Multiple sequence alignment - TraesCS6B01G358600

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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 TraesCS6B01G358600 chr6B 100.000 3548 0 0 1 3548 626811004 626814551 0.000000e+00 6553.0
1 TraesCS6B01G358600 chr6B 96.410 1504 52 2 886 2387 626882479 626883982 0.000000e+00 2477.0
2 TraesCS6B01G358600 chr6B 91.778 1569 116 3 888 2443 626458115 626456547 0.000000e+00 2170.0
3 TraesCS6B01G358600 chr6B 90.839 1561 112 14 886 2433 626590621 626589079 0.000000e+00 2061.0
4 TraesCS6B01G358600 chr6B 91.702 699 51 4 1 697 626880582 626881275 0.000000e+00 963.0
5 TraesCS6B01G358600 chr6B 89.158 701 68 6 5 702 626591890 626591195 0.000000e+00 867.0
6 TraesCS6B01G358600 chr6B 95.349 172 7 1 697 867 626590779 626590608 4.510000e-69 272.0
7 TraesCS6B01G358600 chr6B 90.291 206 12 5 2737 2938 626885593 626885794 2.720000e-66 263.0
8 TraesCS6B01G358600 chr6B 89.216 204 18 2 2655 2857 626588452 626588252 5.880000e-63 252.0
9 TraesCS6B01G358600 chr6B 94.771 153 5 3 718 867 626882341 626882493 5.920000e-58 235.0
10 TraesCS6B01G358600 chr6B 83.333 228 23 7 3060 3287 626819987 626820199 2.790000e-46 196.0
11 TraesCS6B01G358600 chr6B 96.154 52 1 1 2470 2521 626884042 626884092 2.270000e-12 84.2
12 TraesCS6B01G358600 chr6D 92.839 1564 110 2 888 2450 417890745 417892307 0.000000e+00 2266.0
13 TraesCS6B01G358600 chr6D 91.672 1549 109 11 888 2433 417695268 417693737 0.000000e+00 2128.0
14 TraesCS6B01G358600 chr6D 90.000 210 17 2 2649 2857 417893751 417893957 5.840000e-68 268.0
15 TraesCS6B01G358600 chr6D 87.121 132 11 6 2654 2782 417892836 417892964 1.030000e-30 145.0
16 TraesCS6B01G358600 chr6D 91.304 92 1 4 3459 3548 417766657 417766743 6.220000e-23 119.0
17 TraesCS6B01G358600 chr6A 93.226 1491 98 3 888 2376 560567665 560569154 0.000000e+00 2191.0
18 TraesCS6B01G358600 chr6A 90.918 1046 78 9 1389 2433 560104775 560103746 0.000000e+00 1389.0
19 TraesCS6B01G358600 chr6A 94.165 617 26 5 2936 3548 560524249 560524859 0.000000e+00 931.0
20 TraesCS6B01G358600 chr6A 91.843 613 37 8 2936 3547 560407700 560408300 0.000000e+00 843.0
21 TraesCS6B01G358600 chr6A 91.843 613 37 8 2936 3547 560479467 560480067 0.000000e+00 843.0
22 TraesCS6B01G358600 chr6A 86.726 226 15 5 3114 3331 560545125 560545343 1.650000e-58 237.0
23 TraesCS6B01G358600 chr6A 89.412 170 14 2 2689 2857 560569648 560569814 9.980000e-51 211.0


