Multiple sequence alignment - TraesCS7A01G245100

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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 TraesCS7A01G245100 chr7A 100.000 1635 0 0 945 2579 222785795 222784161 0.000000e+00 3020
1 TraesCS7A01G245100 chr7A 100.000 653 0 0 1 653 222786739 222786087 0.000000e+00 1206
2 TraesCS7A01G245100 chr7D 90.190 1682 85 36 950 2579 210125251 210123598 0.000000e+00 2119
3 TraesCS7A01G245100 chr7D 86.545 602 29 13 76 649 210125899 210125322 1.310000e-172 616
4 TraesCS7A01G245100 chr7B 87.468 1540 90 39 945 2416 191139017 191140521 0.000000e+00 1679
5 TraesCS7A01G245100 chr7B 87.755 588 16 10 82 644 191138392 191138948 1.010000e-178 636
6 TraesCS7A01G245100 chr7B 98.305 59 1 0 2521 2579 191140775 191140833 1.260000e-18 104
7 TraesCS7A01G245100 chr5D 80.989 526 66 27 999 1516 374661844 374662343 1.120000e-103 387
8 TraesCS7A01G245100 chr5B 78.887 521 75 24 1000 1516 447402739 447403228 1.150000e-83 320
9 TraesCS7A01G245100 chr5A 81.356 177 24 6 1000 1173 476402840 476403010 4.480000e-28 135


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 TraesCS7A01G245100 chr7A 222784161 222786739 2578 True 2113.000000 3020 100.0000 1 2579 2 chr7A.!!$R1 2578
1 TraesCS7A01G245100 chr7D 210123598 210125899 2301 True 1367.500000 2119 88.3675 76 2579 2 chr7D.!!$R1 2503
2 TraesCS7A01G245100 chr7B 191138392 191140833 2441 False 806.333333 1679 91.1760 82 2579 3 chr7B.!!$F1 2497

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
179 182 0.17691 CCACCACCACCCAAAACAAC 59.823 55.0 0.0 0.0 0.0 3.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1674 1771 0.309612 CCACCGCTACAACAACAACC 59.69 55.0 0.0 0.0 0.0 3.77 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
19 20 2.004583 TTAGTTCGCTTGGACGGATG 57.995 50.000 0.00 0.00 0.00 3.51
20 21 0.459585 TAGTTCGCTTGGACGGATGC 60.460 55.000 0.00 0.00 0.00 3.91
21 22 2.032634 GTTCGCTTGGACGGATGCA 61.033 57.895 0.00 0.00 0.00 3.96
22 23 1.302112 TTCGCTTGGACGGATGCAA 60.302 52.632 0.00 0.00 34.60 4.08
23 24 0.886938 TTCGCTTGGACGGATGCAAA 60.887 50.000 0.00 0.00 35.51 3.68
24 25 0.886938 TCGCTTGGACGGATGCAAAA 60.887 50.000 0.00 0.00 35.51 2.44
25 26 0.454957 CGCTTGGACGGATGCAAAAG 60.455 55.000 0.00 0.00 35.51 2.27
26 27 0.881118 GCTTGGACGGATGCAAAAGA 59.119 50.000 0.00 0.00 35.51 2.52
27 28 1.269448 GCTTGGACGGATGCAAAAGAA 59.731 47.619 0.00 0.00 35.51 2.52
28 29 2.288152 GCTTGGACGGATGCAAAAGAAA 60.288 45.455 0.00 0.00 35.51 2.52
29 30 3.798548 GCTTGGACGGATGCAAAAGAAAA 60.799 43.478 0.00 0.00 35.51 2.29
30 31 4.559153 CTTGGACGGATGCAAAAGAAAAT 58.441 39.130 0.00 0.00 35.51 1.82
31 32 4.599047 TGGACGGATGCAAAAGAAAATT 57.401 36.364 0.00 0.00 0.00 1.82
