Multiple sequence alignment - TraesCS5D01G073700

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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 TraesCS5D01G073700 chr5D 100.000 3687 0 0 1 3687 72898206 72901892 0.000000e+00 6809
1 TraesCS5D01G073700 chr5A 94.118 2261 86 20 1437 3685 67468478 67470703 0.000000e+00 3395
2 TraesCS5D01G073700 chr5A 86.398 397 44 6 919 1309 67468052 67468444 3.400000e-115 425
3 TraesCS5D01G073700 chr5A 96.721 61 2 0 859 919 67467963 67468023 6.510000e-18 102
4 TraesCS5D01G073700 chr5B 92.584 1780 83 21 1920 3685 79802635 79804379 0.000000e+00 2510
5 TraesCS5D01G073700 chr5B 89.934 457 23 12 1437 1892 79802120 79802554 5.340000e-158 568
6 TraesCS5D01G073700 chr5B 85.250 400 34 7 919 1309 79801703 79802086 4.470000e-104 388
7 TraesCS5D01G073700 chr5B 100.000 56 0 0 864 919 79801622 79801677 1.810000e-18 104
8 TraesCS5D01G073700 chr3B 85.329 2004 209 31 866 2803 125784990 125783006 0.000000e+00 1993
9 TraesCS5D01G073700 chr3B 84.670 698 100 7 18 712 187569942 187570635 0.000000e+00 689
10 TraesCS5D01G073700 chr1B 91.865 713 57 1 1 713 683623676 683622965 0.000000e+00 994
11 TraesCS5D01G073700 chr4D 86.536 713 93 3 1 711 414354999 414355710 0.000000e+00 782
12 TraesCS5D01G073700 chr4B 85.615 716 98 5 1 713 510558136 510558849 0.000000e+00 747
13 TraesCS5D01G073700 chr2D 85.077 717 98 8 1 712 139054346 139055058 0.000000e+00 723
14 TraesCS5D01G073700 chr7D 84.263 699 104 6 18 713 611068622 611069317 0.000000e+00 676
15 TraesCS5D01G073700 chr7A 84.362 697 101 8 19 712 615372248 615372939 0.000000e+00 676
16 TraesCS5D01G073700 chr3D 87.500 592 54 11 1315 1897 79510920 79510340 0.000000e+00 665
17 TraesCS5D01G073700 chr3D 82.378 715 121 5 1 712 300935931 300935219 5.230000e-173 617
18 TraesCS5D01G073700 chr3D 88.224 501 57 2 2382 2881 79509739 79509240 6.820000e-167 597
19 TraesCS5D01G073700 chr3D 87.158 475 44 10 1915 2385 79510296 79509835 1.170000e-144 523
20 TraesCS5D01G073700 chr3D 80.727 275 32 11 2992 3257 79509157 79508895 1.040000e-45 195
21 TraesCS5D01G073700 chr4A 81.958 715 122 7 1 712 727265619 727266329 1.890000e-167 599


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 TraesCS5D01G073700 chr5D 72898206 72901892 3686 False 6809.000000 6809 100.000000 1 3687 1 chr5D.!!$F1 3686
1 TraesCS5D01G073700 chr5A 67467963 67470703 2740 False 1307.333333 3395 92.412333 859 3685 3 chr5A.!!$F1 2826
2 TraesCS5D01G073700 chr5B 79801622 79804379 2757 False 892.500000 2510 91.942000 864 3685 4 chr5B.!!$F1 2821
