTGAGCATGTATG 59.796 42.308 0.00 0.00 0.00 2.39


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

AutoCloner maintained by Alex Coulton.