32 33 4.954875 TGGACGGATGCAAAAGAAAATTT 58.045 34.783 0.00 0.00 0.00 1.82
33 34 4.749099 TGGACGGATGCAAAAGAAAATTTG 59.251 37.500 0.00 0.00 42.01 2.32
42 43 4.517287 CAAAAGAAAATTTGCGAGTTGCC 58.483 39.130 0.00 0.00 45.60 4.52
43 44 2.050477 AGAAAATTTGCGAGTTGCCG 57.950 45.000 0.00 0.00 45.60 5.69
44 45 1.336755 AGAAAATTTGCGAGTTGCCGT 59.663 42.857 0.00 0.00 45.60 5.68
45 46 2.124122 GAAAATTTGCGAGTTGCCGTT 58.876 42.857 0.00 0.00 45.60 4.44
46 47 1.486439 AAATTTGCGAGTTGCCGTTG 58.514 45.000 0.00 0.00 45.60 4.10
47 48 0.665835 AATTTGCGAGTTGCCGTTGA 59.334 45.000 0.00 0.00 45.60 3.18
48 49 0.665835 ATTTGCGAGTTGCCGTTGAA 59.334 45.000 0.00 0.00 45.60 2.69
49 50 0.452184 TTTGCGAGTTGCCGTTGAAA 59.548 45.000 0.00 0.00 45.60 2.69
50 51 0.452184 TTGCGAGTTGCCGTTGAAAA 59.548 45.000 0.00 0.00 45.60 2.29
51 52 0.665835 TGCGAGTTGCCGTTGAAAAT 59.334 45.000 0.00 0.00 45.60 1.82
52 53 1.052287 GCGAGTTGCCGTTGAAAATG 58.948 50.000 0.00 0.00 37.76 2.32
62 63 2.928694 CGTTGAAAATGGCTAAAGCGT 58.071 42.857 0.00 0.00 43.26 5.07
63 64 2.908626 CGTTGAAAATGGCTAAAGCGTC 59.091 45.455 0.00 0.00 43.26 5.19
64 65 3.608241 CGTTGAAAATGGCTAAAGCGTCA 60.608 43.478 0.00 0.00 43.26 4.35
65 66 4.295051 GTTGAAAATGGCTAAAGCGTCAA 58.705 39.130 0.00 0.00 43.26 3.18
66 67 4.159377 TGAAAATGGCTAAAGCGTCAAG 57.841 40.909 0.00 0.00 43.26 3.02
67 68 3.057596 TGAAAATGGCTAAAGCGTCAAGG 60.058 43.478 0.00 0.00 43.26 3.61
68 69 2.489938 AATGGCTAAAGCGTCAAGGA 57.510 45.000 0.00 0.00 43.26 3.36
69 70 2.717639 ATGGCTAAAGCGTCAAGGAT 57.282 45.000 0.00 0.00 43.26 3.24
70 71 3.838244 ATGGCTAAAGCGTCAAGGATA 57.162 42.857 0.00 0.00 43.26 2.59
71 72 2.901249 TGGCTAAAGCGTCAAGGATAC 58.099 47.619 0.00 0.00 43.26 2.24
72 73 2.235155 TGGCTAAAGCGTCAAGGATACA 59.765 45.455 0.00 0.00 43.26 2.29
73 74 3.267483 GGCTAAAGCGTCAAGGATACAA 58.733 45.455 0.00 0.00 43.26 2.41
74 75 3.309954 GGCTAAAGCGTCAAGGATACAAG 59.690 47.826 0.00 0.00 43.26 3.16
82 83 4.271291 GCGTCAAGGATACAAGAAAGATCC 59.729 45.833 0.00 0.00 39.65 3.36
86 87 5.824624 TCAAGGATACAAGAAAGATCCATGC 59.175 40.000 3.15 0.00 41.48 4.06
152 153 0.454600 CCGCCTACGAAGCAGAGTAA 59.545 55.000 0.00 0.00 43.93 2.24
179 182 0.176910 CCACCACCACCCAAAACAAC 59.823 55.000 0.00 0.00 0.00 3.32
255 259 2.960688 GCGCACTCCCCTTCCTTCT 61.961 63.158 0.30 0.00 0.00 2.85
262 266 1.078143 CCCCTTCCTTCTCCTTGCG 60.078 63.158 0.00 0.00 0.00 4.85
292 296 2.359478 ACCACCCGTCGCCATTTC 60.359 61.111 0.00 0.00 0.00 2.17
293 297 3.131478 CCACCCGTCGCCATTTCC 61.131 66.667 0.00 0.00 0.00 3.13
294 298 3.131478 CACCCGTCGCCATTTCCC 61.131 66.667 0.00 0.00 0.00 3.97
295 299 3.327404 ACCCGTCGCCATTTCCCT 61.327 61.111 0.00 0.00 0.00 4.20