3 TraesCS5D01G073700 chr3B 125783006 125784990 1984 True 1993.000000 1993 85.329000 866 2803 1 chr3B.!!$R1 1937
4 TraesCS5D01G073700 chr3B 187569942 187570635 693 False 689.000000 689 84.670000 18 712 1 chr3B.!!$F1 694
5 TraesCS5D01G073700 chr1B 683622965 683623676 711 True 994.000000 994 91.865000 1 713 1 chr1B.!!$R1 712
6 TraesCS5D01G073700 chr4D 414354999 414355710 711 False 782.000000 782 86.536000 1 711 1 chr4D.!!$F1 710
7 TraesCS5D01G073700 chr4B 510558136 510558849 713 False 747.000000 747 85.615000 1 713 1 chr4B.!!$F1 712
8 TraesCS5D01G073700 chr2D 139054346 139055058 712 False 723.000000 723 85.077000 1 712 1 chr2D.!!$F1 711
9 TraesCS5D01G073700 chr7D 611068622 611069317 695 False 676.000000 676 84.263000 18 713 1 chr7D.!!$F1 695
10 TraesCS5D01G073700 chr7A 615372248 615372939 691 False 676.000000 676 84.362000 19 712 1 chr7A.!!$F1 693
11 TraesCS5D01G073700 chr3D 300935219 300935931 712 True 617.000000 617 82.378000 1 712 1 chr3D.!!$R1 711
12 TraesCS5D01G073700 chr3D 79508895 79510920 2025 True 495.000000 665 85.902250 1315 3257 4 chr3D.!!$R2 1942
13 TraesCS5D01G073700 chr4A 727265619 727266329 710 False 599.000000 599 81.958000 1 712 1 chr4A.!!$F1 711

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
622 624 0.674895 GACGGAAAGCTGGCTCACAT 60.675 55.000 0.0 0.0 0.00 3.21 F
1410 1475 1.471287 GCAAATCGGGTTACTGTTCCC 59.529 52.381 9.7 9.7 40.26 3.97 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1522 1587 0.034380 AGAAGGCTGACATGCTGCAT 60.034 50.0 9.81 9.81 42.62 3.96 R
3142 3385 0.602372 GGGCCTCAGCGATTCATCTC 60.602 60.0 0.84 0.00 41.24 2.75 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
104 105 4.021102 ACGAAGGTGACAAAATGGATCT 57.979 40.909 0.00 0.00 0.00 2.75
142 143 3.726517 CCCGTGAAGCGTTGGCAG 61.727 66.667 0.00 0.00 43.41 4.85
150 151 1.130561 GAAGCGTTGGCAGTATTGGAC 59.869 52.381 0.00 0.00 43.41 4.02
156 157 3.088532 GTTGGCAGTATTGGACATTCCA 58.911 45.455 0.00 0.00 46.61 3.53
234 235 6.128063 GCCAGATCAAGATAAATACAGATGCC 60.128 42.308 0.00 0.00 0.00 4.40
332 333 3.883822 AACCCCACCCCGGAGTGAT 62.884 63.158 19.00 0.00 40.34 3.06
454 455 1.843851 TGGTCAACCTCTGGAACACTT 59.156 47.619 0.10 0.00 36.82 3.16
470 471 1.069568 CACTTGCCGCAACAATCGTTA 60.070 47.619 0.38 0.00 32.75 3.18
507 508 9.334947 CCTATTCTTCAAGAAATTGATGAGCTA 57.665 33.333 3.35 0.00 37.82 3.32
552 554 6.040247 TGTAATTCAGCATGTAAGTAGGTCG 58.960 40.000 0.00 0.00 37.40 4.79
