Multiple sequence alignment - TraesCS2B01G387100

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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 TraesCS2B01G387100 chr2B 100.000 2753 0 0 1 2753 550396165 550398917 0.000000e+00 5084.0
1 TraesCS2B01G387100 chr2B 79.832 119 20 4 2053 2171 777074196 777074082 1.760000e-12 84.2
2 TraesCS2B01G387100 chr2D 88.534 1971 111 53 1 1887 471062376 471064315 0.000000e+00 2281.0
3 TraesCS2B01G387100 chr2D 92.213 809 51 10 1951 2753 471214509 471215311 0.000000e+00 1134.0
4 TraesCS2B01G387100 chr2A 89.843 1398 112 22 553 1927 612842871 612844261 0.000000e+00 1768.0
5 TraesCS2B01G387100 chr2A 91.143 350 16 7 121 460 612842465 612842809 6.950000e-126 460.0
6 TraesCS2B01G387100 chr2A 88.835 206 18 2 2549 2753 612844695 612844896 5.890000e-62 248.0
7 TraesCS2B01G387100 chr2A 90.476 105 6 3 6 108 612842319 612842421 4.780000e-28 135.0
8 TraesCS2B01G387100 chr2A 86.792 53 7 0 2052 2104 712588566 712588618 2.960000e-05 60.2
9 TraesCS2B01G387100 chr2A 100.000 29 0 0 2030 2058 80614634 80614662 1.000000e-03 54.7
10 TraesCS2B01G387100 chrUn 80.931 1096 183 23 725 1811 10650721 10651799 0.000000e+00 843.0
11 TraesCS2B01G387100 chrUn 81.256 987 155 18 775 1752 10695574 10696539 0.000000e+00 771.0
12 TraesCS2B01G387100 chrUn 82.193 921 131 21 961 1854 10644050 10644964 0.000000e+00 761.0
13 TraesCS2B01G387100 chr1D 83.045 926 131 20 880 1788 35788908 35787992 0.000000e+00 817.0
14 TraesCS2B01G387100 chr1D 82.347 963 137 23 797 1752 35927349 35926413 0.000000e+00 806.0
15 TraesCS2B01G387100 chr1A 81.154 1040 156 28 722 1752 34708328 34707320 0.000000e+00 798.0
16 TraesCS2B01G387100 chr1A 80.754 1034 159 28 728 1752 34860824 34859822 0.000000e+00 771.0
17 TraesCS2B01G387100 chr1A 80.765 993 158 23 775 1752 34891930 34890956 0.000000e+00 745.0
18 TraesCS2B01G387100 chr1A 87.097 62 8 0 2169 2230 560252683 560252744 1.370000e-08 71.3
19 TraesCS2B01G387100 chr1B 80.172 1044 178 24 725 1752 55242247 55241217 0.000000e+00 754.0
20 TraesCS2B01G387100 chr1B 79.924 1046 177 29 725 1752 55206459 55205429 0.000000e+00 737.0
21 TraesCS2B01G387100 chr1B 81.170 940 152 18 977 1906 54978646 54977722 0.000000e+00 732.0
22 TraesCS2B01G387100 chr4B 86.207 87 8 3 2053 2138 610571428 610571511 1.050000e-14 91.6
23 TraesCS2B01G387100 chr7B 95.918 49 2 0 2173 2221 13758264 13758312 2.270000e-11 80.5
24 TraesCS2B01G387100 chr5D 91.071 56 4 1 2173 2228 469062804 469062750 1.060000e-09 75.0
25 TraesCS2B01G387100 chr5D 86.667 60 4 3 2182 2238 476275243 476275185 2.290000e-06 63.9
26 TraesCS2B01G387100 chr4A 95.556 45 2 0 2182 2226 741472602 741472558 3.800000e-09 73.1
27 TraesCS2B01G387100 chr4A 100.000 30 0 0 2053 2082 614261011 614261040 3.830000e-04 56.5
