Multiple sequence alignment - TraesCS7B01G141000

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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 TraesCS7B01G141000 chr7B 100.000 5159 0 0 1 5159 179245857 179251015 0.000000e+00 9527
1 TraesCS7B01G141000 chr7B 92.455 729 51 4 1 727 679104333 679105059 0.000000e+00 1038
2 TraesCS7B01G141000 chr7B 92.632 190 14 0 3776 3965 443646512 443646323 1.830000e-69 274
3 TraesCS7B01G141000 chr7A 92.001 3863 176 62 732 4505 232597959 232594141 0.000000e+00 5299
4 TraesCS7B01G141000 chr7A 95.807 644 22 2 4516 5159 232594052 232593414 0.000000e+00 1035
5 TraesCS7B01G141000 chr7D 97.526 1859 42 2 2650 4505 220288531 220286674 0.000000e+00 3175
6 TraesCS7B01G141000 chr7D 92.269 1966 77 28 732 2654 220290498 220288565 0.000000e+00 2719
7 TraesCS7B01G141000 chr7D 96.118 644 18 4 4516 5159 220286592 220285956 0.000000e+00 1044
8 TraesCS7B01G141000 chr2D 93.631 738 43 4 1 736 520039429 520040164 0.000000e+00 1099
9 TraesCS7B01G141000 chr4B 92.828 739 46 7 1 736 377799548 377798814 0.000000e+00 1064
10 TraesCS7B01G141000 chr4B 90.968 310 28 0 3770 4079 605162688 605162997 7.990000e-113 418
11 TraesCS7B01G141000 chr1B 93.122 727 48 2 1 727 639087450 639086726 0.000000e+00 1064
12 TraesCS7B01G141000 chr1B 90.691 376 26 8 2121 2490 608360728 608361100 4.640000e-135 492
13 TraesCS7B01G141000 chr1B 96.053 76 3 0 2038 2113 608360611 608360686 1.950000e-24 124
14 TraesCS7B01G141000 chr2B 93.004 729 47 4 1 727 406114021 406114747 0.000000e+00 1061
15 TraesCS7B01G141000 chr5D 92.740 730 47 5 1 728 30811468 30812193 0.000000e+00 1050
16 TraesCS7B01G141000 chr3B 92.141 738 51 7 1 735 421109950 421110683 0.000000e+00 1035
17 TraesCS7B01G141000 chr3B 90.957 376 25 8 2121 2490 12027114 12027486 9.980000e-137 497
18 TraesCS7B01G141000 chr3B 96.053 76 3 0 2038 2113 12026997 12027072 1.950000e-24 124
19 TraesCS7B01G141000 chr5B 92.318 729 52 4 1 727 710360703 710361429 0.000000e+00 1033
20 TraesCS7B01G141000 chr5B 90.576 382 27 8 2121 2496 6849496 6849118 9.980000e-137 497
21 TraesCS7B01G141000 chr5B 94.737 76 4 0 2038 2113 6849613 6849538 9.070000e-23 119
22 TraesCS7B01G141000 chr6B 91.973 735 55 4 2 734 652706840 652706108 0.000000e+00 1027
23 TraesCS7B01G141000 chr6D 90.929 463 29 10 2041 2496 226683360 226682904 1.230000e-170 610
24 TraesCS7B01G141000 chr6A 91.223 376 24 8 2121 2490 607431977 607432349 2.140000e-138 503
25 TraesCS7B01G141000 chr6A 90.314 382 26 9 2121 2496 61396382 61396006 1.670000e-134 490
26 TraesCS7B01G141000 chr6A 89.137 313 34 0 3770 4082 449815563 449815875 1.740000e-104 390