296 300 2.513897 CCCGTCGCCATTTCCCTC 60.514 66.667 0.00 0.00 0.00 4.30
297 301 2.513897 CCGTCGCCATTTCCCTCC 60.514 66.667 0.00 0.00 0.00 4.30
375 391 5.239359 ACGAAAACTCCACTTGTTTAACC 57.761 39.130 0.00 0.00 36.72 2.85
376 392 4.701171 ACGAAAACTCCACTTGTTTAACCA 59.299 37.500 0.00 0.00 36.72 3.67
377 393 5.183522 ACGAAAACTCCACTTGTTTAACCAA 59.816 36.000 0.00 0.00 36.72 3.67
378 394 5.513849 CGAAAACTCCACTTGTTTAACCAAC 59.486 40.000 0.00 0.00 36.72 3.77
379 395 4.625972 AACTCCACTTGTTTAACCAACG 57.374 40.909 0.00 0.00 38.36 4.10
380 396 2.356695 ACTCCACTTGTTTAACCAACGC 59.643 45.455 0.00 0.00 38.36 4.84
381 397 2.356382 CTCCACTTGTTTAACCAACGCA 59.644 45.455 0.00 0.00 38.36 5.24
382 398 2.753452 TCCACTTGTTTAACCAACGCAA 59.247 40.909 0.00 0.00 38.36 4.85
383 399 2.855370 CCACTTGTTTAACCAACGCAAC 59.145 45.455 0.00 0.00 38.36 4.17
384 400 2.528287 CACTTGTTTAACCAACGCAACG 59.472 45.455 0.00 0.00 38.36 4.10
385 401 1.515221 CTTGTTTAACCAACGCAACGC 59.485 47.619 0.00 0.00 38.36 4.84
386 402 0.450583 TGTTTAACCAACGCAACGCA 59.549 45.000 0.00 0.00 38.36 5.24
387 403 1.135489 TGTTTAACCAACGCAACGCAA 60.135 42.857 0.00 0.00 38.36 4.85
388 404 1.253289 GTTTAACCAACGCAACGCAAC 59.747 47.619 0.00 0.00 0.00 4.17
389 405 0.589229 TTAACCAACGCAACGCAACG 60.589 50.000 0.00 0.00 0.00 4.10
419 435 3.353836 CGCACCCCGTTCCTTGTG 61.354 66.667 0.00 0.00 0.00 3.33
427 443 3.423154 GTTCCTTGTGGAGCGCGG 61.423 66.667 8.83 0.00 44.24 6.46
428 444 4.697756 TTCCTTGTGGAGCGCGGG 62.698 66.667 8.83 0.00 44.24 6.13
621 655 2.768344 TCCTCCTCCGCCCCATTC 60.768 66.667 0.00 0.00 0.00 2.67
644 690 3.973267 AAAGCCTCGACTCGCTCGC 62.973 63.158 0.00 0.00 42.62 5.03
647 693 4.583254 CCTCGACTCGCTCGCTCG 62.583 72.222 0.00 3.77 42.62 5.03
648 694 3.555619 CTCGACTCGCTCGCTCGA 61.556 66.667 10.07 10.07 42.62 4.04
649 695 2.876879 CTCGACTCGCTCGCTCGAT 61.877 63.158 10.65 0.00 42.62 3.59
650 696 2.424479 CGACTCGCTCGCTCGATC 60.424 66.667 0.00 0.00 37.87 3.69
652 698 3.530398 GACTCGCTCGCTCGATCCC 62.530 68.421 0.00 0.00 37.87 3.85
1142 1198 2.125350 CTGCTTCCTGGCGTCCTC 60.125 66.667 0.00 0.00 34.52 3.71
1143 1199 3.672295 CTGCTTCCTGGCGTCCTCC 62.672 68.421 0.00 0.00 34.52 4.30
1144 1200 3.394836 GCTTCCTGGCGTCCTCCT 61.395 66.667 0.00 0.00 0.00 3.69
1323 1388 2.049433 AAGGCGTCCAAGTCGTCG 60.049 61.111 0.00 0.00 37.99 5.12
1326 1391 3.103911 GCGTCCAAGTCGTCGGTG 61.104 66.667 0.00 0.00 0.00 4.94
1519 1584 1.405821 AGATCGTCCGGTTCTGATCAC 59.594 52.381 21.17 3.83 39.70 3.06
1522 1587 0.736325 CGTCCGGTTCTGATCACCAC 60.736 60.000 0.00 0.00 33.36 4.16
1526 1591 0.243907 CGGTTCTGATCACCACGACT 59.756 55.000 0.00 0.00 33.36 4.18
1527 1592 1.471287 CGGTTCTGATCACCACGACTA 59.529 52.381 0.00 0.00 33.36 2.59