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 TraesCS6B01G358600 chr6B 626811004 626814551 3547 False 6553.00 6553 100.000000 1 3548 1 chr6B.!!$F1 3547
1 TraesCS6B01G358600 chr6B 626456547 626458115 1568 True 2170.00 2170 91.778000 888 2443 1 chr6B.!!$R1 1555
2 TraesCS6B01G358600 chr6B 626588252 626591890 3638 True 863.00 2061 91.140500 5 2857 4 chr6B.!!$R2 2852
3 TraesCS6B01G358600 chr6B 626880582 626885794 5212 False 804.44 2477 93.865600 1 2938 5 chr6B.!!$F3 2937
4 TraesCS6B01G358600 chr6D 417693737 417695268 1531 True 2128.00 2128 91.672000 888 2433 1 chr6D.!!$R1 1545
5 TraesCS6B01G358600 chr6D 417890745 417893957 3212 False 893.00 2266 89.986667 888 2857 3 chr6D.!!$F2 1969
6 TraesCS6B01G358600 chr6A 560103746 560104775 1029 True 1389.00 1389 90.918000 1389 2433 1 chr6A.!!$R1 1044
7 TraesCS6B01G358600 chr6A 560567665 560569814 2149 False 1201.00 2191 91.319000 888 2857 2 chr6A.!!$F5 1969
8 TraesCS6B01G358600 chr6A 560524249 560524859 610 False 931.00 931 94.165000 2936 3548 1 chr6A.!!$F3 612
9 TraesCS6B01G358600 chr6A 560407700 560408300 600 False 843.00 843 91.843000 2936 3547 1 chr6A.!!$F1 611
10 TraesCS6B01G358600 chr6A 560479467 560480067 600 False 843.00 843 91.843000 2936 3547 1 chr6A.!!$F2 611

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
525 528 0.767375 ATGGACTGGCTCACACTTGT 59.233 50.0 0.00 0.00 0.0 3.16 F
1530 2589 0.824109 TCACGCTGGTAGCTGCTATT 59.176 50.0 19.58 3.46 39.6 1.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1790 2849 0.402121 GTCTGGCTTGAACCCCTTCT 59.598 55.0 0.0 0.0 0.0 2.85 R
3033 6164 0.233848 CGCCGCTTCTTTTTGTACGT 59.766 50.0 0.0 0.0 0.0 3.57 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
33 34 1.071814 TAGGCTTTTTGGTCGGCGT 59.928 52.632 6.85 0.00 0.00 5.68
77 78 0.895100 TTGCACCATTCAGACCCTGC 60.895 55.000 0.00 0.00 0.00 4.85
104 105 2.270850 GCGGTGATGGGGCACTAA 59.729 61.111 0.00 0.00 38.78 2.24
105 106 1.377987 GCGGTGATGGGGCACTAAA 60.378 57.895 0.00 0.00 38.78 1.85
180 181 1.336148 CGTGGCTGTACAACGAGGTTA 60.336 52.381 12.16 0.00 0.00 2.85
182 183 1.687660 TGGCTGTACAACGAGGTTACA 59.312 47.619 0.00 0.00 0.00 2.41
190 191 4.395959 ACAACGAGGTTACAACAGAGAA 57.604 40.909 0.00 0.00 0.00 2.87
199 200 1.956170 CAACAGAGAAGCACGGCGT 60.956 57.895 6.77 6.77 0.00 5.68