27 TraesCS7B01G141000 chr6A 86.581 313 35 5 3770 4082 22031165 22030860 6.400000e-89 339
28 TraesCS7B01G141000 chr6A 96.053 76 3 0 2038 2113 607431860 607431935 1.950000e-24 124
29 TraesCS7B01G141000 chr5A 91.223 376 24 8 2121 2490 324949128 324949500 2.140000e-138 503
30 TraesCS7B01G141000 chr5A 96.053 76 3 0 2038 2113 324949011 324949086 1.950000e-24 124
31 TraesCS7B01G141000 chr4A 91.964 224 17 1 3769 3992 564740352 564740574 3.880000e-81 313
32 TraesCS7B01G141000 chrUn 94.382 89 5 0 2408 2496 434647769 434647681 2.510000e-28 137


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 TraesCS7B01G141000 chr7B 179245857 179251015 5158 False 9527.000000 9527 100.000000 1 5159 1 chr7B.!!$F1 5158
1 TraesCS7B01G141000 chr7B 679104333 679105059 726 False 1038.000000 1038 92.455000 1 727 1 chr7B.!!$F2 726
2 TraesCS7B01G141000 chr7A 232593414 232597959 4545 True 3167.000000 5299 93.904000 732 5159 2 chr7A.!!$R1 4427
3 TraesCS7B01G141000 chr7D 220285956 220290498 4542 True 2312.666667 3175 95.304333 732 5159 3 chr7D.!!$R1 4427
4 TraesCS7B01G141000 chr2D 520039429 520040164 735 False 1099.000000 1099 93.631000 1 736 1 chr2D.!!$F1 735
5 TraesCS7B01G141000 chr4B 377798814 377799548 734 True 1064.000000 1064 92.828000 1 736 1 chr4B.!!$R1 735
6 TraesCS7B01G141000 chr1B 639086726 639087450 724 True 1064.000000 1064 93.122000 1 727 1 chr1B.!!$R1 726
7 TraesCS7B01G141000 chr2B 406114021 406114747 726 False 1061.000000 1061 93.004000 1 727 1 chr2B.!!$F1 726
8 TraesCS7B01G141000 chr5D 30811468 30812193 725 False 1050.000000 1050 92.740000 1 728 1 chr5D.!!$F1 727
9 TraesCS7B01G141000 chr3B 421109950 421110683 733 False 1035.000000 1035 92.141000 1 735 1 chr3B.!!$F1 734
10 TraesCS7B01G141000 chr5B 710360703 710361429 726 False 1033.000000 1033 92.318000 1 727 1 chr5B.!!$F1 726
11 TraesCS7B01G141000 chr6B 652706108 652706840 732 True 1027.000000 1027 91.973000 2 734 1 chr6B.!!$R1 732


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
865 876 0.315869 CTCGCACGCGACAAAAGTTT 60.316 50.000 15.93 0.0 44.01 2.66 F
1444 1506 0.662619 TACCGTACCAATCGCTACCG 59.337 55.000 0.00 0.0 0.00 4.02 F
1953 2027 0.460987 GGATCAGTGACTCCCTTGCG 60.461 60.000 0.00 0.0 0.00 4.85 F
2061 2135 1.144936 GCTTGAGTCCCGCATAGCT 59.855 57.895 0.00 0.0 0.00 3.32 F
3903 4029 1.068541 GCAAGTTACAAAAGGCTCCGG 60.069 52.381 0.00 0.0 0.00 5.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1692 1766 0.459237 CTGCAACTACAGCCTCTCCG 60.459 60.000 0.00 0.00 0.00 4.63 R
2393 2476 0.532115 ATTTTGGAAGCGATGGCACC 59.468 50.000 1.50 5.77 43.41 5.01 R
3107 3233 1.129917 ATCTGACTGGGAGCCATGAG 58.870 55.000 0.00 0.00 30.82 2.90 R
