Multiple sequence alignment - TraesCS3B01G407500

Loading Multiple Alignment...

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 TraesCS3B01G407500 chr3B 100.000 2648 0 0 1 2648 642825802 642828449 0.000000e+00 4891.0
1 TraesCS3B01G407500 chr3B 85.065 154 19 2 1972 2124 760442679 760442829 1.270000e-33 154.0
2 TraesCS3B01G407500 chr3D 92.534 1634 98 13 711 2333 481534136 481535756 0.000000e+00 2320.0
3 TraesCS3B01G407500 chr3D 86.544 654 55 18 41 665 481533480 481534129 0.000000e+00 689.0
4 TraesCS3B01G407500 chr3D 91.509 318 18 2 2331 2648 481535833 481536141 1.880000e-116 429.0
5 TraesCS3B01G407500 chr3A 90.869 1588 79 17 773 2333 624541395 624542943 0.000000e+00 2069.0
6 TraesCS3B01G407500 chr3A 88.287 794 74 8 1541 2333 6653952 6654727 0.000000e+00 933.0
7 TraesCS3B01G407500 chr3A 87.304 575 50 6 1019 1585 6653349 6653908 1.030000e-178 636.0
8 TraesCS3B01G407500 chr3A 93.769 321 17 1 2331 2648 624543023 624543343 1.840000e-131 479.0
9 TraesCS3B01G407500 chr3A 90.909 319 27 2 2331 2648 6654805 6655122 6.770000e-116 427.0
10 TraesCS3B01G407500 chr3A 85.065 154 22 1 1972 2124 705297240 705297393 3.530000e-34 156.0
11 TraesCS3B01G407500 chr4A 87.031 987 100 13 1356 2333 16846861 16845894 0.000000e+00 1088.0
12 TraesCS3B01G407500 chr4A 89.557 316 31 2 2334 2648 16845813 16845499 1.480000e-107 399.0
13 TraesCS3B01G407500 chr5A 88.146 793 76 7 1541 2333 396390664 396391438 0.000000e+00 928.0
14 TraesCS3B01G407500 chr5A 87.375 602 52 7 992 1585 396390079 396390664 0.000000e+00 669.0
15 TraesCS3B01G407500 chr5A 89.969 319 30 2 2331 2648 396391718 396392035 6.820000e-111 411.0
16 TraesCS3B01G407500 chr1A 86.255 793 73 14 1541 2333 309686459 309687215 0.000000e+00 828.0
17 TraesCS3B01G407500 chr1A 87.708 602 51 6 992 1585 309685873 309686459 0.000000e+00 680.0
18 TraesCS3B01G407500 chr1A 75.159 314 42 13 2336 2648 82661211 82660933 5.990000e-22 115.0
19 TraesCS3B01G407500 chr5D 76.190 189 40 4 41 226 509672111 509672297 7.800000e-16 95.3
20 TraesCS3B01G407500 chrUn 77.344 128 27 2 49 175 334256566 334256440 1.020000e-09 75.0
21 TraesCS3B01G407500 chr2A 85.507 69 8 2 253 319 213090183 213090251 1.320000e-08 71.3


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 TraesCS3B01G407500 chr3B 642825802 642828449 2647 False 4891.000000 4891 100.000000 1 2648 1 chr3B.!!$F1 2647
1 TraesCS3B01G407500 chr3D 481533480 481536141 2661 False 1146.000000 2320 90.195667 41 2648 3 chr3D.!!$F1 2607
2 TraesCS3B01G407500 chr3A 624541395 624543343 1948 False 1274.000000 2069 92.319000 773 2648 2 chr3A.!!$F3 1875
3 TraesCS3B01G407500 chr3A 6653349 6655122 1773 False 665.333333 933 88.833333 1019 2648 3 chr3A.!!$F2 1629
4 TraesCS3B01G407500 chr4A 16845499 16846861 1362 True 743.500000 1088 88.294000 1356 2648 2 chr4A.!!$R1 1292
5 TraesCS3B01G407500 chr5A 396390079 396392035 1956 False 669.333333 928 88.496667 992 2648 3 chr5A.!!$F1 1656
6 TraesCS3B01G407500 chr1A 309685873 309687215 1342 False 754.000000 828 86.981500 992 2333 2 chr1A.!!$F1 1341

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