234 235 1.192146 TGGTTGGGGAGAGAAGACGG 61.192 60.000 0.00 0.00 0.00 4.79
365 366 2.750637 GAGAGTGACTCCGGCCGA 60.751 66.667 30.73 12.25 39.53 5.54
387 390 5.220854 CGACATTCTTATTTTCCCGATGCTT 60.221 40.000 0.00 0.00 0.00 3.91
414 417 7.549488 CGAACTGGTTTAAGGTTGAGATAAGAT 59.451 37.037 0.00 0.00 0.00 2.40
473 476 7.998964 GGATTAAGAGGATAAGGTTTGATTCCA 59.001 37.037 0.00 0.00 0.00 3.53
478 481 6.660949 AGAGGATAAGGTTTGATTCCAACAAG 59.339 38.462 3.36 0.00 30.88 3.16
479 482 6.552008 AGGATAAGGTTTGATTCCAACAAGA 58.448 36.000 3.36 0.00 30.88 3.02
494 497 5.104374 CCAACAAGACATATGAATTGGTGC 58.896 41.667 24.73 2.97 38.69 5.01
499 502 6.015180 ACAAGACATATGAATTGGTGCTGTTT 60.015 34.615 20.78 3.51 0.00 2.83
525 528 0.767375 ATGGACTGGCTCACACTTGT 59.233 50.000 0.00 0.00 0.00 3.16
531 534 1.112916 TGGCTCACACTTGTCCGAGA 61.113 55.000 1.82 0.00 0.00 4.04
577 580 4.715534 TCCACACCAAGAACTATGGAAA 57.284 40.909 0.00 0.00 40.56 3.13
588 591 3.066291 ACTATGGAAACGAACATGCCA 57.934 42.857 0.00 0.00 0.00 4.92
753 1803 2.766345 TTTTATAAGCGGTCACGGGT 57.234 45.000 0.00 0.00 41.36 5.28
857 1909 1.067565 CGTTCTAGTGCTCCAGCTGAA 60.068 52.381 17.39 0.00 42.66 3.02
858 1910 2.610479 CGTTCTAGTGCTCCAGCTGAAA 60.610 50.000 17.39 1.42 42.66 2.69
859 1911 2.999355 GTTCTAGTGCTCCAGCTGAAAG 59.001 50.000 17.39 13.33 42.66 2.62
872 1924 1.871080 CTGAAAGCTTGTCGACACCT 58.129 50.000 19.90 14.71 0.00 4.00
873 1925 1.795286 CTGAAAGCTTGTCGACACCTC 59.205 52.381 19.90 10.16 0.00 3.85
874 1926 1.138069 TGAAAGCTTGTCGACACCTCA 59.862 47.619 19.90 13.10 0.00 3.86
875 1927 2.210116 GAAAGCTTGTCGACACCTCAA 58.790 47.619 19.90 1.61 0.00 3.02
876 1928 2.325583 AAGCTTGTCGACACCTCAAA 57.674 45.000 19.90 0.76 0.00 2.69
877 1929 2.325583 AGCTTGTCGACACCTCAAAA 57.674 45.000 19.90 0.00 0.00 2.44
878 1930 2.639065 AGCTTGTCGACACCTCAAAAA 58.361 42.857 19.90 0.00 0.00 1.94
928 1980 2.420890 GCCGCCTCTCCATCTCTG 59.579 66.667 0.00 0.00 0.00 3.35
949 2001 4.697756 CTTCCTCCACCCGCGCAA 62.698 66.667 8.75 0.00 0.00 4.85
970 2022 3.353836 GCCACTTCAAAGCCGCGA 61.354 61.111 8.23 0.00 0.00 5.87
1530 2589 0.824109 TCACGCTGGTAGCTGCTATT 59.176 50.000 19.58 3.46 39.60 1.73
1790 2849 0.451383 CATTTCGAGGCAATGCGGAA 59.549 50.000 0.00 0.00 0.00 4.30
1830 2889 2.963320 GTGACGTTCACGGGCGTT 60.963 61.111 4.07 0.00 44.95 4.84
1881 2940 0.395448 ACGAGGGGCTGAGGTACTAC 60.395 60.000 0.00 0.00 41.55 2.73