28 TraesCS2B01G387100 chr6D 89.286 56 4 1 2173 2226 86643241 86643296 4.920000e-08 69.4
29 TraesCS2B01G387100 chr6A 89.286 56 4 1 2173 2226 104308494 104308549 4.920000e-08 69.4
30 TraesCS2B01G387100 chr4D 84.615 65 8 2 2164 2228 6594594 6594656 2.290000e-06 63.9
31 TraesCS2B01G387100 chr4D 100.000 29 0 0 2023 2051 306302710 306302738 1.000000e-03 54.7
32 TraesCS2B01G387100 chr7A 100.000 33 0 0 2027 2059 192986911 192986879 8.230000e-06 62.1


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 TraesCS2B01G387100 chr2B 550396165 550398917 2752 False 5084.00 5084 100.00000 1 2753 1 chr2B.!!$F1 2752
1 TraesCS2B01G387100 chr2D 471062376 471064315 1939 False 2281.00 2281 88.53400 1 1887 1 chr2D.!!$F1 1886
2 TraesCS2B01G387100 chr2D 471214509 471215311 802 False 1134.00 1134 92.21300 1951 2753 1 chr2D.!!$F2 802
3 TraesCS2B01G387100 chr2A 612842319 612844896 2577 False 652.75 1768 90.07425 6 2753 4 chr2A.!!$F3 2747
4 TraesCS2B01G387100 chrUn 10650721 10651799 1078 False 843.00 843 80.93100 725 1811 1 chrUn.!!$F2 1086
5 TraesCS2B01G387100 chrUn 10695574 10696539 965 False 771.00 771 81.25600 775 1752 1 chrUn.!!$F3 977
6 TraesCS2B01G387100 chrUn 10644050 10644964 914 False 761.00 761 82.19300 961 1854 1 chrUn.!!$F1 893
7 TraesCS2B01G387100 chr1D 35787992 35788908 916 True 817.00 817 83.04500 880 1788 1 chr1D.!!$R1 908
8 TraesCS2B01G387100 chr1D 35926413 35927349 936 True 806.00 806 82.34700 797 1752 1 chr1D.!!$R2 955
9 TraesCS2B01G387100 chr1A 34707320 34708328 1008 True 798.00 798 81.15400 722 1752 1 chr1A.!!$R1 1030
10 TraesCS2B01G387100 chr1A 34859822 34860824 1002 True 771.00 771 80.75400 728 1752 1 chr1A.!!$R2 1024
11 TraesCS2B01G387100 chr1A 34890956 34891930 974 True 745.00 745 80.76500 775 1752 1 chr1A.!!$R3 977
12 TraesCS2B01G387100 chr1B 55241217 55242247 1030 True 754.00 754 80.17200 725 1752 1 chr1B.!!$R3 1027
13 TraesCS2B01G387100 chr1B 55205429 55206459 1030 True 737.00 737 79.92400 725 1752 1 chr1B.!!$R2 1027
14 TraesCS2B01G387100 chr1B 54977722 54978646 924 True 732.00 732 81.17000 977 1906 1 chr1B.!!$R1 929

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
328 376 0.238553 GCTCTTGTCTTTTCACCGCC 59.761 55.0 0.0 0.0 0.00 6.13 F
499 551 0.251341 GGAGCTGAAAGGCAAAGGGA 60.251 55.0 0.0 0.0 34.17 4.20 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1252 1425 0.533032 AAGTCTTCTACCTCCGCAGC 59.467 55.0 0.0 0.0 0.0 5.25 R
2471 2670 1.002069 ATGGGAGATGGCTGGTTGAA 58.998 50.0 0.0 0.0 0.0 2.69 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
20 21 3.636231 CGCTGGGAGTGTGGGGAA 61.636 66.667 0.00 0.00 0.00 3.97
40 41 3.815569 GATCGAGCGTCGCAGAGGG 62.816 68.421 21.09 3.40 43.38 4.30