1534 1622 3.857052 TGATCACCACGACTACAAATCC 58.143 45.455 0.00 0.00 0.00 3.01
1546 1634 1.446907 ACAAATCCGAAGCAGCAGAG 58.553 50.000 0.00 0.00 0.00 3.35
1644 1741 2.516930 AAAGATGGCGATGGGGCG 60.517 61.111 0.00 0.00 46.04 6.13
1674 1771 4.327357 ACGAAGAAACAGTGCGATGATAAG 59.673 41.667 0.00 0.00 0.00 1.73
1709 1814 3.961414 GGTTGGCGGTGGAGGGAA 61.961 66.667 0.00 0.00 0.00 3.97
1710 1815 2.359975 GTTGGCGGTGGAGGGAAG 60.360 66.667 0.00 0.00 0.00 3.46
1711 1816 2.528127 TTGGCGGTGGAGGGAAGA 60.528 61.111 0.00 0.00 0.00 2.87
1725 1830 2.589664 AGGGAAGAGAGGAGATGAGGAA 59.410 50.000 0.00 0.00 0.00 3.36
1755 1860 1.214367 GTGTGTACTGTTGTCCCACG 58.786 55.000 0.00 0.00 33.51 4.94
1826 1934 4.444388 TCATTTCTACGATGCAGTATTCGC 59.556 41.667 7.32 0.00 0.00 4.70
1828 1936 3.000082 TCTACGATGCAGTATTCGCTG 58.000 47.619 7.32 1.46 39.37 5.18
1842 1950 0.390340 TCGCTGGCTTTAGCTGTCAG 60.390 55.000 0.00 0.00 41.51 3.51
1845 1953 3.911137 GGCTTTAGCTGTCAGCCC 58.089 61.111 21.32 11.02 46.55 5.19
1850 1958 2.095008 GCTTTAGCTGTCAGCCCTTTTC 60.095 50.000 21.32 3.28 43.77 2.29
1851 1959 3.416156 CTTTAGCTGTCAGCCCTTTTCT 58.584 45.455 21.32 3.46 43.77 2.52
1852 1960 2.770164 TAGCTGTCAGCCCTTTTCTC 57.230 50.000 21.32 0.00 43.77 2.87
1853 1961 0.037447 AGCTGTCAGCCCTTTTCTCC 59.963 55.000 21.32 0.00 43.77 3.71
1877 1992 3.864686 CTGGCCGCGAATTGTCCG 61.865 66.667 8.23 0.00 0.00 4.79
1910 2025 1.062587 CATTGACGTTTGGATCGCTCC 59.937 52.381 0.00 0.00 42.45 4.70
1928 2043 3.861263 GTTGGATCGGTTCGGCGC 61.861 66.667 0.00 0.00 0.00 6.53
1951 2066 1.691196 ATCATTATTGGGTGGGTGCG 58.309 50.000 0.00 0.00 0.00 5.34
2013 2155 6.187480 GTCTGTTTGAGAAAAATTTGCAAGC 58.813 36.000 0.00 0.00 30.26 4.01
2025 2167 1.164411 TTGCAAGCCGTATGGTGAAG 58.836 50.000 2.17 0.00 37.67 3.02
2029 2171 0.108329 AAGCCGTATGGTGAAGTCGG 60.108 55.000 2.17 0.00 43.37 4.79
2032 2174 1.082117 CCGTATGGTGAAGTCGGCAC 61.082 60.000 0.00 0.00 35.01 5.01
2045 2187 3.666253 GGCACGTTTCGGTTGGGG 61.666 66.667 0.00 0.00 0.00 4.96
2085 2227 0.796312 CGTCCGTGATTTTCTGTGGG 59.204 55.000 0.00 0.00 0.00 4.61
2139 2281 3.733960 GACGCCCCGTTTTCTGCC 61.734 66.667 0.00 0.00 41.37 4.85
2229 2377 4.129737 AGCGACGTCCATCCACCG 62.130 66.667 10.58 0.00 0.00 4.94
2231 2379 3.445687 CGACGTCCATCCACCGGA 61.446 66.667 9.46 0.00 35.55 5.14
2232 2380 2.975536 GACGTCCATCCACCGGAA 59.024 61.111 9.46 0.00 34.34 4.30
2280 2428 4.752514 CCTCGGCGGGTAGAAATC 57.247 61.111 5.83 0.00 0.00 2.17
2419 2567 7.479352 TTAATCCATCTCATCTCATCTCCTC 57.521 40.000 0.00 0.00 0.00 3.71
2420 2568 4.745484 TCCATCTCATCTCATCTCCTCT 57.255 45.455 0.00 0.00 0.00 3.69
2421 2569 4.665451 TCCATCTCATCTCATCTCCTCTC 58.335 47.826 0.00 0.00 0.00 3.20