1884 2943 0.333993 AGGGGCTGAGGTACTACGAA 59.666 55.000 0.00 0.00 41.55 3.85
1904 2969 2.580815 CATGAGGGCAGAGCACGA 59.419 61.111 0.00 0.00 36.86 4.35
2289 3354 1.832608 CGGGGATCGGTCTCATCCA 60.833 63.158 0.00 0.00 41.68 3.41
2412 3528 2.613223 GGCTTTCAGTAGTCACCAGGTC 60.613 54.545 0.00 0.00 0.00 3.85
2451 3747 0.528249 AAAAGCTGCTGTTGTTGCGG 60.528 50.000 3.82 0.00 39.61 5.69
2467 3763 1.376683 CGGCTCCCGTTTCATCCAA 60.377 57.895 0.00 0.00 42.73 3.53
2468 3764 1.644786 CGGCTCCCGTTTCATCCAAC 61.645 60.000 0.00 0.00 42.73 3.77
2510 3828 5.191426 ACAGGTGATGAGATGGATCTTTTG 58.809 41.667 0.00 0.00 37.25 2.44
2515 3833 2.632377 TGAGATGGATCTTTTGCCGTC 58.368 47.619 0.00 0.00 39.89 4.79
2521 3839 1.429463 GATCTTTTGCCGTCGACAGT 58.571 50.000 17.16 0.00 0.00 3.55
2522 3840 1.126846 GATCTTTTGCCGTCGACAGTG 59.873 52.381 17.16 4.33 0.00 3.66
2526 3863 2.157834 TTTGCCGTCGACAGTGTAAT 57.842 45.000 17.16 0.00 0.00 1.89
2565 3902 3.999001 CACATGGCTTATCATCGTATGCT 59.001 43.478 0.00 0.00 0.00 3.79
2574 3911 3.273919 TCATCGTATGCTCATCTCGTG 57.726 47.619 0.00 0.00 0.00 4.35
2575 3912 2.878406 TCATCGTATGCTCATCTCGTGA 59.122 45.455 0.00 0.00 35.05 4.35
2611 3965 9.467258 GATCAGTTCAATCAAACAAATTTCTGA 57.533 29.630 0.00 0.00 0.00 3.27
2661 5789 8.634475 TGAACTGATAACGTTAGAAGATCATG 57.366 34.615 20.00 13.08 0.00 3.07
2701 5829 5.221742 ACCTACTCCTCTTTCAAAGACAAGG 60.222 44.000 0.00 0.00 33.12 3.61
2707 5835 1.889170 CTTTCAAAGACAAGGGGGAGC 59.111 52.381 0.00 0.00 0.00 4.70
2708 5836 0.250727 TTCAAAGACAAGGGGGAGCG 60.251 55.000 0.00 0.00 0.00 5.03
2772 5901 2.762535 AACTATGGTGACCTCCAACG 57.237 50.000 2.11 0.00 41.09 4.10
2776 5905 1.779061 ATGGTGACCTCCAACGGCTT 61.779 55.000 2.11 0.00 41.09 4.35
2782 5911 1.480954 GACCTCCAACGGCTTGATAGA 59.519 52.381 0.00 0.00 0.00 1.98
2783 5912 2.103263 GACCTCCAACGGCTTGATAGAT 59.897 50.000 0.00 0.00 0.00 1.98
2784 5913 3.305720 ACCTCCAACGGCTTGATAGATA 58.694 45.455 0.00 0.00 0.00 1.98
2785 5914 3.709653 ACCTCCAACGGCTTGATAGATAA 59.290 43.478 0.00 0.00 0.00 1.75
2807 5936 1.446907 AGAAGAGAACATGGCGCAAG 58.553 50.000 10.83 0.00 43.44 4.01
2848 5977 4.584327 AGTTACACCCAAACAAGCATTC 57.416 40.909 0.00 0.00 0.00 2.67
2857 5986 2.101640 AACAAGCATTCCCCTGGTTT 57.898 45.000 0.00 0.00 34.78 3.27
2858 5987 1.341080 ACAAGCATTCCCCTGGTTTG 58.659 50.000 0.00 0.00 34.78 2.93
2892 6021 7.998964 AGAGAAACAAAAAGACCTTCTCCATAA 59.001 33.333 6.52 0.00 41.86 1.90