63 66 1.660333 GCGGAGTGCTAATAAATGCGC 60.660 52.381 0.00 0.00 43.11 6.09
64 67 1.397190 CGGAGTGCTAATAAATGCGCG 60.397 52.381 0.00 0.00 43.55 6.86
65 68 1.660333 GGAGTGCTAATAAATGCGCGC 60.660 52.381 27.26 27.26 43.55 6.86
96 99 2.040544 CCAGGACGGCGAGCATTTT 61.041 57.895 16.62 0.00 0.00 1.82
136 170 2.049526 GGGCTTTCGTTTTGGGCG 60.050 61.111 0.00 0.00 0.00 6.13
165 204 1.982395 TGATGAGACCCTCCGCGTT 60.982 57.895 4.92 0.00 0.00 4.84
166 205 1.519455 GATGAGACCCTCCGCGTTG 60.519 63.158 4.92 0.00 0.00 4.10
307 355 1.459450 CGTGGGGTAAATGAACAGGG 58.541 55.000 0.00 0.00 0.00 4.45
328 376 0.238553 GCTCTTGTCTTTTCACCGCC 59.761 55.000 0.00 0.00 0.00 6.13
334 382 4.404654 CTTTTCACCGCCGCTGGC 62.405 66.667 9.20 9.20 46.75 4.85
366 414 4.162690 GCTCGGGGAACGCTCCAT 62.163 66.667 7.26 0.00 44.51 3.41
389 437 1.912417 CCGTTTTGTATGGGTTGGGA 58.088 50.000 0.00 0.00 0.00 4.37
476 528 2.974623 CTCCTGAGAGTCTGGCAGT 58.025 57.895 15.27 0.00 35.69 4.40
477 529 0.817013 CTCCTGAGAGTCTGGCAGTC 59.183 60.000 15.27 9.24 35.69 3.51
478 530 0.407528 TCCTGAGAGTCTGGCAGTCT 59.592 55.000 14.10 14.10 37.52 3.24
484 536 2.237534 GAGTCTGGCAGTCTGGGAGC 62.238 65.000 18.84 0.55 0.00 4.70
485 537 2.121385 TCTGGCAGTCTGGGAGCT 59.879 61.111 15.27 0.00 0.00 4.09
486 538 2.268280 CTGGCAGTCTGGGAGCTG 59.732 66.667 6.28 0.00 35.93 4.24
487 539 2.203832 TGGCAGTCTGGGAGCTGA 60.204 61.111 1.14 0.00 34.87 4.26
489 541 1.376466 GGCAGTCTGGGAGCTGAAA 59.624 57.895 1.14 0.00 34.87 2.69
490 542 0.676151 GGCAGTCTGGGAGCTGAAAG 60.676 60.000 1.14 0.00 34.87 2.62
491 543 0.676151 GCAGTCTGGGAGCTGAAAGG 60.676 60.000 1.14 0.00 34.87 3.11
492 544 0.676151 CAGTCTGGGAGCTGAAAGGC 60.676 60.000 0.00 0.00 34.87 4.35
495 547 0.478072 TCTGGGAGCTGAAAGGCAAA 59.522 50.000 0.00 0.00 34.17 3.68
496 548 0.886563 CTGGGAGCTGAAAGGCAAAG 59.113 55.000 0.00 0.00 34.17 2.77
498 550 1.253593 GGGAGCTGAAAGGCAAAGGG 61.254 60.000 0.00 0.00 34.17 3.95
499 551 0.251341 GGAGCTGAAAGGCAAAGGGA 60.251 55.000 0.00 0.00 34.17 4.20
500 552 1.618074 GGAGCTGAAAGGCAAAGGGAT 60.618 52.381 0.00 0.00 34.17 3.85
501 553 1.747924 GAGCTGAAAGGCAAAGGGATC 59.252 52.381 0.00 0.00 34.17 3.36
502 554 0.453390 GCTGAAAGGCAAAGGGATCG 59.547 55.000 0.00 0.00 0.00 3.69
503 555 0.453390 CTGAAAGGCAAAGGGATCGC 59.547 55.000 0.54 0.54 0.00 4.58
506 558 0.967380 AAAGGCAAAGGGATCGCAGG 60.967 55.000 12.83 1.99 0.00 4.85
507 559 3.521796 GGCAAAGGGATCGCAGGC 61.522 66.667 12.83 11.47 0.00 4.85
529 589 2.916702 TACCAGATCGCAAGCATGAT 57.083 45.000 0.00 0.00 37.18 2.45
604 676 8.569641 ACCGAGCACTTTAATAATGTGTTTAAA 58.430 29.630 16.82 0.00 38.43 1.52
637 710 1.588403 CAGCATCGCCTCAGACGAG 60.588 63.158 0.00 0.00 43.74 4.18
690 788 7.227314 GTGACTTGATCAAACCATGCATATCTA 59.773 37.037 9.88 0.00 39.72 1.98