2422 2570 3.765511 CCATCTCATCTCATCTCCTCTCC 59.234 52.174 0.00 0.00 0.00 3.71
2423 2571 4.509663 CCATCTCATCTCATCTCCTCTCCT 60.510 50.000 0.00 0.00 0.00 3.69
2427 2575 5.013079 TCTCATCTCATCTCCTCTCCTAGTC 59.987 48.000 0.00 0.00 0.00 2.59
2434 2582 2.370519 TCTCCTCTCCTAGTCGATCCAG 59.629 54.545 0.00 0.00 0.00 3.86
2457 2605 4.429212 TCGGCGTCGTGGATGTGG 62.429 66.667 10.18 0.00 37.69 4.17
2486 2634 3.661648 GCCCAGGCTGGAAGGGAA 61.662 66.667 34.84 0.00 45.80 3.97
2487 2635 2.679716 CCCAGGCTGGAAGGGAAG 59.320 66.667 34.84 12.25 45.80 3.46
2488 2636 2.679716 CCAGGCTGGAAGGGAAGG 59.320 66.667 29.96 0.00 40.96 3.46
2489 2637 2.679716 CAGGCTGGAAGGGAAGGG 59.320 66.667 6.61 0.00 0.00 3.95
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.004583 CATCCGTCCAAGCGAACTAA 57.995 50.000 0.00 0.00 0.00 2.24
1 2 0.459585 GCATCCGTCCAAGCGAACTA 60.460 55.000 0.00 0.00 0.00 2.24
3 4 1.573829 TTGCATCCGTCCAAGCGAAC 61.574 55.000 0.00 0.00 0.00 3.95
4 5 0.886938 TTTGCATCCGTCCAAGCGAA 60.887 50.000 0.00 0.00 0.00 4.70
5 6 0.886938 TTTTGCATCCGTCCAAGCGA 60.887 50.000 0.00 0.00 0.00 4.93
6 7 0.454957 CTTTTGCATCCGTCCAAGCG 60.455 55.000 0.00 0.00 0.00 4.68
7 8 0.881118 TCTTTTGCATCCGTCCAAGC 59.119 50.000 0.00 0.00 0.00 4.01
8 9 3.641437 TTTCTTTTGCATCCGTCCAAG 57.359 42.857 0.00 0.00 0.00 3.61
9 10 4.599047 ATTTTCTTTTGCATCCGTCCAA 57.401 36.364 0.00 0.00 0.00 3.53
10 11 4.599047 AATTTTCTTTTGCATCCGTCCA 57.401 36.364 0.00 0.00 0.00 4.02
11 12 5.268107 CAAATTTTCTTTTGCATCCGTCC 57.732 39.130 0.00 0.00 30.51 4.79
20 21 4.517287 GGCAACTCGCAAATTTTCTTTTG 58.483 39.130 0.00 0.00 45.17 2.44
21 22 3.245048 CGGCAACTCGCAAATTTTCTTTT 59.755 39.130 0.00 0.00 45.17 2.27
22 23 2.794350 CGGCAACTCGCAAATTTTCTTT 59.206 40.909 0.00 0.00 45.17 2.52
23 24 2.223711 ACGGCAACTCGCAAATTTTCTT 60.224 40.909 0.00 0.00 45.17 2.52
24 25 1.336755 ACGGCAACTCGCAAATTTTCT 59.663 42.857 0.00 0.00 45.17 2.52
25 26 1.766069 ACGGCAACTCGCAAATTTTC 58.234 45.000 0.00 0.00 45.17 2.29
26 27 1.857837 CAACGGCAACTCGCAAATTTT 59.142 42.857 0.00 0.00 45.17 1.82
27 28 1.066303 TCAACGGCAACTCGCAAATTT 59.934 42.857 0.00 0.00 45.17 1.82
28 29 0.665835 TCAACGGCAACTCGCAAATT 59.334 45.000 0.00 0.00 45.17 1.82
29 30 0.665835 TTCAACGGCAACTCGCAAAT 59.334 45.000 0.00 0.00 45.17 2.32
30 31 0.452184 TTTCAACGGCAACTCGCAAA 59.548 45.000 0.00 0.00 45.17 3.68
31 32 0.452184 TTTTCAACGGCAACTCGCAA 59.548 45.000 0.00 0.00 45.17 4.85
32 33 0.665835 ATTTTCAACGGCAACTCGCA 59.334 45.000 0.00 0.00 45.17 5.10
33 34 1.052287 CATTTTCAACGGCAACTCGC 58.948 50.000 0.00 0.00 41.28 5.03
34 35 1.685302 CCATTTTCAACGGCAACTCG 58.315 50.000 0.00 0.00 0.00 4.18
35 36 1.418373 GCCATTTTCAACGGCAACTC 58.582 50.000 0.00 0.00 45.52 3.01