622 624 0.674895 GACGGAAAGCTGGCTCACAT 60.675 55.000 0.00 0.00 0.00 3.21
780 783 8.575649 AAAAACTAGTCCTGAAAAAGAAGTCA 57.424 30.769 0.00 0.00 0.00 3.41
781 784 8.575649 AAAACTAGTCCTGAAAAAGAAGTCAA 57.424 30.769 0.00 0.00 0.00 3.18
782 785 8.753497 AAACTAGTCCTGAAAAAGAAGTCAAT 57.247 30.769 0.00 0.00 0.00 2.57
783 786 8.753497 AACTAGTCCTGAAAAAGAAGTCAATT 57.247 30.769 0.00 0.00 0.00 2.32
784 787 8.384607 ACTAGTCCTGAAAAAGAAGTCAATTC 57.615 34.615 0.00 0.00 38.28 2.17
785 788 6.641169 AGTCCTGAAAAAGAAGTCAATTCC 57.359 37.500 0.00 0.00 38.84 3.01
786 789 6.368805 AGTCCTGAAAAAGAAGTCAATTCCT 58.631 36.000 0.00 0.00 38.84 3.36
787 790 6.836007 AGTCCTGAAAAAGAAGTCAATTCCTT 59.164 34.615 0.00 0.00 38.84 3.36
788 791 7.343057 AGTCCTGAAAAAGAAGTCAATTCCTTT 59.657 33.333 0.00 0.00 38.84 3.11
789 792 7.981789 GTCCTGAAAAAGAAGTCAATTCCTTTT 59.018 33.333 0.00 0.00 41.90 2.27
790 793 8.539544 TCCTGAAAAAGAAGTCAATTCCTTTTT 58.460 29.630 10.31 10.31 40.18 1.94
824 827 7.610580 AAAAATCAATTCCTCACCAGGTAAA 57.389 32.000 0.00 0.00 41.28 2.01
825 828 6.840780 AAATCAATTCCTCACCAGGTAAAG 57.159 37.500 0.00 0.00 41.28 1.85
826 829 4.993705 TCAATTCCTCACCAGGTAAAGT 57.006 40.909 0.00 0.00 41.28 2.66
827 830 5.319043 TCAATTCCTCACCAGGTAAAGTT 57.681 39.130 0.00 0.00 41.28 2.66
828 831 5.313712 TCAATTCCTCACCAGGTAAAGTTC 58.686 41.667 0.00 0.00 41.28 3.01
829 832 4.993705 ATTCCTCACCAGGTAAAGTTCA 57.006 40.909 0.00 0.00 41.28 3.18
830 833 4.993705 TTCCTCACCAGGTAAAGTTCAT 57.006 40.909 0.00 0.00 41.28 2.57
831 834 4.286297 TCCTCACCAGGTAAAGTTCATG 57.714 45.455 0.00 0.00 41.28 3.07
832 835 2.749621 CCTCACCAGGTAAAGTTCATGC 59.250 50.000 0.00 0.00 34.60 4.06
833 836 2.416547 CTCACCAGGTAAAGTTCATGCG 59.583 50.000 0.00 0.00 0.00 4.73
834 837 2.151202 CACCAGGTAAAGTTCATGCGT 58.849 47.619 0.00 0.00 0.00 5.24
835 838 2.095768 CACCAGGTAAAGTTCATGCGTG 60.096 50.000 0.00 0.00 0.00 5.34
836 839 2.224426 ACCAGGTAAAGTTCATGCGTGA 60.224 45.455 3.97 3.97 0.00 4.35
837 840 2.159627 CCAGGTAAAGTTCATGCGTGAC 59.840 50.000 8.48 4.31 33.11 3.67
838 841 2.805671 CAGGTAAAGTTCATGCGTGACA 59.194 45.455 8.48 0.00 33.11 3.58
839 842 3.249799 CAGGTAAAGTTCATGCGTGACAA 59.750 43.478 8.48 0.00 33.11 3.18
840 843 3.498397 AGGTAAAGTTCATGCGTGACAAG 59.502 43.478 8.48 0.00 33.11 3.16
841 844 3.250040 GGTAAAGTTCATGCGTGACAAGT 59.750 43.478 8.48 0.00 33.11 3.16
842 845 4.449743 GGTAAAGTTCATGCGTGACAAGTA 59.550 41.667 8.48 0.00 33.11 2.24
843 846 5.121768 GGTAAAGTTCATGCGTGACAAGTAT 59.878 40.000 8.48 0.00 33.11 2.12