2908 6037 6.811954 TCTCCATAAGTTGGTTTGGAAAAAC 58.188 36.000 0.00 0.00 46.52 2.43
2912 6043 7.883311 TCCATAAGTTGGTTTGGAAAAACAAAA 59.117 29.630 4.85 0.00 46.52 2.44
2925 6056 8.073467 TGGAAAAACAAAAGTTAGGAATGAGT 57.927 30.769 0.00 0.00 0.00 3.41
2975 6106 2.317609 GCACGAGCGGCTCTTCAAA 61.318 57.895 25.96 0.00 0.00 2.69
3020 6151 8.592155 CGTCGTATGTTGATTTCTTGAAGAATA 58.408 33.333 8.64 0.76 33.67 1.75
3028 6159 8.725148 GTTGATTTCTTGAAGAATAGAAGCAGA 58.275 33.333 8.64 0.00 33.67 4.26
3033 6164 6.455647 TCTTGAAGAATAGAAGCAGACGAAA 58.544 36.000 0.00 0.00 0.00 3.46
3040 6171 3.088194 AGAAGCAGACGAAACGTACAA 57.912 42.857 0.00 0.00 41.37 2.41
3079 6210 3.039134 CCGGTTGGTGTTGGCTTC 58.961 61.111 0.00 0.00 0.00 3.86
3085 6216 0.187117 TTGGTGTTGGCTTCATGGGA 59.813 50.000 0.00 0.00 0.00 4.37
3086 6217 0.251297 TGGTGTTGGCTTCATGGGAG 60.251 55.000 0.00 0.00 0.00 4.30
3092 6223 3.209410 GTTGGCTTCATGGGAGTGATAG 58.791 50.000 0.00 0.00 0.00 2.08
3117 6248 5.435291 CTGCTTGGTAGAGAAATGGAGATT 58.565 41.667 0.00 0.00 0.00 2.40
3127 6258 7.429374 AGAGAAATGGAGATTGTCTATGTGA 57.571 36.000 0.00 0.00 0.00 3.58
3152 6283 2.104967 TGGAGTCGACCGGTTCATAAT 58.895 47.619 9.42 0.00 0.00 1.28
3153 6284 2.498481 TGGAGTCGACCGGTTCATAATT 59.502 45.455 9.42 0.00 0.00 1.40
3154 6285 3.700539 TGGAGTCGACCGGTTCATAATTA 59.299 43.478 9.42 0.00 0.00 1.40
3155 6286 4.160065 TGGAGTCGACCGGTTCATAATTAA 59.840 41.667 9.42 0.00 0.00 1.40
3167 6298 6.367695 CGGTTCATAATTAAGATCCATACGCA 59.632 38.462 14.89 0.00 0.00 5.24
3233 6364 1.453669 CCTCCCTCCTAGCCATTGC 59.546 63.158 0.00 0.00 37.95 3.56
3286 6417 5.529800 TGCATGTGATTATGGATGAGTCTTG 59.470 40.000 0.00 0.00 0.00 3.02
3299 6430 0.615331 AGTCTTGGATGATGCACCGT 59.385 50.000 0.00 0.00 0.00 4.83
3378 6509 8.696374 TGTTCCCTATTAAATCACAAAACAACA 58.304 29.630 0.00 0.00 0.00 3.33
3430 6562 0.837272 AACATACACCATCCCTCCCG 59.163 55.000 0.00 0.00 0.00 5.14
3501 6636 0.036732 TGCTGGAGGCTACAAGTTGG 59.963 55.000 7.96 0.00 42.39 3.77
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 4.387559 CACTTATTTCGATCAACACACGGA 59.612 41.667 0.00 0.00 0.00 4.69
94 95 1.072266 ACCATCACTTTAGTGCCCCA 58.928 50.000 5.00 0.00 45.25 4.96
104 105 3.452264 TGTCTAGCTATGCACCATCACTT 59.548 43.478 0.00 0.00 0.00 3.16
105 106 3.033909 TGTCTAGCTATGCACCATCACT 58.966 45.455 0.00 0.00 0.00 3.41
118 119 0.399233 GGATCCCCACCTGTCTAGCT 60.399 60.000 0.00 0.00 0.00 3.32