36 37 3.586430 GCCATTTTCAACGGCAACT 57.414 47.368 0.00 0.00 45.52 3.16
40 41 1.992667 GCTTTAGCCATTTTCAACGGC 59.007 47.619 0.00 0.00 46.62 5.68
41 42 2.250188 CGCTTTAGCCATTTTCAACGG 58.750 47.619 0.00 0.00 37.91 4.44
42 43 2.908626 GACGCTTTAGCCATTTTCAACG 59.091 45.455 0.00 0.00 37.91 4.10
43 44 3.896122 TGACGCTTTAGCCATTTTCAAC 58.104 40.909 0.00 0.00 37.91 3.18
44 45 4.545610 CTTGACGCTTTAGCCATTTTCAA 58.454 39.130 0.00 0.00 37.91 2.69
45 46 3.057596 CCTTGACGCTTTAGCCATTTTCA 60.058 43.478 0.00 0.00 37.91 2.69
46 47 3.190535 TCCTTGACGCTTTAGCCATTTTC 59.809 43.478 0.00 0.00 37.91 2.29
47 48 3.153919 TCCTTGACGCTTTAGCCATTTT 58.846 40.909 0.00 0.00 37.91 1.82
48 49 2.790433 TCCTTGACGCTTTAGCCATTT 58.210 42.857 0.00 0.00 37.91 2.32
49 50 2.489938 TCCTTGACGCTTTAGCCATT 57.510 45.000 0.00 0.00 37.91 3.16
50 51 2.717639 ATCCTTGACGCTTTAGCCAT 57.282 45.000 0.00 0.00 37.91 4.40
51 52 2.235155 TGTATCCTTGACGCTTTAGCCA 59.765 45.455 0.00 0.00 37.91 4.75
52 53 2.901249 TGTATCCTTGACGCTTTAGCC 58.099 47.619 0.00 0.00 37.91 3.93
53 54 4.181578 TCTTGTATCCTTGACGCTTTAGC 58.818 43.478 0.00 0.00 37.78 3.09
54 55 6.590292 TCTTTCTTGTATCCTTGACGCTTTAG 59.410 38.462 0.00 0.00 0.00 1.85
55 56 6.460781 TCTTTCTTGTATCCTTGACGCTTTA 58.539 36.000 0.00 0.00 0.00 1.85
56 57 5.305585 TCTTTCTTGTATCCTTGACGCTTT 58.694 37.500 0.00 0.00 0.00 3.51
57 58 4.894784 TCTTTCTTGTATCCTTGACGCTT 58.105 39.130 0.00 0.00 0.00 4.68
58 59 4.537135 TCTTTCTTGTATCCTTGACGCT 57.463 40.909 0.00 0.00 0.00 5.07
59 60 4.271291 GGATCTTTCTTGTATCCTTGACGC 59.729 45.833 0.00 0.00 36.93 5.19
60 61 5.419542 TGGATCTTTCTTGTATCCTTGACG 58.580 41.667 0.00 0.00 39.97 4.35
61 62 6.238593 GCATGGATCTTTCTTGTATCCTTGAC 60.239 42.308 16.36 7.45 42.95 3.18
62 63 5.824624 GCATGGATCTTTCTTGTATCCTTGA 59.175 40.000 16.36 0.00 42.95 3.02
63 64 5.591472 TGCATGGATCTTTCTTGTATCCTTG 59.409 40.000 10.51 10.51 43.07 3.61
64 65 5.759059 TGCATGGATCTTTCTTGTATCCTT 58.241 37.500 0.00 0.00 39.97 3.36
65 66 5.378230 TGCATGGATCTTTCTTGTATCCT 57.622 39.130 0.00 0.00 39.97 3.24
66 67 6.455360 TTTGCATGGATCTTTCTTGTATCC 57.545 37.500 0.00 0.00 39.76 2.59
152 153 2.277404 GTGGTGGTGGTGGTGGTT 59.723 61.111 0.00 0.00 0.00 3.67
179 182 0.392193 GGTGGACTCATCTGGTGCTG 60.392 60.000 0.00 0.00 0.00 4.41
255 259 2.527671 CGTGTGAATGACGCAAGGA 58.472 52.632 0.00 0.00 46.39 3.36
262 266 1.574428 GGTGGTGCGTGTGAATGAC 59.426 57.895 0.00 0.00 0.00 3.06
292 296 2.040359 GGGAAGGGAGGAGGAGGG 60.040 72.222 0.00 0.00 0.00 4.30
293 297 1.074850 GAGGGAAGGGAGGAGGAGG 60.075 68.421 0.00 0.00 0.00 4.30
294 298 1.074850 GGAGGGAAGGGAGGAGGAG 60.075 68.421 0.00 0.00 0.00 3.69