844 847 5.689383 AAAGTTCATGCGTGACAAGTATT 57.311 34.783 8.48 0.00 33.11 1.89
845 848 6.795098 AAAGTTCATGCGTGACAAGTATTA 57.205 33.333 8.48 0.00 33.11 0.98
846 849 6.795098 AAGTTCATGCGTGACAAGTATTAA 57.205 33.333 8.48 0.00 33.11 1.40
847 850 6.165659 AGTTCATGCGTGACAAGTATTAAC 57.834 37.500 8.48 7.92 33.11 2.01
848 851 4.833469 TCATGCGTGACAAGTATTAACG 57.167 40.909 3.97 0.00 37.32 3.18
849 852 3.615056 TCATGCGTGACAAGTATTAACGG 59.385 43.478 3.97 0.00 34.91 4.44
850 853 3.300852 TGCGTGACAAGTATTAACGGA 57.699 42.857 0.00 0.00 34.91 4.69
851 854 2.988493 TGCGTGACAAGTATTAACGGAC 59.012 45.455 0.00 0.00 34.91 4.79
852 855 3.248266 GCGTGACAAGTATTAACGGACT 58.752 45.455 0.00 0.00 34.91 3.85
853 856 3.302699 GCGTGACAAGTATTAACGGACTC 59.697 47.826 0.00 0.00 34.91 3.36
854 857 4.730657 CGTGACAAGTATTAACGGACTCT 58.269 43.478 0.00 0.00 0.00 3.24
855 858 4.557690 CGTGACAAGTATTAACGGACTCTG 59.442 45.833 0.00 0.00 0.00 3.35
856 859 5.467705 GTGACAAGTATTAACGGACTCTGT 58.532 41.667 0.00 0.00 0.00 3.41
857 860 5.924825 GTGACAAGTATTAACGGACTCTGTT 59.075 40.000 8.34 8.34 0.00 3.16
861 864 8.302965 ACAAGTATTAACGGACTCTGTTAAAC 57.697 34.615 21.73 19.26 42.95 2.01
966 998 4.722700 CACAAGTCCAGCCCCCGG 62.723 72.222 0.00 0.00 0.00 5.73
1011 1043 1.817099 CGAGAGCATGGTTCCTGCC 60.817 63.158 0.00 0.00 40.56 4.85
1278 1325 3.557228 ATTCCAATGAGTCTCTCAGCC 57.443 47.619 0.65 0.00 44.08 4.85
1298 1345 2.791560 CCACGAAGAGATGCGTCATTAG 59.208 50.000 8.99 5.68 38.92 1.73
1304 1351 4.927978 AGAGATGCGTCATTAGCTAGTT 57.072 40.909 8.99 0.00 35.28 2.24
1311 1358 4.328983 TGCGTCATTAGCTAGTTGTAAAGC 59.671 41.667 0.00 3.07 39.08 3.51
1358 1405 2.613691 CCAATGCTTTGTTGATGAGGC 58.386 47.619 11.03 0.00 0.00 4.70
1359 1406 2.232941 CCAATGCTTTGTTGATGAGGCT 59.767 45.455 11.03 0.00 0.00 4.58
1365 1412 3.985925 GCTTTGTTGATGAGGCTTTCTTG 59.014 43.478 0.00 0.00 0.00 3.02
1378 1425 5.888105 AGGCTTTCTTGATGATTTTGATCG 58.112 37.500 0.00 0.00 0.00 3.69
1409 1474 2.433436 AGCAAATCGGGTTACTGTTCC 58.567 47.619 0.00 0.00 0.00 3.62
1410 1475 1.471287 GCAAATCGGGTTACTGTTCCC 59.529 52.381 9.70 9.70 40.26 3.97
1415 1480 3.173953 TCGGGTTACTGTTCCCTTCTA 57.826 47.619 15.33 1.00 41.40 2.10
1432 1497 6.828273 TCCCTTCTACACAATATTTGTCATGG 59.172 38.462 6.56 6.88 43.23 3.66
1433 1498 6.460123 CCCTTCTACACAATATTTGTCATGGC 60.460 42.308 0.00 0.00 43.23 4.40
1434 1499 6.449635 TTCTACACAATATTTGTCATGGCC 57.550 37.500 0.00 0.00 43.23 5.36
1471 1536 7.625828 AGGTAGCTCCAAATAATTTGTGTAC 57.374 36.000 0.00 0.00 38.98 2.90