691 789 7.774625 TGACTTGATCAAACCATGCATATCTAA 59.225 33.333 9.88 0.00 33.02 2.10
692 790 8.162878 ACTTGATCAAACCATGCATATCTAAG 57.837 34.615 9.88 7.08 0.00 2.18
695 793 8.837788 TGATCAAACCATGCATATCTAAGTAG 57.162 34.615 0.00 0.00 0.00 2.57
696 794 7.879677 TGATCAAACCATGCATATCTAAGTAGG 59.120 37.037 0.00 0.00 0.00 3.18
739 837 2.167693 TCAATCGATTAGTTGGCCGTCT 59.832 45.455 10.97 0.85 0.00 4.18
800 905 1.807142 GTTGCTCACTTGGGAACTAGC 59.193 52.381 0.00 0.00 36.60 3.42
850 956 1.953686 CCCCGACAGAACAAACACAAT 59.046 47.619 0.00 0.00 0.00 2.71
871 983 3.081804 TGCTTTTCGATCCTCCTTTTCC 58.918 45.455 0.00 0.00 0.00 3.13
872 984 3.244911 TGCTTTTCGATCCTCCTTTTCCT 60.245 43.478 0.00 0.00 0.00 3.36
974 1103 9.042450 TCCCTAGAGATTAAACACACTCAATTA 57.958 33.333 0.00 0.00 32.59 1.40
998 1132 2.667969 TGAGAATCAACGCTCACATTCG 59.332 45.455 0.00 0.00 45.97 3.34
1021 1155 0.889186 GGCGGCAAAGTTCTTCCTCA 60.889 55.000 3.07 0.00 0.00 3.86
1080 1214 3.706373 GACCCGAGCCAGCTCCAA 61.706 66.667 13.83 0.00 39.77 3.53
1115 1249 2.571653 CTGACAGGACATCCCAAGGTAA 59.428 50.000 0.00 0.00 37.41 2.85
1116 1250 3.189606 TGACAGGACATCCCAAGGTAAT 58.810 45.455 0.00 0.00 37.41 1.89
1157 1317 2.479389 CGTGTGTGGTGAAATGTTTGCT 60.479 45.455 0.00 0.00 0.00 3.91
1158 1318 2.859538 GTGTGTGGTGAAATGTTTGCTG 59.140 45.455 0.00 0.00 0.00 4.41
1168 1328 8.363390 TGGTGAAATGTTTGCTGTAATTATCAA 58.637 29.630 0.00 0.00 0.00 2.57
1236 1409 4.319694 GCAGTTTTTGTCAATGGATTTGCC 60.320 41.667 0.00 0.00 35.16 4.52
1294 1467 1.980765 TCTTCTCTGGCCTTCACATGT 59.019 47.619 3.32 0.00 0.00 3.21
1648 1821 2.845659 ACCCTGGAGTGATCACCATAA 58.154 47.619 22.21 5.19 34.11 1.90
1674 1847 1.883021 GGTGTTTGGATCCAAGCCG 59.117 57.895 31.27 0.00 36.52 5.52
1790 1966 8.706035 GGTGATATGCTTATTTGATTCATTTGC 58.294 33.333 0.00 0.00 0.00 3.68
1794 1970 7.766219 ATGCTTATTTGATTCATTTGCTGTC 57.234 32.000 0.00 0.00 0.00 3.51
1869 2049 9.643693 ATTATGTTAATCAAAGCTTTTGTGGAG 57.356 29.630 9.53 0.00 0.00 3.86
1888 2068 8.862325 TGTGGAGTAAAATCAATGATGTACTT 57.138 30.769 16.32 4.25 29.55 2.24
1889 2069 8.729756 TGTGGAGTAAAATCAATGATGTACTTG 58.270 33.333 16.32 0.00 29.55 3.16
1943 2137 3.714798 ACACTAGAAAGGGGAGTTTGTGA 59.285 43.478 0.00 0.00 0.00 3.58
1944 2138 4.351111 ACACTAGAAAGGGGAGTTTGTGAT 59.649 41.667 0.00 0.00 0.00 3.06
1949 2143 4.043310 AGAAAGGGGAGTTTGTGATCATCA 59.957 41.667 0.00 0.00 0.00 3.07
1951 2145 4.598036 AGGGGAGTTTGTGATCATCATT 57.402 40.909 0.00 0.00 0.00 2.57
1953 2147 4.019174 GGGGAGTTTGTGATCATCATTGT 58.981 43.478 0.00 0.00 0.00 2.71
1979 2173 0.030908 GGTGATACTTCCTCTCCGCG 59.969 60.000 0.00 0.00 0.00 6.46
2006 2202 3.511540 TCACCTCCTCCTATATTCATGCG 59.488 47.826 0.00 0.00 0.00 4.73
2106 2302 6.767902 TGGATTATAGACAACCTGAAATGAGC 59.232 38.462 0.00 0.00 0.00 4.26