425 434 0.258774 AACCCCAATGCTCGGCTTAT 59.741 50.0 0.0 0.0 0.0 1.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2403 2868 1.137872 CACAGCTCCATAGACCTGACC 59.862 57.143 0.0 0.0 0.0 4.02 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
27 28 7.760131 ATAATCGAATTTGCCATGTTCTTTG 57.240 32.000 0.00 0.00 0.00 2.77
28 29 4.582701 TCGAATTTGCCATGTTCTTTGT 57.417 36.364 0.00 0.00 0.00 2.83
29 30 4.942852 TCGAATTTGCCATGTTCTTTGTT 58.057 34.783 0.00 0.00 0.00 2.83
30 31 4.744137 TCGAATTTGCCATGTTCTTTGTTG 59.256 37.500 0.00 0.00 0.00 3.33
31 32 4.507388 CGAATTTGCCATGTTCTTTGTTGT 59.493 37.500 0.00 0.00 0.00 3.32
32 33 5.332506 CGAATTTGCCATGTTCTTTGTTGTC 60.333 40.000 0.00 0.00 0.00 3.18
33 34 4.462508 TTTGCCATGTTCTTTGTTGTCA 57.537 36.364 0.00 0.00 0.00 3.58
34 35 4.462508 TTGCCATGTTCTTTGTTGTCAA 57.537 36.364 0.00 0.00 0.00 3.18
35 36 3.779759 TGCCATGTTCTTTGTTGTCAAC 58.220 40.909 8.86 8.86 32.93 3.18
36 37 3.123050 GCCATGTTCTTTGTTGTCAACC 58.877 45.455 13.13 0.00 32.93 3.77
37 38 3.430098 GCCATGTTCTTTGTTGTCAACCA 60.430 43.478 13.13 0.00 32.93 3.67
38 39 4.753233 CCATGTTCTTTGTTGTCAACCAA 58.247 39.130 13.13 7.58 32.93 3.67
39 40 5.174395 CCATGTTCTTTGTTGTCAACCAAA 58.826 37.500 13.13 11.67 34.07 3.28
40 41 5.291614 CCATGTTCTTTGTTGTCAACCAAAG 59.708 40.000 21.91 21.91 34.07 2.77
41 42 5.713792 TGTTCTTTGTTGTCAACCAAAGA 57.286 34.783 24.23 24.23 37.07 2.52
42 43 5.708948 TGTTCTTTGTTGTCAACCAAAGAG 58.291 37.500 25.33 13.92 38.49 2.85
43 44 5.242838 TGTTCTTTGTTGTCAACCAAAGAGT 59.757 36.000 25.33 0.00 38.49 3.24
90 91 1.481363 GGTGGAACTAGCCTACCAGAC 59.519 57.143 11.71 0.87 36.74 3.51
123 124 7.290948 TCCTAGACTTGACAATGGTGATCATAT 59.709 37.037 0.00 0.00 34.44 1.78
127 128 8.680903 AGACTTGACAATGGTGATCATATTTTC 58.319 33.333 0.00 6.75 34.44 2.29
151 152 7.736031 CTAAAACTATTTTAGGCTTTTCGGC 57.264 36.000 11.59 0.00 45.21 5.54
157 158 3.296322 TTTAGGCTTTTCGGCAATGTG 57.704 42.857 0.00 0.00 41.46 3.21
176 177 1.187087 GTCGTTCAGTGGGAGGAGAT 58.813 55.000 0.00 0.00 0.00 2.75
179 180 1.276421 CGTTCAGTGGGAGGAGATGTT 59.724 52.381 0.00 0.00 0.00 2.71
181 182 3.756117 GTTCAGTGGGAGGAGATGTTTT 58.244 45.455 0.00 0.00 0.00 2.43
188 189 4.952335 GTGGGAGGAGATGTTTTCATTGAT 59.048 41.667 0.00 0.00 41.05 2.57
191 192 7.286316 GTGGGAGGAGATGTTTTCATTGATTAT 59.714 37.037 0.00 0.00 41.05 1.28
193 194 7.286316 GGGAGGAGATGTTTTCATTGATTATGT 59.714 37.037 0.00 0.00 41.05 2.29
200 201 5.124617 TGTTTTCATTGATTATGTAGGCGCA 59.875 36.000 10.83 0.00 35.64 6.09
205 206 6.405538 TCATTGATTATGTAGGCGCATATGA 58.594 36.000 10.83 1.50 35.64 2.15
232 233 5.702670 ACTTCGTCAATCAAGATGTGATGTT 59.297 36.000 10.99 0.00 46.80 2.71
249 252 4.701651 TGATGTTGGCTCAGTATTTTGGAG 59.298 41.667 0.00 0.00 0.00 3.86
258 261 4.133820 TCAGTATTTTGGAGGTGTGTGTG 58.866 43.478 0.00 0.00 0.00 3.82
293 297 5.880332 AGTGAGTGTTTGTGTTTGTATGAGT 59.120 36.000 0.00 0.00 0.00 3.41
297 301 5.067674 AGTGTTTGTGTTTGTATGAGTGCAT 59.932 36.000 0.00 0.00 38.54 3.96
298 302 5.173673 GTGTTTGTGTTTGTATGAGTGCATG 59.826 40.000 0.00 0.00 35.94 4.06
309 313 2.510615 GAGTGCATGCGTTTGTACTC 57.489 50.000 14.09 14.81 46.91 2.59
353 362 6.711277 ACTATAAAGCAGGAAGACACATTCA 58.289 36.000 0.00 0.00 0.00 2.57