145 146 0.809636 CCACGTTGTGCAGAGTCACA 60.810 55.000 0.00 0.00 44.39 3.58
151 152 0.878523 GTACAGCCACGTTGTGCAGA 60.879 55.000 1.62 0.00 30.98 4.26
159 160 1.006571 CCTCGTTGTACAGCCACGT 60.007 57.895 15.93 0.00 0.00 4.49
180 181 1.956170 CGCCGTGCTTCTCTGTTGT 60.956 57.895 0.00 0.00 0.00 3.32
182 183 0.032952 TTACGCCGTGCTTCTCTGTT 59.967 50.000 0.00 0.00 0.00 3.16
308 309 1.553308 GTCCGCACGTATTACCTCAC 58.447 55.000 0.00 0.00 0.00 3.51
309 310 0.457035 GGTCCGCACGTATTACCTCA 59.543 55.000 0.00 0.00 0.00 3.86
345 346 1.979693 GGCCGGAGTCACTCTCTGT 60.980 63.158 5.05 0.00 45.40 3.41
365 366 5.220854 CGAAGCATCGGGAAAATAAGAATGT 60.221 40.000 2.82 0.00 45.32 2.71
387 390 4.675976 TCTCAACCTTAAACCAGTTCGA 57.324 40.909 0.00 0.00 0.00 3.71
434 437 7.374975 TCCTCTTAATCCCTAAAATCGACAT 57.625 36.000 0.00 0.00 0.00 3.06
437 440 8.594550 CCTTATCCTCTTAATCCCTAAAATCGA 58.405 37.037 0.00 0.00 0.00 3.59
466 469 7.396907 ACCAATTCATATGTCTTGTTGGAATCA 59.603 33.333 21.96 0.00 38.33 2.57
473 476 5.477984 ACAGCACCAATTCATATGTCTTGTT 59.522 36.000 1.90 0.00 0.00 2.83
499 502 3.068024 GTGTGAGCCAGTCCATTCAAAAA 59.932 43.478 0.00 0.00 0.00 1.94
525 528 1.136774 CATCGTCGTGCTTCTCGGA 59.863 57.895 0.00 0.00 0.00 4.55
531 534 1.157257 TTGTGTGCATCGTCGTGCTT 61.157 50.000 16.80 0.00 45.27 3.91
577 580 1.152860 TGGTTGGTGGCATGTTCGT 60.153 52.632 0.00 0.00 0.00 3.85
739 1789 1.290955 CTTGACCCGTGACCGCTTA 59.709 57.895 0.00 0.00 0.00 3.09
753 1803 2.075355 AAATGGGCCGGTCCACTTGA 62.075 55.000 34.46 7.41 39.97 3.02
829 1881 2.122783 AGCACTAGAACGAGAGCTCT 57.877 50.000 18.28 18.28 38.82 4.09
857 1909 2.325583 TTTGAGGTGTCGACAAGCTT 57.674 45.000 21.95 4.99 0.00 3.74
858 1910 2.325583 TTTTGAGGTGTCGACAAGCT 57.674 45.000 21.95 18.37 0.00 3.74
879 1931 2.481276 GCCGACAAGCTTTCAGGTTTTT 60.481 45.455 0.00 0.00 32.99 1.94
880 1932 1.067060 GCCGACAAGCTTTCAGGTTTT 59.933 47.619 0.00 0.00 32.99 2.43
881 1933 0.668535 GCCGACAAGCTTTCAGGTTT 59.331 50.000 0.00 0.00 32.99 3.27
882 1934 1.172812 GGCCGACAAGCTTTCAGGTT 61.173 55.000 0.00 0.00 36.17 3.50
883 1935 1.600916 GGCCGACAAGCTTTCAGGT 60.601 57.895 0.00 0.00 0.00 4.00
884 1936 0.962356 ATGGCCGACAAGCTTTCAGG 60.962 55.000 0.00 0.88 0.00 3.86
885 1937 0.169672 CATGGCCGACAAGCTTTCAG 59.830 55.000 0.00 0.00 0.00 3.02
886 1938 1.243342 CCATGGCCGACAAGCTTTCA 61.243 55.000 0.00 0.00 0.00 2.69