3980 4106 0.536006 AGCGGCTTCAGCTTCTTTGT 60.536 50.000 0.00 0.00 43.24 2.83 R
4824 5032 2.575993 CCAGAGGCTCCAGTGACG 59.424 66.667 11.71 0.00 0.00 4.35 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
25 26 2.009774 GTAGTTGCCATGTCGCTGAAT 58.990 47.619 0.00 0.00 0.00 2.57
103 105 5.540337 CCATGTATGGTCTGGTCTACTGTAT 59.460 44.000 2.66 0.00 43.05 2.29
302 309 1.446907 AAAGAGAGTTGCCATCTGCG 58.553 50.000 0.00 0.00 45.60 5.18
315 322 1.008875 ATCTGCGTACGTGCACACTG 61.009 55.000 18.64 2.84 40.62 3.66
317 324 2.355363 GCGTACGTGCACACTGGA 60.355 61.111 18.64 0.00 34.15 3.86
462 471 1.304217 GTGTGGGAGAGGAGACGGA 60.304 63.158 0.00 0.00 0.00 4.69
509 518 1.301716 CACTAGCCCTTGTGCGTGT 60.302 57.895 0.00 0.00 36.02 4.49
520 529 0.391793 TGTGCGTGTGTGGAAAGTGA 60.392 50.000 0.00 0.00 0.00 3.41
545 554 2.721231 GCAAACTGCTGAACGCCA 59.279 55.556 0.00 0.00 40.96 5.69
579 588 4.347096 CGTGTGGTGAAACGGCTA 57.653 55.556 0.00 0.00 38.12 3.93
623 632 1.152118 ACACCAGGCCAGTCCTACA 60.152 57.895 5.01 0.00 45.52 2.74
644 653 5.375417 CATGGCACTAGAAACATGTCAAA 57.625 39.130 0.00 0.00 36.76 2.69
674 683 3.437795 ACGAACGGACGCGGATCT 61.438 61.111 12.47 0.00 36.70 2.75
766 775 7.387673 TCTTGATAACGATGATGACACACTTTT 59.612 33.333 0.00 0.00 0.00 2.27
778 787 3.011119 ACACACTTTTGCGGTTTGAGTA 58.989 40.909 0.00 0.00 0.00 2.59
783 792 1.144969 TTTGCGGTTTGAGTAGAGCG 58.855 50.000 0.00 0.00 39.54 5.03
786 795 0.388134 GCGGTTTGAGTAGAGCGTCA 60.388 55.000 0.00 0.00 38.84 4.35
865 876 0.315869 CTCGCACGCGACAAAAGTTT 60.316 50.000 15.93 0.00 44.01 2.66
878 889 5.220719 CGACAAAAGTTTAACCCGAGTTTCT 60.221 40.000 0.00 0.00 37.42 2.52
885 896 2.434359 CCCGAGTTTCTCCCGCAC 60.434 66.667 0.00 0.00 0.00 5.34
910 929 2.700897 AGCCAAAGTATGATCCGCTAGT 59.299 45.455 0.00 0.00 0.00 2.57
911 930 3.060602 GCCAAAGTATGATCCGCTAGTC 58.939 50.000 0.00 0.00 0.00 2.59
912 931 3.654414 CCAAAGTATGATCCGCTAGTCC 58.346 50.000 0.00 0.00 0.00 3.85
913 932 3.069586 CCAAAGTATGATCCGCTAGTCCA 59.930 47.826 0.00 0.00 0.00 4.02
914 933 4.262635 CCAAAGTATGATCCGCTAGTCCAT 60.263 45.833 0.00 0.00 0.00 3.41
915 934 5.300752 CAAAGTATGATCCGCTAGTCCATT 58.699 41.667 0.00 0.00 0.00 3.16
916 935 6.455647 CAAAGTATGATCCGCTAGTCCATTA 58.544 40.000 0.00 0.00 0.00 1.90
917 936 5.906113 AGTATGATCCGCTAGTCCATTAG 57.094 43.478 0.00 0.00 0.00 1.73
918 937 3.601443 ATGATCCGCTAGTCCATTAGC 57.399 47.619 0.00 0.00 42.05 3.09
919 938 2.316108 TGATCCGCTAGTCCATTAGCA 58.684 47.619 5.94 0.00 44.98 3.49
921 940 1.480789 TCCGCTAGTCCATTAGCACA 58.519 50.000 5.94 0.00 44.98 4.57
922 941 1.409064 TCCGCTAGTCCATTAGCACAG 59.591 52.381 5.94 0.00 44.98 3.66
933 971 0.685097 TTAGCACAGACAGGTCCACC 59.315 55.000 0.00 0.00 0.00 4.61