1511 1576 2.561478 TTACCACCTGAACTGAAGCC 57.439 50.000 0.00 0.00 0.00 4.35
1546 1614 3.276857 CAGCATGTCAGCCTTCTATTGT 58.723 45.455 0.00 0.00 34.23 2.71
1561 1629 5.309323 TCTATTGTTTGCTTGTATGGTGC 57.691 39.130 0.00 0.00 0.00 5.01
1588 1657 0.874390 TGGCGAATGACACTCTTTGC 59.126 50.000 0.00 0.00 0.00 3.68
1593 1662 3.751621 CGAATGACACTCTTTGCATTCC 58.248 45.455 0.00 0.00 41.19 3.01
1660 1730 0.178975 ATTCGTGGGGTTGGCAGAAA 60.179 50.000 0.00 0.00 0.00 2.52
1771 1841 3.383185 CACCGGTTTATACATTGGGCAAT 59.617 43.478 2.97 0.00 0.00 3.56
1788 1858 2.095059 GCAATGGCAACGATGAGAAGTT 60.095 45.455 0.00 0.00 40.72 2.66
2043 2169 8.524870 CCTTTTTGGTTAGATCAAACAATGAG 57.475 34.615 8.53 9.02 43.31 2.90
2091 2224 7.487484 TGCTGACTTTTGAAATATTGAACACA 58.513 30.769 0.00 0.00 0.00 3.72
2195 2328 2.774439 ACCCGATTATCAATTTGCGC 57.226 45.000 0.00 0.00 0.00 6.09
2203 2336 6.011879 CGATTATCAATTTGCGCTATCAGAC 58.988 40.000 9.73 0.00 0.00 3.51
2240 2373 4.065789 GGTACCAAAGGTCACTTGAAGAG 58.934 47.826 7.15 0.00 36.93 2.85
2241 2374 3.933861 ACCAAAGGTCACTTGAAGAGT 57.066 42.857 0.00 0.00 39.89 3.24
2494 2730 1.061546 TCACAACTGACCTAACCCCC 58.938 55.000 0.00 0.00 0.00 5.40
2515 2751 3.384467 CCTTTCAACACATTGTTCCCTGT 59.616 43.478 0.00 0.00 38.77 4.00
2521 2757 1.619827 CACATTGTTCCCTGTGGCATT 59.380 47.619 0.00 0.00 39.24 3.56
2525 2761 3.517296 TTGTTCCCTGTGGCATTAAGA 57.483 42.857 0.00 0.00 0.00 2.10
2571 2807 5.591877 AGCAGATATTACAAAAGGCTTCCAG 59.408 40.000 0.00 0.00 0.00 3.86
2872 3109 4.140536 CAAGAACTCAAGCTTTTCCTCCT 58.859 43.478 0.00 0.00 0.00 3.69
2919 3156 5.645067 CCATTCTCAGTAAATCTGTCTTGCA 59.355 40.000 0.00 0.00 43.97 4.08
2938 3175 5.381174 TGCAATTCTGGACAGATGAAAAG 57.619 39.130 2.42 0.00 37.29 2.27
2939 3176 5.072055 TGCAATTCTGGACAGATGAAAAGA 58.928 37.500 2.42 0.00 37.29 2.52
2940 3177 5.535783 TGCAATTCTGGACAGATGAAAAGAA 59.464 36.000 2.42 0.00 37.29 2.52
3131 3374 3.262420 CACCTTGTAGCACATCCTGTAC 58.738 50.000 0.00 0.00 0.00 2.90
3133 3376 3.583086 ACCTTGTAGCACATCCTGTACTT 59.417 43.478 0.00 0.00 0.00 2.24
3142 3385 5.471456 AGCACATCCTGTACTTTTCTTCTTG 59.529 40.000 0.00 0.00 0.00 3.02
3158 3404 3.449528 TCTTGAGATGAATCGCTGAGG 57.550 47.619 0.00 0.00 0.00 3.86
3166 3412 0.178068 GAATCGCTGAGGCCCTGTTA 59.822 55.000 0.00 0.00 34.44 2.41
3169 3416 1.142748 CGCTGAGGCCCTGTTAGAG 59.857 63.158 0.00 0.00 34.44 2.43
3406 3663 0.249031 GTATTTCCAATGCTGCGGCC 60.249 55.000 16.57 0.00 37.74 6.13
3413 3670 0.669619 CAATGCTGCGGCCAATATGA 59.330 50.000 16.57 0.00 37.74 2.15