358 367 2.490903 GCAGGAAGACACATTCAAGCAT 59.509 45.455 0.00 0.00 33.37 3.79
359 368 3.427233 GCAGGAAGACACATTCAAGCATC 60.427 47.826 0.00 0.00 33.37 3.91
373 382 8.982685 ACATTCAAGCATCTATCTATTACAACG 58.017 33.333 0.00 0.00 0.00 4.10
386 395 7.169035 TCTATTACAACGAACTTGTGTGTTC 57.831 36.000 0.49 0.00 43.38 3.18
390 399 4.658071 ACAACGAACTTGTGTGTTCATTC 58.342 39.130 7.91 0.00 44.59 2.67
412 421 8.757877 CATTCTATTTTTCTAATTCCAACCCCA 58.242 33.333 0.00 0.00 0.00 4.96
419 428 1.185315 AATTCCAACCCCAATGCTCG 58.815 50.000 0.00 0.00 0.00 5.03
421 430 3.451894 CCAACCCCAATGCTCGGC 61.452 66.667 0.00 0.00 0.00 5.54
422 431 2.361610 CAACCCCAATGCTCGGCT 60.362 61.111 0.00 0.00 0.00 5.52
424 433 0.679640 CAACCCCAATGCTCGGCTTA 60.680 55.000 0.00 0.00 0.00 3.09
425 434 0.258774 AACCCCAATGCTCGGCTTAT 59.741 50.000 0.00 0.00 0.00 1.73
426 435 1.136828 ACCCCAATGCTCGGCTTATA 58.863 50.000 0.00 0.00 0.00 0.98
432 441 4.338118 CCCAATGCTCGGCTTATAAAAAGA 59.662 41.667 0.00 0.00 0.00 2.52
462 471 6.855836 TCACTATTGCACCTTGAATCAAATC 58.144 36.000 0.00 0.00 0.00 2.17
466 475 4.038271 TGCACCTTGAATCAAATCCTCT 57.962 40.909 0.00 0.00 0.00 3.69
468 477 5.569355 TGCACCTTGAATCAAATCCTCTTA 58.431 37.500 0.00 0.00 0.00 2.10
498 507 5.625311 GTGATCAACATCCAAAGTTCGAAAC 59.375 40.000 0.00 0.00 0.00 2.78
506 515 4.963373 TCCAAAGTTCGAAACCATACTCA 58.037 39.130 0.00 0.00 0.00 3.41
507 516 4.994852 TCCAAAGTTCGAAACCATACTCAG 59.005 41.667 0.00 0.00 0.00 3.35
508 517 4.755123 CCAAAGTTCGAAACCATACTCAGT 59.245 41.667 0.00 0.00 0.00 3.41
525 534 5.657474 ACTCAGTCTCAAGTTCGTTTTACA 58.343 37.500 0.00 0.00 0.00 2.41
526 535 5.749109 ACTCAGTCTCAAGTTCGTTTTACAG 59.251 40.000 0.00 0.00 0.00 2.74
527 536 5.657474 TCAGTCTCAAGTTCGTTTTACAGT 58.343 37.500 0.00 0.00 0.00 3.55
528 537 6.103997 TCAGTCTCAAGTTCGTTTTACAGTT 58.896 36.000 0.00 0.00 0.00 3.16
530 539 7.118680 TCAGTCTCAAGTTCGTTTTACAGTTTT 59.881 33.333 0.00 0.00 0.00 2.43
531 540 8.385111 CAGTCTCAAGTTCGTTTTACAGTTTTA 58.615 33.333 0.00 0.00 0.00 1.52
532 541 9.106070 AGTCTCAAGTTCGTTTTACAGTTTTAT 57.894 29.630 0.00 0.00 0.00 1.40
575 603 1.792367 GTTTGGCCGCATTCTCAAAAC 59.208 47.619 0.00 0.00 32.01 2.43
577 605 1.801512 GGCCGCATTCTCAAAACGC 60.802 57.895 0.00 0.00 0.00 4.84
586 614 2.018542 TCTCAAAACGCGGGAATAGG 57.981 50.000 12.47 0.00 0.00 2.57
589 617 2.745281 CTCAAAACGCGGGAATAGGAAA 59.255 45.455 12.47 0.00 0.00 3.13
626 656 1.208052 AGTGACATCGCCTAGTGCATT 59.792 47.619 0.00 0.00 41.33 3.56
634 664 1.535226 CGCCTAGTGCATTAGCGTGTA 60.535 52.381 18.13 0.00 46.23 2.90
641 671 2.096909 GTGCATTAGCGTGTATAAGCGG 60.097 50.000 0.00 0.00 46.23 5.52
642 672 1.459592 GCATTAGCGTGTATAAGCGGG 59.540 52.381 0.00 0.00 36.36 6.13
643 673 1.459592 CATTAGCGTGTATAAGCGGGC 59.540 52.381 0.00 0.00 36.36 6.13
648 678 1.666311 GCGTGTATAAGCGGGCTCTAG 60.666 57.143 0.00 0.00 0.00 2.43
653 683 1.759459 ATAAGCGGGCTCTAGGCACC 61.759 60.000 5.85 4.00 42.35 5.01
656 686 3.771160 CGGGCTCTAGGCACCGTT 61.771 66.667 17.06 0.00 44.13 4.44
680 710 7.412853 TTTTTGCAAAAGAGGGTAGTAGTTT 57.587 32.000 22.78 0.00 0.00 2.66
681 711 7.412853 TTTTGCAAAAGAGGGTAGTAGTTTT 57.587 32.000 20.46 0.00 0.00 2.43