1362 1424 2.674033 TCCTCGTCGCTCCGGAAA 60.674 61.111 5.23 0.00 0.00 3.13
1431 1493 3.524606 GCTCTGCCGCCTACCGTA 61.525 66.667 0.00 0.00 34.38 4.02
1442 1504 1.601412 GCCTACCGTACCAATCGCTAC 60.601 57.143 0.00 0.00 0.00 3.58
1444 1506 0.662619 TACCGTACCAATCGCTACCG 59.337 55.000 0.00 0.00 0.00 4.02
1489 1563 2.417933 ACGGCTACTGTACTTCGTACTG 59.582 50.000 8.79 8.79 41.50 2.74
1682 1756 2.303022 AGGCGAAAGAAGAAGATGGTGA 59.697 45.455 0.00 0.00 0.00 4.02
1725 1799 1.139058 GTTGCAGTAGTGGGGATCGAT 59.861 52.381 0.00 0.00 0.00 3.59
1785 1859 2.630158 CTTGATTCAGTCCAGCAGAGG 58.370 52.381 0.00 0.00 0.00 3.69
1953 2027 0.460987 GGATCAGTGACTCCCTTGCG 60.461 60.000 0.00 0.00 0.00 4.85
1989 2063 2.254546 AAGATCGGTTGTTGACTGCA 57.745 45.000 0.00 0.00 34.46 4.41
2031 2105 6.125719 TGATTATGATTCGGTGGATTTGGAA 58.874 36.000 0.00 0.00 0.00 3.53
2061 2135 1.144936 GCTTGAGTCCCGCATAGCT 59.855 57.895 0.00 0.00 0.00 3.32
2096 2170 4.434483 TGCCCTTCTCGAGCAGTA 57.566 55.556 7.81 0.00 31.65 2.74
2115 2189 6.199937 CAGTATGCAAAGGTAAATCAGCTT 57.800 37.500 0.00 0.00 46.92 3.74
2258 2336 8.999431 CCTAGTATTTCTAGAGAGCTACTCAAG 58.001 40.741 13.42 1.44 46.53 3.02
2322 2400 7.948034 TTTTTATTGGATAACACTAGTGGGG 57.052 36.000 26.12 2.30 34.19 4.96
2323 2401 5.640158 TTATTGGATAACACTAGTGGGGG 57.360 43.478 26.12 1.91 34.19 5.40
2343 2421 5.998363 GGGGGCTACTATGCTTATATAATGC 59.002 44.000 0.00 3.26 0.00 3.56
2393 2476 4.937696 TTGTGTTGATGGCACTATTACG 57.062 40.909 0.00 0.00 37.70 3.18
2410 2493 2.331893 CGGTGCCATCGCTTCCAAA 61.332 57.895 0.00 0.00 35.36 3.28
2490 2576 4.627035 TCGAACAGCATGATAGTTGTGAAG 59.373 41.667 0.00 0.00 39.69 3.02
2597 2684 3.582647 TGTTTACCTGAGCCAGAGAATGA 59.417 43.478 4.00 0.00 32.44 2.57
2612 2700 6.036953 CCAGAGAATGATTTGTCTGTTAGAGC 59.963 42.308 13.94 0.00 46.60 4.09
2631 2719 9.004717 GTTAGAGCTATTCCCCTTATGAAATTC 57.995 37.037 0.00 0.00 0.00 2.17
2706 2832 8.970859 ATTATGAACCTCTAAAGGATTCACTG 57.029 34.615 0.00 0.00 46.67 3.66
2958 3084 8.754096 CATTTGATTGAAGACGATAAGAGAGAG 58.246 37.037 0.00 0.00 0.00 3.20
3107 3233 1.153549 GTGCGGTGGTCTCCAGATC 60.154 63.158 0.00 0.00 32.34 2.75
3330 3456 2.821969 TGAAATCAGAAGGAAGCTTGCC 59.178 45.455 15.04 10.33 0.00 4.52
3342 3468 4.080129 AGGAAGCTTGCCTCATCAATCTTA 60.080 41.667 15.04 0.00 33.95 2.10
3354 3480 6.151648 CCTCATCAATCTTAAAGTCAAGGCAA 59.848 38.462 0.00 0.00 0.00 4.52
3370 3496 5.885912 TCAAGGCAAGATAGAATTGGGTTAC 59.114 40.000 0.00 0.00 0.00 2.50
3507 3633 8.947115 GCTGATAAAGAACATTGGGTATATACC 58.053 37.037 21.88 21.88 45.71 2.73
3814 3940 9.621239 ATCTGGAGGTTATAGAAAAGGATATCA 57.379 33.333 4.83 0.00 0.00 2.15