295 299 2.647949 GGGAGGGAAGGGAGGAGGA 61.648 68.421 0.00 0.00 0.00 3.71
296 300 2.040359 GGGAGGGAAGGGAGGAGG 60.040 72.222 0.00 0.00 0.00 4.30
297 301 1.074850 GAGGGAGGGAAGGGAGGAG 60.075 68.421 0.00 0.00 0.00 3.69
375 391 2.946597 TTGCGTTGCGTTGCGTTG 60.947 55.556 0.00 0.00 0.00 4.10
376 392 2.947109 GTTGCGTTGCGTTGCGTT 60.947 55.556 0.00 0.00 0.00 4.84
380 396 2.946597 TTGCGTTGCGTTGCGTTG 60.947 55.556 0.00 0.00 0.00 4.10
381 397 2.947109 GTTGCGTTGCGTTGCGTT 60.947 55.556 0.00 0.00 0.00 4.84
385 401 3.667486 GTGCGTTGCGTTGCGTTG 61.667 61.111 0.00 0.00 0.00 4.10
400 416 3.353836 CAAGGAACGGGGTGCGTG 61.354 66.667 0.00 0.00 0.00 5.34
621 655 2.269241 GAGTCGAGGCTTTGGGGG 59.731 66.667 0.00 0.00 0.00 5.40
979 1025 2.716864 GCCTACGAGCCGAGAGAC 59.283 66.667 1.50 0.00 0.00 3.36
980 1026 2.895865 CGCCTACGAGCCGAGAGA 60.896 66.667 1.50 0.00 43.93 3.10
1323 1388 2.904866 TTGTGGCAGCGGTTCACC 60.905 61.111 13.19 3.74 0.00 4.02
1326 1391 2.639286 CAGTTGTGGCAGCGGTTC 59.361 61.111 0.00 0.00 0.00 3.62
1506 1571 0.736325 GTCGTGGTGATCAGAACCGG 60.736 60.000 0.00 0.00 40.86 5.28
1519 1584 1.659098 GCTTCGGATTTGTAGTCGTGG 59.341 52.381 0.00 0.00 0.00 4.94
1522 1587 1.324736 GCTGCTTCGGATTTGTAGTCG 59.675 52.381 0.00 0.00 0.00 4.18
1526 1591 2.621338 CTCTGCTGCTTCGGATTTGTA 58.379 47.619 0.00 0.00 0.00 2.41
1527 1592 1.446907 CTCTGCTGCTTCGGATTTGT 58.553 50.000 0.00 0.00 0.00 2.83
1534 1622 3.123620 GTGGGCTCTGCTGCTTCG 61.124 66.667 0.00 0.00 0.00 3.79
1546 1634 3.005897 GGAAAGAAAGGAAAAGAGTGGGC 59.994 47.826 0.00 0.00 0.00 5.36
1619 1716 0.394352 ATCGCCATCTTTCACCCACC 60.394 55.000 0.00 0.00 0.00 4.61
1620 1717 0.734889 CATCGCCATCTTTCACCCAC 59.265 55.000 0.00 0.00 0.00 4.61
1621 1718 0.394216 CCATCGCCATCTTTCACCCA 60.394 55.000 0.00 0.00 0.00 4.51
1644 1741 0.878961 ACTGTTTCTTCGTCGTGGCC 60.879 55.000 0.00 0.00 0.00 5.36
1674 1771 0.309612 CCACCGCTACAACAACAACC 59.690 55.000 0.00 0.00 0.00 3.77
1706 1811 3.909732 TCTTCCTCATCTCCTCTCTTCC 58.090 50.000 0.00 0.00 0.00 3.46
1708 1813 4.225573 CCATCTTCCTCATCTCCTCTCTT 58.774 47.826 0.00 0.00 0.00 2.85
1709 1814 3.438372 CCCATCTTCCTCATCTCCTCTCT 60.438 52.174 0.00 0.00 0.00 3.10
1710 1815 2.899256 CCCATCTTCCTCATCTCCTCTC 59.101 54.545 0.00 0.00 0.00 3.20
1711 1816 2.427593 CCCCATCTTCCTCATCTCCTCT 60.428 54.545 0.00 0.00 0.00 3.69
1725 1830 1.351017 CAGTACACACCAACCCCATCT 59.649 52.381 0.00 0.00 0.00 2.90
1812 1920 0.877649 AGCCAGCGAATACTGCATCG 60.878 55.000 3.09 3.09 41.81 3.84
1842 1950 1.000771 GTGGGAGGGAGAAAAGGGC 60.001 63.158 0.00 0.00 0.00 5.19
1845 1953 0.322906 GCCAGTGGGAGGGAGAAAAG 60.323 60.000 12.15 0.00 35.59 2.27
1877 1992 1.195448 CGTCAATGGTTGAGCTGTCAC 59.805 52.381 0.00 0.00 41.01 3.67