682 712 7.412853 TTTGCAAAAGAGGGTAGTAGTTTTT 57.587 32.000 10.02 0.00 0.00 1.94
704 734 4.921644 TTTTTGAGGGGTAAGAGGGTAG 57.078 45.455 0.00 0.00 0.00 3.18
705 735 3.572661 TTTGAGGGGTAAGAGGGTAGT 57.427 47.619 0.00 0.00 0.00 2.73
706 736 4.697802 TTTGAGGGGTAAGAGGGTAGTA 57.302 45.455 0.00 0.00 0.00 1.82
707 737 3.967467 TGAGGGGTAAGAGGGTAGTAG 57.033 52.381 0.00 0.00 0.00 2.57
708 738 3.204760 TGAGGGGTAAGAGGGTAGTAGT 58.795 50.000 0.00 0.00 0.00 2.73
709 739 3.599698 TGAGGGGTAAGAGGGTAGTAGTT 59.400 47.826 0.00 0.00 0.00 2.24
710 740 3.959449 GAGGGGTAAGAGGGTAGTAGTTG 59.041 52.174 0.00 0.00 0.00 3.16
711 741 3.339130 AGGGGTAAGAGGGTAGTAGTTGT 59.661 47.826 0.00 0.00 0.00 3.32
712 742 4.545786 AGGGGTAAGAGGGTAGTAGTTGTA 59.454 45.833 0.00 0.00 0.00 2.41
713 743 4.892345 GGGGTAAGAGGGTAGTAGTTGTAG 59.108 50.000 0.00 0.00 0.00 2.74
714 744 5.514169 GGGTAAGAGGGTAGTAGTTGTAGT 58.486 45.833 0.00 0.00 0.00 2.73
715 745 6.353951 GGGGTAAGAGGGTAGTAGTTGTAGTA 60.354 46.154 0.00 0.00 0.00 1.82
726 756 9.136952 GGTAGTAGTTGTAGTACAAAGAATGTG 57.863 37.037 17.16 0.00 43.77 3.21
727 757 9.136952 GTAGTAGTTGTAGTACAAAGAATGTGG 57.863 37.037 17.16 0.00 43.77 4.17
728 758 7.959175 AGTAGTTGTAGTACAAAGAATGTGGA 58.041 34.615 17.16 0.00 43.77 4.02
730 760 9.048446 GTAGTTGTAGTACAAAGAATGTGGAAA 57.952 33.333 17.16 0.00 43.77 3.13
802 834 1.369091 CGGATCTGAAAACCCCAGCG 61.369 60.000 0.00 0.00 0.00 5.18
977 1015 2.511600 GCCAGCCGTTACATCGCT 60.512 61.111 0.00 0.00 0.00 4.93
978 1016 2.526120 GCCAGCCGTTACATCGCTC 61.526 63.158 0.00 0.00 0.00 5.03
979 1017 2.230940 CCAGCCGTTACATCGCTCG 61.231 63.158 0.00 0.00 0.00 5.03
980 1018 1.516386 CAGCCGTTACATCGCTCGT 60.516 57.895 0.00 0.00 0.00 4.18
1195 1244 2.503061 CCCTGCTCATGTCCTCCG 59.497 66.667 0.00 0.00 0.00 4.63
1488 1554 0.748729 ATGAGGAGGAGGACGACGAC 60.749 60.000 0.00 0.00 0.00 4.34
1686 1840 1.376424 CAGCTGCCTTCGACCACAT 60.376 57.895 0.00 0.00 0.00 3.21
1687 1841 0.957395 CAGCTGCCTTCGACCACATT 60.957 55.000 0.00 0.00 0.00 2.71
1775 1930 6.077197 CACCTGTAAAATGTGTGTTGTATCG 58.923 40.000 0.00 0.00 0.00 2.92
1875 2031 9.337396 TGGATTAAGATAATTGCGTTCTTATGT 57.663 29.630 0.00 0.00 33.32 2.29
1888 2044 6.649141 TGCGTTCTTATGTATCTTTCTGTGTT 59.351 34.615 0.00 0.00 0.00 3.32
1889 2045 7.815549 TGCGTTCTTATGTATCTTTCTGTGTTA 59.184 33.333 0.00 0.00 0.00 2.41
1916 2072 8.762481 AATTTACCCCAAGAGATATGGTTTAC 57.238 34.615 0.00 0.00 36.14 2.01
1925 2081 6.749036 AGAGATATGGTTTACCGATCCTTT 57.251 37.500 9.01 0.00 39.43 3.11
1930 2086 8.881262 AGATATGGTTTACCGATCCTTTCTATT 58.119 33.333 9.01 0.00 39.43 1.73
1948 2104 9.968743 CTTTCTATTGTTACATTCCGAAAGTAC 57.031 33.333 15.67 0.00 34.36 2.73
1950 2106 7.537715 TCTATTGTTACATTCCGAAAGTACGA 58.462 34.615 0.00 0.00 35.09 3.43
1952 2108 5.827568 TGTTACATTCCGAAAGTACGAAC 57.172 39.130 0.00 0.00 35.09 3.95
2045 2219 6.825721 CACTTATGGAGCTGGATTCTTTACTT 59.174 38.462 0.00 0.00 0.00 2.24
2084 2259 3.709987 CAGCTTTGTTTGGTGAAGAAGG 58.290 45.455 0.00 0.00 35.20 3.46
2131 2306 5.823209 TGTGATTCTGCAAACTATCCATG 57.177 39.130 0.00 0.00 0.00 3.66
2132 2307 5.499313 TGTGATTCTGCAAACTATCCATGA 58.501 37.500 0.00 0.00 0.00 3.07
2135 2310 7.137426 GTGATTCTGCAAACTATCCATGATTC 58.863 38.462 0.00 0.00 0.00 2.52