3879 4005 3.137533 GCTCAAAGAACAAGAGTCAGCT 58.862 45.455 0.00 0.00 0.00 4.24
3903 4029 1.068541 GCAAGTTACAAAAGGCTCCGG 60.069 52.381 0.00 0.00 0.00 5.14
3960 4086 1.400242 GCAACTGAAACAGATGACGGC 60.400 52.381 11.94 0.00 36.57 5.68
3980 4106 3.321111 GGCGAGGAAGTGGAGATATTACA 59.679 47.826 0.00 0.00 0.00 2.41
3999 4125 0.536006 ACAAAGAAGCTGAAGCCGCT 60.536 50.000 0.00 0.00 43.38 5.52
4044 4170 6.778069 TCAAAACATTGTATAACCTCCAACCA 59.222 34.615 0.00 0.00 0.00 3.67
4130 4256 1.471119 CACTTGGCAGAGATGGCATT 58.529 50.000 0.00 0.00 43.87 3.56
4237 4363 0.684805 CGTAGCAGAACCCTCCTCCT 60.685 60.000 0.00 0.00 0.00 3.69
4249 4375 0.668706 CTCCTCCTGGCGAATATGCG 60.669 60.000 0.00 0.00 35.06 4.73
4257 4383 1.137513 GGCGAATATGCGTACCTCAC 58.862 55.000 4.71 0.00 35.06 3.51
4332 4461 5.554437 TGAGTGTATACCACCTGTTTTGA 57.446 39.130 0.00 0.00 45.74 2.69
4346 4475 6.708054 CACCTGTTTTGAATACTCTGAACTCT 59.292 38.462 0.00 0.00 0.00 3.24
4422 4551 5.021033 TGTTGTGCTGGTTTTTGATTGAT 57.979 34.783 0.00 0.00 0.00 2.57
4423 4552 6.154203 TGTTGTGCTGGTTTTTGATTGATA 57.846 33.333 0.00 0.00 0.00 2.15
4446 4576 0.456221 AGCGACGGGTTATCAGTCAG 59.544 55.000 0.00 0.00 34.80 3.51
4465 4595 9.551734 TCAGTCAGAATGTAATCAGAATAATGG 57.448 33.333 0.00 0.00 37.40 3.16
4466 4596 8.781196 CAGTCAGAATGTAATCAGAATAATGGG 58.219 37.037 0.00 0.00 37.40 4.00
4472 4602 9.082313 GAATGTAATCAGAATAATGGGTCCATT 57.918 33.333 17.97 17.97 46.85 3.16
4505 4635 3.632643 TCTGCTTTGCCATCACATCTA 57.367 42.857 0.00 0.00 0.00 1.98
4507 4637 3.198417 TCTGCTTTGCCATCACATCTAGA 59.802 43.478 0.00 0.00 0.00 2.43
4508 4638 3.273434 TGCTTTGCCATCACATCTAGAC 58.727 45.455 0.00 0.00 0.00 2.59
4509 4639 3.054875 TGCTTTGCCATCACATCTAGACT 60.055 43.478 0.00 0.00 0.00 3.24
4510 4640 3.311871 GCTTTGCCATCACATCTAGACTG 59.688 47.826 0.00 0.00 0.00 3.51
4511 4641 3.548745 TTGCCATCACATCTAGACTGG 57.451 47.619 0.00 0.00 0.00 4.00
4512 4642 2.470990 TGCCATCACATCTAGACTGGT 58.529 47.619 0.00 0.00 0.00 4.00
4541 4749 2.332063 AGACTGGTTTCTGGTGTGTG 57.668 50.000 0.00 0.00 0.00 3.82
4607 4815 7.700322 AATGCGATCTTGTGTAATGTACTAG 57.300 36.000 0.00 0.00 0.00 2.57
4608 4816 6.203808 TGCGATCTTGTGTAATGTACTAGT 57.796 37.500 0.00 0.00 0.00 2.57
4609 4817 7.324354 TGCGATCTTGTGTAATGTACTAGTA 57.676 36.000 0.00 0.00 0.00 1.82
4726 4934 5.238650 GCCTTTCTGCTTGTTCTACTTGTAA 59.761 40.000 0.00 0.00 0.00 2.41
4922 5130 0.610687 GTCAGAGACCCAGGTCCTTG 59.389 60.000 13.27 11.64 45.59 3.61
4952 5160 7.500892 TCTCACTCTAATGATCCACTCTCTTAC 59.499 40.741 0.00 0.00 0.00 2.34
4966 5174 4.193090 CTCTCTTACTCCTCTCGTTGCTA 58.807 47.826 0.00 0.00 0.00 3.49
5006 5214 7.077605 CGTTCTTGTTTCTTCTTGATAATGCA 58.922 34.615 0.00 0.00 0.00 3.96