3448 3705 1.759445 ACTCTGTCTGTGCTCTTGTGT 59.241 47.619 0.00 0.00 0.00 3.72
3449 3706 2.169352 ACTCTGTCTGTGCTCTTGTGTT 59.831 45.455 0.00 0.00 0.00 3.32
3569 3826 0.868406 CCTTCGAACCTGTGAGTTGC 59.132 55.000 0.00 0.00 0.00 4.17
3602 3861 7.064134 GCTAGTAATACATGTGCAACTGTACAA 59.936 37.037 9.11 1.83 43.49 2.41
3610 3869 3.623960 TGTGCAACTGTACAAGTACAACC 59.376 43.478 13.45 4.17 44.47 3.77
3613 3872 4.274705 TGCAACTGTACAAGTACAACCATG 59.725 41.667 13.45 10.63 44.47 3.66
3685 3945 1.380403 TTTCTTGTGTGCACGTGGGG 61.380 55.000 18.88 1.42 0.00 4.96
3686 3946 2.515991 CTTGTGTGCACGTGGGGT 60.516 61.111 18.88 0.00 0.00 4.95
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
97 98 3.209410 GAACTGAATTCGCCAGATCCAT 58.791 45.455 0.04 0.00 35.69 3.41
150 151 3.243805 TGTTCACCTGTTGCAATGGAATG 60.244 43.478 22.77 13.98 0.00 2.67
156 157 3.553508 GCAAGATGTTCACCTGTTGCAAT 60.554 43.478 0.59 0.00 39.38 3.56
234 235 3.891977 TCCCTTCCAGATGAATAGTCGAG 59.108 47.826 0.00 0.00 31.06 4.04
332 333 2.825532 GCTTCAGCAATAAAGGGGTCAA 59.174 45.455 0.00 0.00 41.59 3.18
454 455 1.160989 ACATAACGATTGTTGCGGCA 58.839 45.000 8.70 0.00 39.12 5.69
470 471 4.574674 TGAAGAATAGGAGCCACAACAT 57.425 40.909 0.00 0.00 0.00 2.71
552 554 2.048603 GTGAGCTGGGACATTGGCC 61.049 63.158 0.00 0.00 38.20 5.36
622 624 4.100189 GCTGATCAGGAAGCTAGGAGTTTA 59.900 45.833 23.89 0.00 36.47 2.01
755 758 8.575649 TGACTTCTTTTTCAGGACTAGTTTTT 57.424 30.769 0.00 0.00 0.00 1.94
756 759 8.575649 TTGACTTCTTTTTCAGGACTAGTTTT 57.424 30.769 0.00 0.00 0.00 2.43
757 760 8.753497 ATTGACTTCTTTTTCAGGACTAGTTT 57.247 30.769 0.00 0.00 0.00 2.66
758 761 8.753497 AATTGACTTCTTTTTCAGGACTAGTT 57.247 30.769 0.00 0.00 0.00 2.24
759 762 7.445707 GGAATTGACTTCTTTTTCAGGACTAGT 59.554 37.037 0.00 0.00 34.08 2.57
760 763 7.663493 AGGAATTGACTTCTTTTTCAGGACTAG 59.337 37.037 0.00 0.00 34.08 2.57
761 764 7.518188 AGGAATTGACTTCTTTTTCAGGACTA 58.482 34.615 0.00 0.00 34.08 2.59
762 765 6.368805 AGGAATTGACTTCTTTTTCAGGACT 58.631 36.000 0.00 0.00 34.08 3.85
763 766 6.641169 AGGAATTGACTTCTTTTTCAGGAC 57.359 37.500 0.00 0.00 34.08 3.85
764 767 7.660030 AAAGGAATTGACTTCTTTTTCAGGA 57.340 32.000 0.00 0.00 39.39 3.86
765 768 8.722480 AAAAAGGAATTGACTTCTTTTTCAGG 57.278 30.769 5.99 0.00 46.49 3.86
800 803 7.290014 ACTTTACCTGGTGAGGAATTGATTTTT 59.710 33.333 10.23 0.00 42.93 1.94
801 804 6.782494 ACTTTACCTGGTGAGGAATTGATTTT 59.218 34.615 10.23 0.00 42.93 1.82
802 805 6.314917 ACTTTACCTGGTGAGGAATTGATTT 58.685 36.000 10.23 0.00 42.93 2.17