2150 2325 6.356556 TCCATGATTCATCGTATTTGAGGTT 58.643 36.000 0.00 0.00 0.00 3.50
2153 2328 4.940654 TGATTCATCGTATTTGAGGTTGCA 59.059 37.500 0.00 0.00 0.00 4.08
2185 2360 3.581770 TGGAAATGGATCATTGGTGCAAA 59.418 39.130 0.00 0.00 34.04 3.68
2237 2413 6.392354 CAATTGATGGTGCTGTTCAGTATTT 58.608 36.000 0.00 0.00 0.00 1.40
2242 2419 4.980573 TGGTGCTGTTCAGTATTTAGGTT 58.019 39.130 1.78 0.00 0.00 3.50
2313 2491 8.020819 TCGAATTTTCATTGTGATGTTTACCTC 58.979 33.333 0.00 0.00 34.77 3.85
2403 2868 8.613060 ACACTATCTTTTATGTATGCCAGATG 57.387 34.615 0.00 0.00 0.00 2.90
2428 2893 2.363680 AGGTCTATGGAGCTGTGATTCG 59.636 50.000 10.27 0.00 46.88 3.34
2432 2897 0.911769 ATGGAGCTGTGATTCGGGAA 59.088 50.000 0.00 0.00 0.00 3.97
2462 2927 2.246719 AATCGATGGCTTAGCTGTCC 57.753 50.000 3.59 0.00 0.00 4.02
2473 2938 4.333926 GGCTTAGCTGTCCAAATAGTTCAG 59.666 45.833 3.59 0.00 0.00 3.02
2620 3085 3.259123 GTCCTGATGGAAAACTGGCAATT 59.741 43.478 0.00 0.00 45.18 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 9.299963 CAAAGAACATGGCAAATTCGATTATAA 57.700 29.630 0.00 0.00 0.00 0.98
2 3 8.465999 ACAAAGAACATGGCAAATTCGATTATA 58.534 29.630 0.00 0.00 0.00 0.98
3 4 7.322664 ACAAAGAACATGGCAAATTCGATTAT 58.677 30.769 0.00 0.00 0.00 1.28
4 5 6.686630 ACAAAGAACATGGCAAATTCGATTA 58.313 32.000 0.00 0.00 0.00 1.75
5 6 5.540911 ACAAAGAACATGGCAAATTCGATT 58.459 33.333 0.00 0.00 0.00 3.34
6 7 5.138125 ACAAAGAACATGGCAAATTCGAT 57.862 34.783 0.00 0.00 0.00 3.59
7 8 4.582701 ACAAAGAACATGGCAAATTCGA 57.417 36.364 0.00 0.00 0.00 3.71
8 9 4.507388 ACAACAAAGAACATGGCAAATTCG 59.493 37.500 0.00 0.00 0.00 3.34
9 10 5.523188 TGACAACAAAGAACATGGCAAATTC 59.477 36.000 0.00 0.00 0.00 2.17
10 11 5.426504 TGACAACAAAGAACATGGCAAATT 58.573 33.333 0.00 0.00 0.00 1.82
11 12 5.021033 TGACAACAAAGAACATGGCAAAT 57.979 34.783 0.00 0.00 0.00 2.32
12 13 4.462508 TGACAACAAAGAACATGGCAAA 57.537 36.364 0.00 0.00 0.00 3.68
13 14 4.180057 GTTGACAACAAAGAACATGGCAA 58.820 39.130 13.52 0.00 38.42 4.52
14 15 3.430098 GGTTGACAACAAAGAACATGGCA 60.430 43.478 19.58 0.00 37.77 4.92
15 16 3.123050 GGTTGACAACAAAGAACATGGC 58.877 45.455 19.58 0.00 37.77 4.40
16 17 4.383850 TGGTTGACAACAAAGAACATGG 57.616 40.909 19.58 0.00 37.77 3.66
24 25 5.588648 CCTAGACTCTTTGGTTGACAACAAA 59.411 40.000 19.58 12.26 39.19 2.83
25 26 5.123227 CCTAGACTCTTTGGTTGACAACAA 58.877 41.667 19.58 5.93 39.19 2.83
26 27 4.163458 ACCTAGACTCTTTGGTTGACAACA 59.837 41.667 19.58 3.77 39.19 3.33
27 28 4.704965 ACCTAGACTCTTTGGTTGACAAC 58.295 43.478 9.97 9.97 39.19 3.32
28 29 4.407621 TGACCTAGACTCTTTGGTTGACAA 59.592 41.667 0.00 0.00 37.28 3.18
29 30 3.964688 TGACCTAGACTCTTTGGTTGACA 59.035 43.478 0.00 0.00 32.30 3.58
30 31 4.281182 TCTGACCTAGACTCTTTGGTTGAC 59.719 45.833 0.00 0.00 32.30 3.18
31 32 4.480115 TCTGACCTAGACTCTTTGGTTGA 58.520 43.478 0.00 5.02 32.30 3.18
32 33 4.873746 TCTGACCTAGACTCTTTGGTTG 57.126 45.455 0.00 3.35 32.30 3.77
33 34 4.223923 CCATCTGACCTAGACTCTTTGGTT 59.776 45.833 0.00 0.00 38.49 3.67
34 35 3.772025 CCATCTGACCTAGACTCTTTGGT 59.228 47.826 0.00 3.80 38.49 3.67
35 36 3.772025 ACCATCTGACCTAGACTCTTTGG 59.228 47.826 0.00 0.00 38.49 3.28