5035 5243 5.530543 TGTTGAAAGTGATAGCAATGTGACA 59.469 36.000 0.00 0.00 0.00 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 2.401583 ATTCAGCGACATGGCAACTA 57.598 45.000 0.00 0.00 34.64 2.24
25 26 0.671163 GTCCGACATGGCAACCGTAA 60.671 55.000 0.00 0.00 37.80 3.18
103 105 9.748708 CTCCTAAAGTTTTGAAATCATGACAAA 57.251 29.630 0.00 1.31 0.00 2.83
133 135 2.094854 ACTGCCTAGTGTTACTACGTGC 60.095 50.000 0.00 0.00 35.34 5.34
137 139 5.415077 TCTCTCAACTGCCTAGTGTTACTAC 59.585 44.000 0.00 0.00 37.19 2.73
302 309 0.249322 ACTGTCCAGTGTGCACGTAC 60.249 55.000 13.13 5.72 40.75 3.67
315 322 0.396811 AGGGTACACAGCAACTGTCC 59.603 55.000 0.00 0.00 43.43 4.02
317 324 0.535102 GCAGGGTACACAGCAACTGT 60.535 55.000 7.75 0.00 46.51 3.55
476 485 1.129251 CTAGTGTGTGAGCATTTGCCG 59.871 52.381 0.00 0.00 43.38 5.69
486 495 0.250295 GCACAAGGGCTAGTGTGTGA 60.250 55.000 16.39 0.00 45.60 3.58
509 518 0.462937 CCCACACGTCACTTTCCACA 60.463 55.000 0.00 0.00 0.00 4.17
520 529 2.124320 AGCAGTTTGCCCACACGT 60.124 55.556 0.00 0.00 46.52 4.49
545 554 3.971702 GGGAAGGGCTGGTGTGCT 61.972 66.667 0.00 0.00 0.00 4.40
558 567 4.128139 CGTTTCACCACACGGGAA 57.872 55.556 0.00 0.00 41.15 3.97
578 587 1.121378 TTTATCCGGTCGCCCACATA 58.879 50.000 0.00 0.00 0.00 2.29
579 588 0.463116 GTTTATCCGGTCGCCCACAT 60.463 55.000 0.00 0.00 0.00 3.21
623 632 6.594788 ATTTTGACATGTTTCTAGTGCCAT 57.405 33.333 0.00 0.00 0.00 4.40
692 701 2.177580 CACACGTGTGGGCGTTTCT 61.178 57.895 35.65 1.12 43.83 2.52
693 702 2.326550 CACACGTGTGGGCGTTTC 59.673 61.111 35.65 0.00 43.83 2.78
766 775 0.388134 GACGCTCTACTCAAACCGCA 60.388 55.000 0.00 0.00 0.00 5.69
778 787 0.251354 AATCCATGTGCTGACGCTCT 59.749 50.000 0.00 0.00 36.97 4.09
786 795 1.303561 ACACGGCAATCCATGTGCT 60.304 52.632 6.72 0.00 37.40 4.40
865 876 1.186917 TGCGGGAGAAACTCGGGTTA 61.187 55.000 0.00 0.00 43.48 2.85
885 896 1.873903 CGGATCATACTTTGGCTCCGG 60.874 57.143 0.00 0.00 42.48 5.14
910 929 1.555075 GGACCTGTCTGTGCTAATGGA 59.445 52.381 0.00 0.00 0.00 3.41
911 930 1.278985 TGGACCTGTCTGTGCTAATGG 59.721 52.381 0.00 0.00 0.00 3.16
912 931 2.350522 GTGGACCTGTCTGTGCTAATG 58.649 52.381 0.00 0.00 0.00 1.90
913 932 1.279271 GGTGGACCTGTCTGTGCTAAT 59.721 52.381 0.00 0.00 0.00 1.73
914 933 0.685097 GGTGGACCTGTCTGTGCTAA 59.315 55.000 0.00 0.00 0.00 3.09
915 934 1.192146 GGGTGGACCTGTCTGTGCTA 61.192 60.000 0.00 0.00 35.85 3.49
916 935 2.520536 GGGTGGACCTGTCTGTGCT 61.521 63.158 0.00 0.00 35.85 4.40
917 936 2.032681 GGGTGGACCTGTCTGTGC 59.967 66.667 0.00 0.00 35.85 4.57
955 993 4.711949 CTGCTGCGGCTGAAGGGT 62.712 66.667 20.27 0.00 39.31 4.34
959 997 1.746615 GGAATCTGCTGCGGCTGAA 60.747 57.895 27.97 13.68 46.45 3.02