2109 2305 2.693069 AGACAACCTGAAATGAGCGAG 58.307 47.619 0.00 0.00 0.00 5.03
2116 2312 3.997021 ACCTGAAATGAGCGAGTAAACAG 59.003 43.478 0.00 0.00 0.00 3.16
2143 2339 8.139989 ACTAAAACGTGTCTATATACACCATCC 58.860 37.037 13.93 0.00 45.66 3.51
2144 2340 6.474140 AAACGTGTCTATATACACCATCCA 57.526 37.500 13.93 0.00 45.66 3.41
2146 2342 6.474140 ACGTGTCTATATACACCATCCAAA 57.526 37.500 13.93 0.00 45.66 3.28
2160 2356 5.236911 CACCATCCAAATCACAAAAAGTTGG 59.763 40.000 0.00 0.00 39.22 3.77
2171 2367 9.480053 AATCACAAAAAGTTGGAACATCTTATG 57.520 29.630 0.00 0.00 46.30 1.90
2177 2373 5.184892 AGTTGGAACATCTTATGCTCCTT 57.815 39.130 9.95 0.00 44.10 3.36
2178 2374 5.189180 AGTTGGAACATCTTATGCTCCTTC 58.811 41.667 9.95 4.45 44.10 3.46
2179 2375 5.045286 AGTTGGAACATCTTATGCTCCTTCT 60.045 40.000 9.95 6.16 44.10 2.85
2181 2377 6.753913 TGGAACATCTTATGCTCCTTCTAT 57.246 37.500 9.95 0.00 44.10 1.98
2182 2378 7.855784 TGGAACATCTTATGCTCCTTCTATA 57.144 36.000 9.95 0.00 44.10 1.31
2184 2380 8.713971 TGGAACATCTTATGCTCCTTCTATAAA 58.286 33.333 9.95 0.00 44.10 1.40
2185 2381 9.213799 GGAACATCTTATGCTCCTTCTATAAAG 57.786 37.037 2.72 0.00 41.29 1.85
2216 2412 9.685828 AGTGATCTAAACGCTCTTATATTTCTC 57.314 33.333 0.00 0.00 0.00 2.87
2222 2418 9.400638 CTAAACGCTCTTATATTTCTCTACAGG 57.599 37.037 0.00 0.00 0.00 4.00
2255 2451 8.547967 TTTGTGAACAGAGGAAGTATATGTTC 57.452 34.615 8.93 8.93 46.25 3.18
2286 2482 3.517500 GCCCACCCTTTTCCATTAAATCA 59.482 43.478 0.00 0.00 0.00 2.57
2334 2530 6.604795 AGCATGAATTGAATACTATATGCCCC 59.395 38.462 0.00 0.00 40.21 5.80
2399 2598 8.635765 ATTATACATATTTCGCCAGAACCAAT 57.364 30.769 0.00 0.00 35.86 3.16
2547 2788 3.861840 ACCCACTTGTCATACTTCGATG 58.138 45.455 0.00 0.00 0.00 3.84
2556 2797 5.351458 TGTCATACTTCGATGGATCACAAG 58.649 41.667 0.00 0.00 0.00 3.16
2561 2802 1.725641 TCGATGGATCACAAGTGCAC 58.274 50.000 9.40 9.40 0.00 4.57
2607 2848 0.887933 ATGGTACGCTTGCCCAAAAG 59.112 50.000 0.00 0.00 0.00 2.27
2613 2854 2.243810 ACGCTTGCCCAAAAGGAATTA 58.756 42.857 0.00 0.00 38.24 1.40
2621 2862 5.792741 TGCCCAAAAGGAATTACTGAAATG 58.207 37.500 0.00 0.00 38.24 2.32
2623 2864 6.183361 TGCCCAAAAGGAATTACTGAAATGTT 60.183 34.615 0.00 0.00 38.24 2.71
2690 2933 2.036346 AGGTTCAACTTGAATTGCCAGC 59.964 45.455 7.47 0.00 38.79 4.85
2697 2940 1.546923 CTTGAATTGCCAGCACATCCA 59.453 47.619 0.00 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 2.577112 CTGCGACGCTCGATCGTT 60.577 61.111 22.08 0.00 43.74 3.85
20 21 3.441808 CTCTGCGACGCTCGATCGT 62.442 63.158 22.08 14.94 43.74 3.73
96 99 3.053291 GTTCAATCACGCCGGCCA 61.053 61.111 23.46 5.14 0.00 5.36
136 170 0.179124 GTCTCATCACAGGGCTCGTC 60.179 60.000 0.00 0.00 0.00 4.20
145 179 2.710902 CGCGGAGGGTCTCATCACA 61.711 63.158 0.00 0.00 34.98 3.58