36 37 5.413309 AACCATCTGACCTAGACTCTTTG 57.587 43.478 0.00 0.00 38.49 2.77
37 38 6.257586 ACTAACCATCTGACCTAGACTCTTT 58.742 40.000 0.00 0.00 38.49 2.52
38 39 5.833340 ACTAACCATCTGACCTAGACTCTT 58.167 41.667 0.00 0.00 38.49 2.85
39 40 5.459982 ACTAACCATCTGACCTAGACTCT 57.540 43.478 0.00 0.00 38.49 3.24
40 41 6.378848 AGAAACTAACCATCTGACCTAGACTC 59.621 42.308 0.00 0.00 38.49 3.36
41 42 6.257586 AGAAACTAACCATCTGACCTAGACT 58.742 40.000 0.00 0.00 38.49 3.24
42 43 6.532988 AGAAACTAACCATCTGACCTAGAC 57.467 41.667 0.00 0.00 38.49 2.59
43 44 7.016268 ACAAAGAAACTAACCATCTGACCTAGA 59.984 37.037 0.00 0.00 40.37 2.43
136 137 3.068873 ACACATTGCCGAAAAGCCTAAAA 59.931 39.130 0.00 0.00 0.00 1.52
142 143 0.040425 ACGACACATTGCCGAAAAGC 60.040 50.000 0.00 0.00 0.00 3.51
148 149 0.110688 CACTGAACGACACATTGCCG 60.111 55.000 0.00 0.00 0.00 5.69
151 152 1.800586 CTCCCACTGAACGACACATTG 59.199 52.381 0.00 0.00 0.00 2.82
157 158 1.134965 CATCTCCTCCCACTGAACGAC 60.135 57.143 0.00 0.00 0.00 4.34
176 177 5.124617 TGCGCCTACATAATCAATGAAAACA 59.875 36.000 4.18 0.00 39.07 2.83
179 180 7.390162 TCATATGCGCCTACATAATCAATGAAA 59.610 33.333 4.18 0.00 39.07 2.69
181 182 6.405538 TCATATGCGCCTACATAATCAATGA 58.594 36.000 4.18 0.00 39.07 2.57
188 189 5.405935 AGTCATCATATGCGCCTACATAA 57.594 39.130 4.18 0.00 36.17 1.90
191 192 3.653344 GAAGTCATCATATGCGCCTACA 58.347 45.455 4.18 0.00 0.00 2.74
193 194 2.296190 ACGAAGTCATCATATGCGCCTA 59.704 45.455 4.18 0.00 29.74 3.93
232 233 2.375174 ACACCTCCAAAATACTGAGCCA 59.625 45.455 0.00 0.00 0.00 4.75
249 252 3.682858 ACTTATATGAACGCACACACACC 59.317 43.478 0.00 0.00 0.00 4.16
258 261 6.015504 CACAAACACTCACTTATATGAACGC 58.984 40.000 0.00 0.00 0.00 4.84
293 297 1.877637 ACAGAGTACAAACGCATGCA 58.122 45.000 19.57 0.00 0.00 3.96
297 301 9.784680 TTTTATTTTTAACAGAGTACAAACGCA 57.215 25.926 0.00 0.00 0.00 5.24
332 336 5.105997 GCTTGAATGTGTCTTCCTGCTTTAT 60.106 40.000 0.00 0.00 0.00 1.40
353 362 9.035607 CAAGTTCGTTGTAATAGATAGATGCTT 57.964 33.333 0.00 0.00 0.00 3.91
373 382 9.736023 AGAAAAATAGAATGAACACACAAGTTC 57.264 29.630 0.00 0.00 46.22 3.01
386 395 8.757877 TGGGGTTGGAATTAGAAAAATAGAATG 58.242 33.333 0.00 0.00 0.00 2.67
390 399 7.495606 GCATTGGGGTTGGAATTAGAAAAATAG 59.504 37.037 0.00 0.00 0.00 1.73
401 410 2.886382 CGAGCATTGGGGTTGGAAT 58.114 52.632 0.00 0.00 0.00 3.01
412 421 6.027749 CGTTTCTTTTTATAAGCCGAGCATT 58.972 36.000 0.00 0.00 0.00 3.56
419 428 5.939457 AGTGAGCGTTTCTTTTTATAAGCC 58.061 37.500 0.00 0.00 0.00 4.35
421 430 9.000018 GCAATAGTGAGCGTTTCTTTTTATAAG 58.000 33.333 0.00 0.00 0.00 1.73
422 431 8.508062 TGCAATAGTGAGCGTTTCTTTTTATAA 58.492 29.630 0.00 0.00 0.00 0.98
424 433 6.801862 GTGCAATAGTGAGCGTTTCTTTTTAT 59.198 34.615 0.00 0.00 0.00 1.40
425 434 6.140110 GTGCAATAGTGAGCGTTTCTTTTTA 58.860 36.000 0.00 0.00 0.00 1.52
426 435 4.976116 GTGCAATAGTGAGCGTTTCTTTTT 59.024 37.500 0.00 0.00 0.00 1.94
432 441 2.185004 AGGTGCAATAGTGAGCGTTT 57.815 45.000 0.00 0.00 0.00 3.60
462 471 6.430925 TGGATGTTGATCACAAACTTAAGAGG 59.569 38.462 10.09 0.40 39.50 3.69
466 475 8.006298 ACTTTGGATGTTGATCACAAACTTAA 57.994 30.769 0.00 0.00 39.50 1.85
468 477 6.469782 ACTTTGGATGTTGATCACAAACTT 57.530 33.333 0.00 0.00 39.50 2.66