1225 1281 0.784495 TGGTCCTGGTCTAGTGGAGT 59.216 55.000 0.00 0.00 0.00 3.85
1362 1424 2.358737 CGCACGGCCCTCTTCTTT 60.359 61.111 0.00 0.00 0.00 2.52
1489 1563 4.067192 GAGAGGCTACTACTACTACTGGC 58.933 52.174 0.00 0.00 0.00 4.85
1682 1756 3.313874 CCTCTCCGGCATCCTTGT 58.686 61.111 0.00 0.00 0.00 3.16
1692 1766 0.459237 CTGCAACTACAGCCTCTCCG 60.459 60.000 0.00 0.00 0.00 4.63
1953 2027 1.625818 TCTTTGTCCTTCTCCAGAGCC 59.374 52.381 0.00 0.00 0.00 4.70
2001 2075 4.101585 TCCACCGAATCATAATCAAGCTCT 59.898 41.667 0.00 0.00 0.00 4.09
2061 2135 1.537397 AGCAGCTTCCTCCTCCACA 60.537 57.895 0.00 0.00 0.00 4.17
2115 2189 4.340666 TGCAAGGTGAGTAAAAGAATGCAA 59.659 37.500 0.00 0.00 38.22 4.08
2119 2193 8.860088 AGTTTTATGCAAGGTGAGTAAAAGAAT 58.140 29.630 0.00 0.00 0.00 2.40
2170 2244 7.537596 TTTAAAAGGATGCCTGAATTCAAGA 57.462 32.000 9.88 0.00 32.13 3.02
2297 2375 7.563556 CCCCCACTAGTGTTATCCAATAAAAAT 59.436 37.037 21.18 0.00 0.00 1.82
2314 2392 2.016905 AGCATAGTAGCCCCCACTAG 57.983 55.000 0.00 0.00 32.24 2.57
2322 2400 7.500992 TCAGGCATTATATAAGCATAGTAGCC 58.499 38.462 14.68 0.00 37.52 3.93
2323 2401 9.553064 AATCAGGCATTATATAAGCATAGTAGC 57.447 33.333 14.68 0.00 0.00 3.58
2393 2476 0.532115 ATTTTGGAAGCGATGGCACC 59.468 50.000 1.50 5.77 43.41 5.01
2490 2576 8.454894 GTCTAAAACTTCAAATCATCCTTCTCC 58.545 37.037 0.00 0.00 0.00 3.71
2597 2684 5.430089 AGGGGAATAGCTCTAACAGACAAAT 59.570 40.000 0.00 0.00 0.00 2.32
2612 2700 6.015940 GCCAGTGAATTTCATAAGGGGAATAG 60.016 42.308 1.78 0.00 0.00 1.73
2631 2719 9.881649 AACATAGATATCATATAGTTGCCAGTG 57.118 33.333 5.32 0.00 0.00 3.66
2706 2832 6.072783 AGCTAGAAGAACAGAAACTGAAATGC 60.073 38.462 5.76 0.00 35.18 3.56
2874 3000 6.544928 AAAACCAATTCTGTTTCAACCTCT 57.455 33.333 3.73 0.00 34.97 3.69
2958 3084 8.532819 TCTCCTTTCTTACTTAGAATGTCCTTC 58.467 37.037 0.00 0.00 42.32 3.46
3107 3233 1.129917 ATCTGACTGGGAGCCATGAG 58.870 55.000 0.00 0.00 30.82 2.90
3330 3456 6.748333 TGCCTTGACTTTAAGATTGATGAG 57.252 37.500 0.00 0.00 0.00 2.90
3342 3468 5.420104 CCCAATTCTATCTTGCCTTGACTTT 59.580 40.000 0.00 0.00 0.00 2.66
3370 3496 6.036470 GCGAAATTTCCTCCTCCATTTTTAG 58.964 40.000 12.54 0.00 0.00 1.85
3507 3633 6.755141 TCTTAACAGGACCGAAAAATATCTCG 59.245 38.462 0.00 0.00 34.83 4.04
3734 3860 7.382110 CAGTTCTTCCTTCTCAGAATTCAGTA 58.618 38.462 8.44 0.00 31.71 2.74
3814 3940 2.645838 ATCTTGTCAGTGGTTGCTGT 57.354 45.000 0.00 0.00 37.70 4.40
3879 4005 3.761752 GGAGCCTTTTGTAACTTGCCATA 59.238 43.478 0.00 0.00 0.00 2.74
3903 4029 1.326213 TAGCAGCAGAGGAGTCCAGC 61.326 60.000 12.86 12.32 0.00 4.85
3960 4086 5.515797 TGTGTAATATCTCCACTTCCTCG 57.484 43.478 0.00 0.00 0.00 4.63