165 204 1.352404 CGGGACAAAACGAAACGCA 59.648 52.632 0.00 0.00 0.00 5.24
166 205 0.655337 GACGGGACAAAACGAAACGC 60.655 55.000 0.00 0.00 0.00 4.84
168 207 0.041926 CGGACGGGACAAAACGAAAC 60.042 55.000 0.00 0.00 0.00 2.78
169 208 1.774046 GCGGACGGGACAAAACGAAA 61.774 55.000 0.00 0.00 0.00 3.46
170 209 2.246042 GCGGACGGGACAAAACGAA 61.246 57.895 0.00 0.00 0.00 3.85
171 210 2.662527 GCGGACGGGACAAAACGA 60.663 61.111 0.00 0.00 0.00 3.85
204 243 4.813526 CGACGACGACGGAGCCAG 62.814 72.222 12.58 0.00 44.46 4.85
307 355 1.195674 GCGGTGAAAAGACAAGAGCTC 59.804 52.381 5.27 5.27 0.00 4.09
334 382 4.093291 AGCAAGCTCCTCCAGGCG 62.093 66.667 0.00 0.00 34.44 5.52
366 414 1.267261 CAACCCATACAAAACGGCGAA 59.733 47.619 16.62 0.00 0.00 4.70
463 515 0.613292 TCCCAGACTGCCAGACTCTC 60.613 60.000 0.00 0.00 0.00 3.20
468 520 2.121385 AGCTCCCAGACTGCCAGA 59.879 61.111 0.00 0.00 0.00 3.86
469 521 1.834856 TTCAGCTCCCAGACTGCCAG 61.835 60.000 0.00 0.00 33.80 4.85
470 522 1.418097 TTTCAGCTCCCAGACTGCCA 61.418 55.000 0.00 0.00 33.80 4.92
472 524 0.676151 CCTTTCAGCTCCCAGACTGC 60.676 60.000 0.00 0.00 33.80 4.40
473 525 0.676151 GCCTTTCAGCTCCCAGACTG 60.676 60.000 0.00 0.00 35.15 3.51
476 528 0.478072 TTTGCCTTTCAGCTCCCAGA 59.522 50.000 0.00 0.00 0.00 3.86
477 529 0.886563 CTTTGCCTTTCAGCTCCCAG 59.113 55.000 0.00 0.00 0.00 4.45
478 530 0.540365 CCTTTGCCTTTCAGCTCCCA 60.540 55.000 0.00 0.00 0.00 4.37
484 536 0.453390 GCGATCCCTTTGCCTTTCAG 59.547 55.000 0.00 0.00 0.00 3.02
485 537 0.251121 TGCGATCCCTTTGCCTTTCA 60.251 50.000 0.00 0.00 33.31 2.69
486 538 0.453390 CTGCGATCCCTTTGCCTTTC 59.547 55.000 0.00 0.00 33.31 2.62
487 539 0.967380 CCTGCGATCCCTTTGCCTTT 60.967 55.000 0.00 0.00 33.31 3.11
489 541 2.273449 CCTGCGATCCCTTTGCCT 59.727 61.111 0.00 0.00 33.31 4.75
490 542 3.521796 GCCTGCGATCCCTTTGCC 61.522 66.667 0.00 0.00 33.31 4.52
491 543 1.669999 ATTGCCTGCGATCCCTTTGC 61.670 55.000 0.00 0.00 35.05 3.68
492 544 1.334869 GTATTGCCTGCGATCCCTTTG 59.665 52.381 0.00 0.00 0.00 2.77
495 547 1.344953 TGGTATTGCCTGCGATCCCT 61.345 55.000 3.04 0.00 38.35 4.20
496 548 0.886490 CTGGTATTGCCTGCGATCCC 60.886 60.000 0.00 0.00 38.35 3.85
498 550 2.072298 GATCTGGTATTGCCTGCGATC 58.928 52.381 0.00 0.00 38.35 3.69
499 551 1.606480 CGATCTGGTATTGCCTGCGAT 60.606 52.381 0.00 0.00 38.35 4.58
500 552 0.249447 CGATCTGGTATTGCCTGCGA 60.249 55.000 0.00 0.00 38.35 5.10
501 553 1.835483 GCGATCTGGTATTGCCTGCG 61.835 60.000 0.00 0.00 38.35 5.18
502 554 0.815213 TGCGATCTGGTATTGCCTGC 60.815 55.000 0.00 0.00 38.35 4.85
503 555 1.600957 CTTGCGATCTGGTATTGCCTG 59.399 52.381 0.00 0.00 38.35 4.85
506 558 1.016627 TGCTTGCGATCTGGTATTGC 58.983 50.000 0.00 0.00 0.00 3.56
507 559 2.874086 TCATGCTTGCGATCTGGTATTG 59.126 45.455 0.00 0.00 0.00 1.90