803 806 5.892348 ACTTTACCTGGTGAGGAATTGATT 58.108 37.500 10.23 0.00 42.93 2.57
804 807 5.520748 ACTTTACCTGGTGAGGAATTGAT 57.479 39.130 10.23 0.00 42.93 2.57
805 808 4.993705 ACTTTACCTGGTGAGGAATTGA 57.006 40.909 10.23 0.00 42.93 2.57
806 809 5.070001 TGAACTTTACCTGGTGAGGAATTG 58.930 41.667 10.23 0.00 42.93 2.32
807 810 5.319043 TGAACTTTACCTGGTGAGGAATT 57.681 39.130 10.23 0.00 42.93 2.17
808 811 4.993705 TGAACTTTACCTGGTGAGGAAT 57.006 40.909 10.23 0.00 42.93 3.01
809 812 4.651778 CATGAACTTTACCTGGTGAGGAA 58.348 43.478 10.23 0.00 42.93 3.36
810 813 3.559171 GCATGAACTTTACCTGGTGAGGA 60.559 47.826 10.23 0.00 42.93 3.71
811 814 2.749621 GCATGAACTTTACCTGGTGAGG 59.250 50.000 10.23 4.12 46.21 3.86
812 815 2.416547 CGCATGAACTTTACCTGGTGAG 59.583 50.000 10.23 9.87 0.00 3.51
813 816 2.224426 ACGCATGAACTTTACCTGGTGA 60.224 45.455 10.23 0.00 0.00 4.02
814 817 2.095768 CACGCATGAACTTTACCTGGTG 60.096 50.000 10.23 0.00 0.00 4.17
815 818 2.151202 CACGCATGAACTTTACCTGGT 58.849 47.619 4.05 4.05 0.00 4.00
816 819 2.159627 GTCACGCATGAACTTTACCTGG 59.840 50.000 0.00 0.00 36.31 4.45
817 820 2.805671 TGTCACGCATGAACTTTACCTG 59.194 45.455 0.00 0.00 36.31 4.00
818 821 3.120321 TGTCACGCATGAACTTTACCT 57.880 42.857 0.00 0.00 36.31 3.08
819 822 3.250040 ACTTGTCACGCATGAACTTTACC 59.750 43.478 0.00 0.00 36.31 2.85
820 823 4.468095 ACTTGTCACGCATGAACTTTAC 57.532 40.909 0.00 0.00 36.31 2.01
821 824 6.795098 AATACTTGTCACGCATGAACTTTA 57.205 33.333 0.00 0.00 36.31 1.85
822 825 5.689383 AATACTTGTCACGCATGAACTTT 57.311 34.783 0.00 0.00 36.31 2.66
823 826 6.599437 GTTAATACTTGTCACGCATGAACTT 58.401 36.000 0.00 0.00 36.31 2.66
824 827 5.163992 CGTTAATACTTGTCACGCATGAACT 60.164 40.000 0.00 0.00 36.31 3.01
825 828 5.013236 CGTTAATACTTGTCACGCATGAAC 58.987 41.667 0.00 0.00 36.31 3.18
826 829 4.092237 CCGTTAATACTTGTCACGCATGAA 59.908 41.667 0.00 0.00 36.31 2.57
827 830 3.615056 CCGTTAATACTTGTCACGCATGA 59.385 43.478 0.00 0.00 0.00 3.07
828 831 3.615056 TCCGTTAATACTTGTCACGCATG 59.385 43.478 0.00 0.00 0.00 4.06
829 832 3.615496 GTCCGTTAATACTTGTCACGCAT 59.385 43.478 0.00 0.00 0.00 4.73
830 833 2.988493 GTCCGTTAATACTTGTCACGCA 59.012 45.455 0.00 0.00 0.00 5.24
831 834 3.248266 AGTCCGTTAATACTTGTCACGC 58.752 45.455 0.00 0.00 0.00 5.34
832 835 4.557690 CAGAGTCCGTTAATACTTGTCACG 59.442 45.833 0.00 0.00 0.00 4.35
833 836 5.467705 ACAGAGTCCGTTAATACTTGTCAC 58.532 41.667 0.00 0.00 0.00 3.67
834 837 5.717078 ACAGAGTCCGTTAATACTTGTCA 57.283 39.130 0.00 0.00 0.00 3.58