3980 4106 0.536006 AGCGGCTTCAGCTTCTTTGT 60.536 50.000 0.00 0.00 43.24 2.83
3999 4125 3.262420 GAGTTCCAGCGCTTTAGATTCA 58.738 45.455 7.50 0.00 0.00 2.57
4044 4170 7.863375 GGCTGAAATATATATTCGTCGCTATCT 59.137 37.037 8.42 0.00 0.00 1.98
4130 4256 1.158007 AGGGGAGAGGCCAAAAGAAA 58.842 50.000 5.01 0.00 38.95 2.52
4237 4363 0.747852 TGAGGTACGCATATTCGCCA 59.252 50.000 0.00 0.00 29.59 5.69
4249 4375 3.764972 AGCTTAGAGGAACAGTGAGGTAC 59.235 47.826 0.00 0.00 0.00 3.34
4257 4383 2.362397 TGCCGATAGCTTAGAGGAACAG 59.638 50.000 0.00 0.00 44.23 3.16
4332 4461 9.225436 GAAAATTCCTCAAGAGTTCAGAGTATT 57.775 33.333 0.00 0.00 0.00 1.89
4422 4551 3.216800 ACTGATAACCCGTCGCTGTATA 58.783 45.455 0.00 0.00 0.00 1.47
4423 4552 2.029623 ACTGATAACCCGTCGCTGTAT 58.970 47.619 0.00 0.00 0.00 2.29
4446 4576 8.641498 ATGGACCCATTATTCTGATTACATTC 57.359 34.615 0.00 0.00 31.82 2.67
4464 4594 6.460261 GCAGAAGAAGCTTTATTAATGGACCC 60.460 42.308 0.00 0.00 0.00 4.46
4465 4595 6.319911 AGCAGAAGAAGCTTTATTAATGGACC 59.680 38.462 0.00 0.00 39.87 4.46
4466 4596 7.326968 AGCAGAAGAAGCTTTATTAATGGAC 57.673 36.000 0.00 0.00 39.87 4.02
4505 4635 3.829601 CAGTCTACTGAGGAAACCAGTCT 59.170 47.826 3.99 0.00 46.59 3.24
4507 4637 2.900546 CCAGTCTACTGAGGAAACCAGT 59.099 50.000 11.69 0.00 46.59 4.00
4508 4638 2.900546 ACCAGTCTACTGAGGAAACCAG 59.099 50.000 11.69 0.00 46.59 4.00
4509 4639 2.972348 ACCAGTCTACTGAGGAAACCA 58.028 47.619 11.69 0.00 46.59 3.67
4510 4640 4.040584 AGAAACCAGTCTACTGAGGAAACC 59.959 45.833 11.69 0.00 46.59 3.27
4511 4641 4.991687 CAGAAACCAGTCTACTGAGGAAAC 59.008 45.833 11.69 0.00 46.59 2.78
4512 4642 4.040461 CCAGAAACCAGTCTACTGAGGAAA 59.960 45.833 11.69 0.00 46.59 3.13
4571 4779 5.111293 CAAGATCGCATTTTAAAAGCCCAT 58.889 37.500 6.79 4.60 0.00 4.00
4640 4848 3.138839 AGGTAGAGAGTAGGTTAGGAGGC 59.861 52.174 0.00 0.00 0.00 4.70
4824 5032 2.575993 CCAGAGGCTCCAGTGACG 59.424 66.667 11.71 0.00 0.00 4.35
4875 5083 4.895889 CCTAGAACATGATACCCTGACTCA 59.104 45.833 0.00 0.00 0.00 3.41
4922 5130 4.892934 AGTGGATCATTAGAGTGAGAGGAC 59.107 45.833 0.00 0.00 0.00 3.85
4952 5160 4.902443 TCATTAGTAGCAACGAGAGGAG 57.098 45.455 0.00 0.00 0.00 3.69
4966 5174 4.261801 CAAGAACGGGTTCCATCATTAGT 58.738 43.478 7.88 0.00 40.33 2.24
5006 5214 7.383029 CACATTGCTATCACTTTCAACAATTGT 59.617 33.333 4.92 4.92 0.00 2.71
5047 5255 5.655974 TGATTGCCTGTCCAATTAGCAAATA 59.344 36.000 0.00 0.00 38.69 1.40
5048 5256 4.467082 TGATTGCCTGTCCAATTAGCAAAT 59.533 37.500 0.00 0.00 38.69 2.32
5062 5270 2.941720 GCTACCTTCTTCTGATTGCCTG 59.058 50.000 0.00 0.00 0.00 4.85



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

AutoCloner maintained by Alex Coulton.