549 609 1.808945 CTGGCAAACACCACTCTGATC 59.191 52.381 0.00 0.00 35.33 2.92
604 676 0.698238 TGCTGCCATCAACCTTAGGT 59.302 50.000 0.00 0.00 37.65 3.08
631 704 1.733360 GTTGTCGTAGCTCTCTCGTCT 59.267 52.381 0.00 0.00 0.00 4.18
637 710 3.425858 GTGTTTCTGTTGTCGTAGCTCTC 59.574 47.826 0.00 0.00 0.00 3.20
690 788 8.196378 AGTTCTCTTCATTTGTACTCCTACTT 57.804 34.615 0.00 0.00 0.00 2.24
691 789 7.784470 AGTTCTCTTCATTTGTACTCCTACT 57.216 36.000 0.00 0.00 0.00 2.57
695 793 9.436957 TTGATTAGTTCTCTTCATTTGTACTCC 57.563 33.333 0.00 0.00 0.00 3.85
800 905 5.292101 GTGGATATGAAGGAACTGTTCTTCG 59.708 44.000 19.05 0.00 40.86 3.79
850 956 3.081804 GGAAAAGGAGGATCGAAAAGCA 58.918 45.455 0.00 0.00 34.37 3.91
871 983 9.420118 AGGAGGCTCTTATATATAGTGATTGAG 57.580 37.037 15.23 0.00 0.00 3.02
998 1132 1.402852 GGAAGAACTTTGCCGCCATTC 60.403 52.381 0.00 0.00 0.00 2.67
1080 1214 0.038251 TGTCAGCGACGCAGAAATCT 60.038 50.000 23.70 0.00 34.95 2.40
1115 1249 3.799963 CGTACGCATGTGTGGTTATACAT 59.200 43.478 22.00 0.00 38.94 2.29
1116 1250 3.180613 CGTACGCATGTGTGGTTATACA 58.819 45.455 22.00 0.00 32.26 2.29
1168 1328 7.944729 AAGAGTTAACAACTATGATTGGCAT 57.055 32.000 8.61 0.00 43.03 4.40
1196 1365 6.453926 AAACTGCATGCACATTACATGATA 57.546 33.333 18.46 0.00 46.33 2.15
1205 1375 3.455990 TGACAAAAACTGCATGCACAT 57.544 38.095 18.46 4.89 0.00 3.21
1206 1376 2.955477 TGACAAAAACTGCATGCACA 57.045 40.000 18.46 7.85 0.00 4.57
1207 1377 3.059461 CCATTGACAAAAACTGCATGCAC 60.059 43.478 18.46 4.88 0.00 4.57
1208 1378 3.132160 CCATTGACAAAAACTGCATGCA 58.868 40.909 21.29 21.29 0.00 3.96
1209 1379 3.391965 TCCATTGACAAAAACTGCATGC 58.608 40.909 11.82 11.82 0.00 4.06
1210 1380 6.367421 CAAATCCATTGACAAAAACTGCATG 58.633 36.000 0.00 0.00 41.85 4.06
1211 1381 5.049267 GCAAATCCATTGACAAAAACTGCAT 60.049 36.000 0.00 0.00 41.85 3.96
1236 1409 2.747855 GCCTTCGGGTCCTTGCAG 60.748 66.667 0.00 0.00 37.45 4.41
1252 1425 0.533032 AAGTCTTCTACCTCCGCAGC 59.467 55.000 0.00 0.00 0.00 5.25
1294 1467 2.029964 GTTGCTCGTGTTCCCGGA 59.970 61.111 0.73 0.00 0.00 5.14
1674 1847 5.585445 GGCAATGATATCATCTGAGATGGAC 59.415 44.000 21.27 11.08 35.10 4.02
1790 1966 8.509690 ACACAAACATGATCTTTAATCAGACAG 58.490 33.333 0.00 0.00 0.00 3.51
1794 1970 9.132521 GGAAACACAAACATGATCTTTAATCAG 57.867 33.333 0.00 0.00 0.00 2.90
1843 2021 9.643693 CTCCACAAAAGCTTTGATTAACATAAT 57.356 29.630 13.54 0.00 0.00 1.28
1869 2049 9.691362 AACAACCAAGTACATCATTGATTTTAC 57.309 29.630 0.00 2.24 0.00 2.01
1907 2087 9.832445 CCCTTTCTAGTGTAGATTAGCAAAATA 57.168 33.333 0.00 0.00 34.22 1.40
1917 2097 5.785940 ACAAACTCCCCTTTCTAGTGTAGAT 59.214 40.000 0.00 0.00 34.22 1.98
1921 2101 3.714798 TCACAAACTCCCCTTTCTAGTGT 59.285 43.478 0.00 0.00 0.00 3.55
1927 2107 4.335416 TGATGATCACAAACTCCCCTTTC 58.665 43.478 0.00 0.00 0.00 2.62