498 507 4.442375 ACGAACTTGAGACTGAGTATGG 57.558 45.455 0.00 0.00 0.00 2.74
506 515 6.980051 AAACTGTAAAACGAACTTGAGACT 57.020 33.333 0.00 0.00 0.00 3.24
545 573 1.173913 GCGGCCAAACAAATAGTCCT 58.826 50.000 2.24 0.00 0.00 3.85
546 574 0.885196 TGCGGCCAAACAAATAGTCC 59.115 50.000 2.24 0.00 0.00 3.85
559 587 1.801512 GCGTTTTGAGAATGCGGCC 60.802 57.895 0.00 0.00 0.00 6.13
597 625 1.728971 GGCGATGTCACTTCAACTCTG 59.271 52.381 0.00 0.00 0.00 3.35
599 627 2.086054 AGGCGATGTCACTTCAACTC 57.914 50.000 0.00 0.00 0.00 3.01
626 656 0.313043 GAGCCCGCTTATACACGCTA 59.687 55.000 0.00 0.00 0.00 4.26
634 664 1.749033 GTGCCTAGAGCCCGCTTAT 59.251 57.895 0.00 0.00 42.71 1.73
641 671 2.942641 AAAAACGGTGCCTAGAGCC 58.057 52.632 0.00 0.00 42.71 4.70
656 686 7.412853 AAACTACTACCCTCTTTTGCAAAAA 57.587 32.000 23.92 14.27 0.00 1.94
683 713 4.245308 ACTACCCTCTTACCCCTCAAAAA 58.755 43.478 0.00 0.00 0.00 1.94
684 714 3.878086 ACTACCCTCTTACCCCTCAAAA 58.122 45.455 0.00 0.00 0.00 2.44
685 715 3.572661 ACTACCCTCTTACCCCTCAAA 57.427 47.619 0.00 0.00 0.00 2.69
686 716 3.599698 ACTACTACCCTCTTACCCCTCAA 59.400 47.826 0.00 0.00 0.00 3.02
687 717 3.204760 ACTACTACCCTCTTACCCCTCA 58.795 50.000 0.00 0.00 0.00 3.86
688 718 3.959449 CAACTACTACCCTCTTACCCCTC 59.041 52.174 0.00 0.00 0.00 4.30
689 719 3.339130 ACAACTACTACCCTCTTACCCCT 59.661 47.826 0.00 0.00 0.00 4.79
690 720 3.717576 ACAACTACTACCCTCTTACCCC 58.282 50.000 0.00 0.00 0.00 4.95
691 721 5.514169 ACTACAACTACTACCCTCTTACCC 58.486 45.833 0.00 0.00 0.00 3.69
692 722 7.112779 TGTACTACAACTACTACCCTCTTACC 58.887 42.308 0.00 0.00 0.00 2.85
693 723 8.567285 TTGTACTACAACTACTACCCTCTTAC 57.433 38.462 0.00 0.00 32.34 2.34
694 724 9.236006 CTTTGTACTACAACTACTACCCTCTTA 57.764 37.037 0.82 0.00 37.90 2.10
695 725 7.946776 TCTTTGTACTACAACTACTACCCTCTT 59.053 37.037 0.82 0.00 37.90 2.85
696 726 7.465116 TCTTTGTACTACAACTACTACCCTCT 58.535 38.462 0.82 0.00 37.90 3.69
697 727 7.693969 TCTTTGTACTACAACTACTACCCTC 57.306 40.000 0.82 0.00 37.90 4.30
698 728 8.529476 CATTCTTTGTACTACAACTACTACCCT 58.471 37.037 0.82 0.00 37.90 4.34
699 729 8.309656 ACATTCTTTGTACTACAACTACTACCC 58.690 37.037 0.82 0.00 37.90 3.69
700 730 9.136952 CACATTCTTTGTACTACAACTACTACC 57.863 37.037 0.82 0.00 37.90 3.18
701 731 9.136952 CCACATTCTTTGTACTACAACTACTAC 57.863 37.037 0.82 0.00 37.90 2.73
702 732 9.081204 TCCACATTCTTTGTACTACAACTACTA 57.919 33.333 0.82 0.00 37.90 1.82
703 733 7.959175 TCCACATTCTTTGTACTACAACTACT 58.041 34.615 0.82 0.00 37.90 2.57
704 734 8.597662 TTCCACATTCTTTGTACTACAACTAC 57.402 34.615 0.82 0.00 37.90 2.73
705 735 9.616156 TTTTCCACATTCTTTGTACTACAACTA 57.384 29.630 0.82 0.00 37.90 2.24
706 736 8.514330 TTTTCCACATTCTTTGTACTACAACT 57.486 30.769 0.82 0.00 37.90 3.16
754 786 5.359194 ACTTTCACGGTATGGATTCAGAT 57.641 39.130 0.00 0.00 0.00 2.90
764 796 2.602878 CGTGCAGTACTTTCACGGTAT 58.397 47.619 27.19 0.00 46.68 2.73
766 798 2.895039 CGTGCAGTACTTTCACGGT 58.105 52.632 27.19 0.00 46.68 4.83
802 834 0.608308 GGAGCCACCAAGGTTGTACC 60.608 60.000 0.00 0.00 40.61 3.34
804 836 1.373435 CGGAGCCACCAAGGTTGTA 59.627 57.895 0.00 0.00 40.61 2.41