928 1980 2.579738 GCGGGTGGAGGAAGACTC 59.420 66.667 0.00 0.00 45.84 3.36
949 2001 3.660111 GGCTTTGAAGTGGCGCGT 61.660 61.111 8.43 0.00 0.00 6.01
1373 2432 1.669760 GGCATTCCGTCGAACACCA 60.670 57.895 0.00 0.00 0.00 4.17
1790 2849 0.402121 GTCTGGCTTGAACCCCTTCT 59.598 55.000 0.00 0.00 0.00 2.85
1860 2919 1.681327 GTACCTCAGCCCCTCGTCA 60.681 63.158 0.00 0.00 0.00 4.35
1904 2969 2.107750 CCATCCTCGCTGCGATGT 59.892 61.111 26.15 11.42 35.17 3.06
2289 3354 3.537206 GAACACCTCCGCAGCCTGT 62.537 63.158 0.00 0.00 0.00 4.00
2358 3423 3.881089 TGCATTCCAGTGCTCATTCATAG 59.119 43.478 0.34 0.00 45.27 2.23
2412 3528 2.138596 ACAAATGCTTGAAACGCAGG 57.861 45.000 0.00 0.00 41.22 4.85
2451 3747 1.133025 CATGTTGGATGAAACGGGAGC 59.867 52.381 0.00 0.00 32.47 4.70
2464 3760 9.249457 CTGTATCTGTATTACTGTACATGTTGG 57.751 37.037 2.30 0.00 34.33 3.77
2465 3761 9.249457 CCTGTATCTGTATTACTGTACATGTTG 57.751 37.037 2.30 0.00 34.33 3.33
2467 3763 8.414003 CACCTGTATCTGTATTACTGTACATGT 58.586 37.037 2.69 2.69 34.33 3.21
2468 3764 8.630037 TCACCTGTATCTGTATTACTGTACATG 58.370 37.037 0.00 0.00 34.33 3.21
2510 3828 1.992170 AGAATTACACTGTCGACGGC 58.008 50.000 24.25 6.06 0.00 5.68
2515 3833 6.706055 TGCTTCTAAAGAATTACACTGTCG 57.294 37.500 0.00 0.00 33.01 4.35
2521 3839 8.402798 TGTGGATTTGCTTCTAAAGAATTACA 57.597 30.769 0.00 0.00 33.01 2.41
2522 3840 9.294030 CATGTGGATTTGCTTCTAAAGAATTAC 57.706 33.333 0.00 0.00 33.01 1.89
2526 3863 5.336690 GCCATGTGGATTTGCTTCTAAAGAA 60.337 40.000 2.55 0.00 37.39 2.52
2603 3940 7.035612 GTGTTGTTCTTCACCTTTCAGAAATT 58.964 34.615 0.00 0.00 0.00 1.82
2611 3965 3.509575 TGCTTGTGTTGTTCTTCACCTTT 59.490 39.130 0.00 0.00 34.14 3.11
2661 5789 7.783042 AGGAGTAGGTGAGTACAAATGAATAC 58.217 38.462 0.00 0.00 0.00 1.89
2668 5796 5.836898 TGAAAGAGGAGTAGGTGAGTACAAA 59.163 40.000 0.00 0.00 0.00 2.83
2673 5801 5.011227 GTCTTTGAAAGAGGAGTAGGTGAGT 59.989 44.000 8.06 0.00 38.41 3.41
2701 5829 3.963428 AGACATGTATATTCGCTCCCC 57.037 47.619 0.00 0.00 0.00 4.81
2707 5835 9.158364 GTGCACAAATAAAGACATGTATATTCG 57.842 33.333 13.17 0.00 0.00 3.34
2750 5878 4.119862 CGTTGGAGGTCACCATAGTTATG 58.880 47.826 0.00 0.00 39.82 1.90
2772 5901 9.988815 TGTTCTCTTCTTATTATCTATCAAGCC 57.011 33.333 0.00 0.00 0.00 4.35
2776 5905 9.935241 GCCATGTTCTCTTCTTATTATCTATCA 57.065 33.333 0.00 0.00 0.00 2.15
2782 5911 5.368145 TGCGCCATGTTCTCTTCTTATTAT 58.632 37.500 4.18 0.00 0.00 1.28