1910 2025 3.550992 CGCCGAACCGATCCAACG 61.551 66.667 0.00 0.00 0.00 4.10
1928 2043 2.622942 CACCCACCCAATAATGATTCCG 59.377 50.000 0.00 0.00 0.00 4.30
1934 2049 1.437160 GCGCACCCACCCAATAATG 59.563 57.895 0.30 0.00 0.00 1.90
1951 2066 1.664151 GATAAACGTACAGGCACAGGC 59.336 52.381 0.00 0.00 40.13 4.85
1977 2092 6.525121 TCTCAAACAGACGTGAATTTGTAG 57.475 37.500 0.00 1.29 34.40 2.74
1978 2093 6.912203 TTCTCAAACAGACGTGAATTTGTA 57.088 33.333 0.00 0.00 34.40 2.41
1979 2094 5.811399 TTCTCAAACAGACGTGAATTTGT 57.189 34.783 0.00 0.00 34.40 2.83
1988 2103 5.947503 TGCAAATTTTTCTCAAACAGACG 57.052 34.783 0.00 0.00 0.00 4.18
2013 2155 1.082117 GTGCCGACTTCACCATACGG 61.082 60.000 0.00 0.00 45.26 4.02
2025 2167 2.247267 CAACCGAAACGTGCCGAC 59.753 61.111 10.84 0.00 0.00 4.79
2029 2171 2.592287 TCCCCAACCGAAACGTGC 60.592 61.111 0.00 0.00 0.00 5.34
2032 2174 2.025418 CGAGTCCCCAACCGAAACG 61.025 63.158 0.00 0.00 0.00 3.60
2061 2203 1.128692 CAGAAAATCACGGACGCCTTC 59.871 52.381 0.00 0.00 0.00 3.46
2071 2213 2.035832 CCCACAACCCACAGAAAATCAC 59.964 50.000 0.00 0.00 0.00 3.06
2085 2227 2.668550 GCCACCTCGACCCACAAC 60.669 66.667 0.00 0.00 0.00 3.32
2109 2251 2.583593 GCGTCGCTGTCCATCCTC 60.584 66.667 10.68 0.00 0.00 3.71
2139 2281 2.208431 GAATTCTGATCAGCGGTCTGG 58.792 52.381 18.36 0.00 40.69 3.86
2189 2333 2.886391 GCCAACCCAACCTAATTAGCCA 60.886 50.000 6.99 0.00 0.00 4.75
2218 2362 2.298661 ACCCTTCCGGTGGATGGAC 61.299 63.158 16.96 0.00 46.27 4.02
2229 2377 1.298014 CCTGAGCTGTGACCCTTCC 59.702 63.158 0.00 0.00 0.00 3.46
2230 2378 1.298014 CCCTGAGCTGTGACCCTTC 59.702 63.158 0.00 0.00 0.00 3.46
2231 2379 2.900106 GCCCTGAGCTGTGACCCTT 61.900 63.158 0.00 0.00 38.99 3.95
2232 2380 3.325753 GCCCTGAGCTGTGACCCT 61.326 66.667 0.00 0.00 38.99 4.34
2264 2412 0.249489 CTGGATTTCTACCCGCCGAG 60.249 60.000 0.00 0.00 0.00 4.63
2367 2515 4.704833 CTGGAGCGGTGGTGGTGG 62.705 72.222 0.00 0.00 0.00 4.61
2378 2526 5.037385 GGATTAAAGAAAAATCGCTGGAGC 58.963 41.667 0.00 0.00 34.74 4.70
2381 2529 6.799512 AGATGGATTAAAGAAAAATCGCTGG 58.200 36.000 0.00 0.00 34.74 4.85
2383 2531 7.630242 TGAGATGGATTAAAGAAAAATCGCT 57.370 32.000 0.00 0.00 34.74 4.93
2419 2567 1.953017 CCGCTGGATCGACTAGGAG 59.047 63.158 0.00 0.00 0.00 3.69
2420 2568 2.194212 GCCGCTGGATCGACTAGGA 61.194 63.158 0.00 0.00 0.00 2.94
2421 2569 2.336809 GCCGCTGGATCGACTAGG 59.663 66.667 0.00 0.00 0.00 3.02
2422 2570 2.050895 CGCCGCTGGATCGACTAG 60.051 66.667 0.00 0.00 0.00 2.57
2423 2571 2.827190 ACGCCGCTGGATCGACTA 60.827 61.111 0.00 0.00 0.00 2.59
2500 2809 4.217550 AGAGAAGAGGTCACGAGAAAGAAG 59.782 45.833 0.00 0.00 0.00 2.85


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

AutoCloner maintained by Alex Coulton.