1943 2137 8.529424 AGTATCACCATTTTGACAATGATGAT 57.471 30.769 6.43 6.43 42.12 2.45
1944 2138 7.943079 AGTATCACCATTTTGACAATGATGA 57.057 32.000 10.23 0.00 34.88 2.92
1949 2143 7.177878 AGAGGAAGTATCACCATTTTGACAAT 58.822 34.615 0.00 0.00 0.00 2.71
1951 2145 6.126863 AGAGGAAGTATCACCATTTTGACA 57.873 37.500 0.00 0.00 0.00 3.58
1953 2147 5.626809 CGGAGAGGAAGTATCACCATTTTGA 60.627 44.000 0.00 0.00 0.00 2.69
1979 2173 4.284490 TGAATATAGGAGGAGGTGATGTGC 59.716 45.833 0.00 0.00 0.00 4.57
2082 2278 6.073548 CGCTCATTTCAGGTTGTCTATAATCC 60.074 42.308 0.00 0.00 0.00 3.01
2085 2281 5.972935 TCGCTCATTTCAGGTTGTCTATAA 58.027 37.500 0.00 0.00 0.00 0.98
2088 2284 3.258372 ACTCGCTCATTTCAGGTTGTCTA 59.742 43.478 0.00 0.00 0.00 2.59
2090 2286 2.417719 ACTCGCTCATTTCAGGTTGTC 58.582 47.619 0.00 0.00 0.00 3.18
2096 2292 4.926238 AGTCTGTTTACTCGCTCATTTCAG 59.074 41.667 0.00 0.00 0.00 3.02
2106 2302 5.684626 AGACACGTTTTAGTCTGTTTACTCG 59.315 40.000 5.55 0.00 43.09 4.18
2143 2339 7.775397 AGATGTTCCAACTTTTTGTGATTTG 57.225 32.000 0.00 0.00 0.00 2.32
2146 2342 7.599998 GCATAAGATGTTCCAACTTTTTGTGAT 59.400 33.333 8.51 0.00 29.69 3.06
2160 2356 9.988815 TCTTTATAGAAGGAGCATAAGATGTTC 57.011 33.333 0.00 0.00 39.45 3.18
2181 2377 9.871238 AAGAGCGTTTAGATCACTATTTCTTTA 57.129 29.630 0.00 0.00 37.82 1.85
2182 2378 8.779354 AAGAGCGTTTAGATCACTATTTCTTT 57.221 30.769 0.00 0.00 37.82 2.52
2190 2386 9.685828 GAGAAATATAAGAGCGTTTAGATCACT 57.314 33.333 0.00 0.00 37.82 3.41
2222 2418 3.202151 TCCTCTGTTCACAAATATCCCCC 59.798 47.826 0.00 0.00 0.00 5.40
2255 2451 4.653341 TGGAAAAGGGTGGGCAATATATTG 59.347 41.667 19.29 19.29 40.66 1.90
2286 2482 7.772757 TGCTTCAACCAATTAATCCAAAGTTTT 59.227 29.630 0.00 0.00 0.00 2.43
2334 2530 2.474410 AACCCTGCTAAAAGGAGACG 57.526 50.000 0.00 0.00 40.02 4.18
2399 2598 7.484993 AATTCTGGATGTTGGATGATTTTCA 57.515 32.000 0.00 0.00 0.00 2.69
2471 2670 1.002069 ATGGGAGATGGCTGGTTGAA 58.998 50.000 0.00 0.00 0.00 2.69
2523 2722 3.322541 TCGAAGTATGACAAGTGGGTTGA 59.677 43.478 0.00 0.00 38.60 3.18
2527 2726 3.118775 TCCATCGAAGTATGACAAGTGGG 60.119 47.826 0.00 0.00 0.00 4.61
2547 2788 1.589716 GCTGGGTGCACTTGTGATCC 61.590 60.000 17.98 7.97 42.31 3.36
2561 2802 2.939103 GTTGCTACTATGTCTTGCTGGG 59.061 50.000 0.00 0.00 0.00 4.45
2607 2848 9.956720 CTCCAATGATAACATTTCAGTAATTCC 57.043 33.333 0.00 0.00 43.17 3.01
2613 2854 6.660521 TGCTTCTCCAATGATAACATTTCAGT 59.339 34.615 0.00 0.00 43.17 3.41
2621 2862 3.058639 GCCGATGCTTCTCCAATGATAAC 60.059 47.826 0.00 0.00 33.53 1.89
2623 2864 2.104622 TGCCGATGCTTCTCCAATGATA 59.895 45.455 0.00 0.00 38.71 2.15
2690 2933 0.321564 TTCAAGCGGAGGTGGATGTG 60.322 55.000 0.00 0.00 38.01 3.21


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

AutoCloner maintained by Alex Coulton.