2783 5912 4.765273 TGCGCCATGTTCTCTTCTTATTA 58.235 39.130 4.18 0.00 0.00 0.98
2784 5913 3.609853 TGCGCCATGTTCTCTTCTTATT 58.390 40.909 4.18 0.00 0.00 1.40
2785 5914 3.266510 TGCGCCATGTTCTCTTCTTAT 57.733 42.857 4.18 0.00 0.00 1.73
2815 5944 8.266473 TGTTTGGGTGTAACTTTCTAACTAGAA 58.734 33.333 0.00 0.00 40.33 2.10
2848 5977 2.132996 TTGCAGTGCAAACCAGGGG 61.133 57.895 27.79 0.00 45.96 4.79
2857 5986 3.865011 TTTTGTTTCTCTTGCAGTGCA 57.135 38.095 15.37 15.37 36.47 4.57
2858 5987 4.266265 GTCTTTTTGTTTCTCTTGCAGTGC 59.734 41.667 8.58 8.58 0.00 4.40
2892 6021 7.389330 CCTAACTTTTGTTTTTCCAAACCAACT 59.611 33.333 0.00 0.00 41.60 3.16
2908 6037 5.530915 TGGTGTCACTCATTCCTAACTTTTG 59.469 40.000 2.35 0.00 0.00 2.44
2912 6043 4.160329 TCTGGTGTCACTCATTCCTAACT 58.840 43.478 2.35 0.00 0.00 2.24
2925 6056 2.754472 CACATCGTCTTTCTGGTGTCA 58.246 47.619 0.00 0.00 0.00 3.58
3020 6151 2.787601 TGTACGTTTCGTCTGCTTCT 57.212 45.000 0.00 0.00 41.54 2.85
3028 6159 3.544637 CCGCTTCTTTTTGTACGTTTCGT 60.545 43.478 0.00 0.00 44.35 3.85
3033 6164 0.233848 CGCCGCTTCTTTTTGTACGT 59.766 50.000 0.00 0.00 0.00 3.57
3040 6171 0.889186 ACCATGTCGCCGCTTCTTTT 60.889 50.000 0.00 0.00 0.00 2.27
3079 6210 0.763652 AGCAGCCTATCACTCCCATG 59.236 55.000 0.00 0.00 0.00 3.66
3085 6216 2.697751 CTCTACCAAGCAGCCTATCACT 59.302 50.000 0.00 0.00 0.00 3.41
3086 6217 2.695666 TCTCTACCAAGCAGCCTATCAC 59.304 50.000 0.00 0.00 0.00 3.06
3092 6223 2.019984 CCATTTCTCTACCAAGCAGCC 58.980 52.381 0.00 0.00 0.00 4.85
3152 6283 4.746535 TGTCCTTGCGTATGGATCTTAA 57.253 40.909 11.22 0.00 33.24 1.85
3153 6284 4.746535 TTGTCCTTGCGTATGGATCTTA 57.253 40.909 11.22 0.00 33.24 2.10
3154 6285 3.627395 TTGTCCTTGCGTATGGATCTT 57.373 42.857 11.22 0.00 33.24 2.40
3155 6286 3.627395 TTTGTCCTTGCGTATGGATCT 57.373 42.857 11.22 0.00 33.24 2.75
3286 6417 3.565482 ACAAATATGACGGTGCATCATCC 59.435 43.478 4.58 0.00 37.89 3.51
3333 6464 8.650490 AGGGAACATAAACATCATTTTCTTTGT 58.350 29.630 0.00 0.00 0.00 2.83
3370 6501 4.220602 GCTGGATGGGACTTATGTTGTTTT 59.779 41.667 0.00 0.00 0.00 2.43
3371 6502 3.763897 GCTGGATGGGACTTATGTTGTTT 59.236 43.478 0.00 0.00 0.00 2.83
3378 6509 2.053244 CTCTGGCTGGATGGGACTTAT 58.947 52.381 0.00 0.00 0.00 1.73
3430 6562 1.375523 ACGGGCAAATCTCACGACC 60.376 57.895 0.00 0.00 0.00 4.79


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

AutoCloner maintained by Alex Coulton.