806 838 1.515521 GAACGGAGCCACCAAGGTTG 61.516 60.000 0.00 0.00 40.61 3.77
937 975 1.701545 GGATTCGCGATTGACGGCAA 61.702 55.000 10.88 5.94 42.83 4.52
1180 1229 1.142748 GGACGGAGGACATGAGCAG 59.857 63.158 0.00 0.00 0.00 4.24
1289 1338 4.421479 AGGCGGACGAAGCAGACG 62.421 66.667 0.00 0.00 36.08 4.18
1290 1339 2.507324 GAGGCGGACGAAGCAGAC 60.507 66.667 0.00 0.00 36.08 3.51
1291 1340 4.116328 CGAGGCGGACGAAGCAGA 62.116 66.667 0.00 0.00 36.08 4.26
1292 1341 4.116328 TCGAGGCGGACGAAGCAG 62.116 66.667 0.00 0.00 36.84 4.24
1293 1342 4.415332 GTCGAGGCGGACGAAGCA 62.415 66.667 0.00 0.00 41.31 3.91
1375 1433 4.178214 CATTTGCATCGCCGGCGT 62.178 61.111 44.16 30.06 40.74 5.68
1450 1508 1.299620 CCGGTTCACTCACGAACGT 60.300 57.895 0.00 0.00 45.12 3.99
1457 1515 1.186200 CTCCTCATCCGGTTCACTCA 58.814 55.000 0.00 0.00 0.00 3.41
1686 1840 9.814899 ATAATTCAAACACACAAACTCAATCAA 57.185 25.926 0.00 0.00 0.00 2.57
1687 1841 9.814899 AATAATTCAAACACACAAACTCAATCA 57.185 25.926 0.00 0.00 0.00 2.57
1775 1930 1.745115 TAATGCCGCACTGGTGAGC 60.745 57.895 4.79 7.01 41.21 4.26
1878 2034 9.238368 TCTTGGGGTAAATTATAACACAGAAAG 57.762 33.333 0.00 0.00 0.00 2.62
1916 2072 6.073765 CGGAATGTAACAATAGAAAGGATCGG 60.074 42.308 0.00 0.00 0.00 4.18
1925 2081 7.537715 TCGTACTTTCGGAATGTAACAATAGA 58.462 34.615 15.49 7.93 0.00 1.98
1930 2086 5.531634 AGTTCGTACTTTCGGAATGTAACA 58.468 37.500 15.49 5.37 0.00 2.41
1966 2122 9.905713 TCTCAAAATATGCCTAAGTTTACATCT 57.094 29.630 0.00 0.00 0.00 2.90
1978 2134 8.701908 ACATCACAATATCTCAAAATATGCCT 57.298 30.769 0.00 0.00 0.00 4.75
2015 2171 1.208052 TCCAGCTCCATAAGTGCAGTC 59.792 52.381 0.00 0.00 37.44 3.51
2045 2219 2.964740 CTGCAGTAGCTAACAAGCTCA 58.035 47.619 5.25 0.00 45.00 4.26
2084 2259 4.026886 CGGCAAAAAGAACTGCAAAACTAC 60.027 41.667 0.00 0.00 40.46 2.73
2131 2306 5.266242 GTGCAACCTCAAATACGATGAATC 58.734 41.667 0.00 0.00 0.00 2.52
2132 2307 4.201812 CGTGCAACCTCAAATACGATGAAT 60.202 41.667 0.00 0.00 33.78 2.57
2135 2310 2.415168 ACGTGCAACCTCAAATACGATG 59.585 45.455 0.00 0.00 35.69 3.84
2150 2325 2.355197 CATTTCCACATCCTACGTGCA 58.645 47.619 0.00 0.00 32.85 4.57
2153 2328 3.454447 TGATCCATTTCCACATCCTACGT 59.546 43.478 0.00 0.00 0.00 3.57
2208 2384 1.542915 ACAGCACCATCAATTGCAGTC 59.457 47.619 0.00 0.00 41.48 3.51
2237 2413 6.257849 CGCAGAGCATATTTAACTCAAACCTA 59.742 38.462 0.00 0.00 32.71 3.08
2242 2419 4.201812 GCACGCAGAGCATATTTAACTCAA 60.202 41.667 0.00 0.00 45.32 3.02
2372 2834 7.274367 GCATACATAAAAGATAGTGTTCGACG 58.726 38.462 0.00 0.00 0.00 5.12
2403 2868 1.137872 CACAGCTCCATAGACCTGACC 59.862 57.143 0.00 0.00 0.00 4.02
2428 2893 5.351458 CCATCGATTTCTTTTGGAATTCCC 58.649 41.667 21.90 4.57 33.31 3.97
2432 2897 5.665916 AAGCCATCGATTTCTTTTGGAAT 57.334 34.783 0.00 0.00 33.53 3.01
2462 2927 7.951530 ATTTTCTGTTTGCCTGAACTATTTG 57.048 32.000 0.00 0.00 31.55 2.32
2473 2938 8.413229 TCCATTAAGCTATATTTTCTGTTTGCC 58.587 33.333 0.00 0.00 0.00 4.52
2511 2976 8.364894 GTTCCTTGATAATAAAAACAAGTGGGT 58.635 33.333 0.00 0.00 38.28 4.51
2620 3085 5.661056 ACGAAGAAGATCCTCAACACATA 57.339 39.130 0.00 0.00 0.00 2.29


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

AutoCloner maintained by Alex Coulton.