835 838 8.430828 GTTTAACAGAGTCCGTTAATACTTGTC 58.569 37.037 11.54 0.00 38.32 3.18
836 839 7.386025 GGTTTAACAGAGTCCGTTAATACTTGT 59.614 37.037 11.54 0.00 38.32 3.16
837 840 7.385752 TGGTTTAACAGAGTCCGTTAATACTTG 59.614 37.037 11.54 0.00 38.32 3.16
838 841 7.444299 TGGTTTAACAGAGTCCGTTAATACTT 58.556 34.615 11.54 0.00 38.32 2.24
839 842 6.996509 TGGTTTAACAGAGTCCGTTAATACT 58.003 36.000 11.54 0.00 38.32 2.12
840 843 6.870439 ACTGGTTTAACAGAGTCCGTTAATAC 59.130 38.462 11.54 11.64 40.97 1.89
841 844 6.869913 CACTGGTTTAACAGAGTCCGTTAATA 59.130 38.462 11.54 2.48 40.97 0.98
842 845 5.699458 CACTGGTTTAACAGAGTCCGTTAAT 59.301 40.000 11.54 0.00 40.97 1.40
843 846 5.051816 CACTGGTTTAACAGAGTCCGTTAA 58.948 41.667 7.47 7.47 40.97 2.01
844 847 4.099881 ACACTGGTTTAACAGAGTCCGTTA 59.900 41.667 1.02 0.00 37.69 3.18
845 848 3.118519 ACACTGGTTTAACAGAGTCCGTT 60.119 43.478 1.02 0.00 37.69 4.44
846 849 2.433239 ACACTGGTTTAACAGAGTCCGT 59.567 45.455 1.02 0.00 37.69 4.69
847 850 2.800544 CACACTGGTTTAACAGAGTCCG 59.199 50.000 1.02 0.00 39.70 4.79
848 851 4.067972 TCACACTGGTTTAACAGAGTCC 57.932 45.455 1.02 0.00 39.70 3.85
849 852 5.542779 AGATCACACTGGTTTAACAGAGTC 58.457 41.667 1.02 0.00 39.70 3.36
850 853 5.542779 GAGATCACACTGGTTTAACAGAGT 58.457 41.667 1.02 0.00 41.86 3.24
851 854 4.623167 CGAGATCACACTGGTTTAACAGAG 59.377 45.833 1.02 0.00 40.97 3.35
852 855 4.556233 CGAGATCACACTGGTTTAACAGA 58.444 43.478 1.02 0.00 40.97 3.41
853 856 3.679980 CCGAGATCACACTGGTTTAACAG 59.320 47.826 0.00 0.00 44.03 3.16
854 857 3.659786 CCGAGATCACACTGGTTTAACA 58.340 45.455 0.00 0.00 0.00 2.41
855 858 2.415512 GCCGAGATCACACTGGTTTAAC 59.584 50.000 0.00 0.00 0.00 2.01
856 859 2.695359 GCCGAGATCACACTGGTTTAA 58.305 47.619 0.00 0.00 0.00 1.52
857 860 1.403647 CGCCGAGATCACACTGGTTTA 60.404 52.381 0.00 0.00 0.00 2.01
861 864 1.079819 AACGCCGAGATCACACTGG 60.080 57.895 0.00 0.00 0.00 4.00
966 998 4.144703 GGAGCGGAACCGAGTCCC 62.145 72.222 17.63 7.51 42.83 4.46
984 1016 3.207677 CATGCTCTCGAGTATGGCC 57.792 57.895 13.13 0.00 44.42 5.36
1183 1215 1.076632 AGTACCTCCTCCTGCCGAG 60.077 63.158 0.00 0.00 38.46 4.63
1204 1240 8.519526 ACCAGAGCAATTAAAATTAACGAATCA 58.480 29.630 0.00 0.00 0.00 2.57
1278 1325 2.217393 GCTAATGACGCATCTCTTCGTG 59.783 50.000 0.00 0.00 39.22 4.35
1298 1345 1.531883 GCCGCATGCTTTACAACTAGC 60.532 52.381 17.13 0.00 36.87 3.42
1358 1405 7.025365 TCAAGCGATCAAAATCATCAAGAAAG 58.975 34.615 0.00 0.00 31.76 2.62
1359 1406 6.912082 TCAAGCGATCAAAATCATCAAGAAA 58.088 32.000 0.00 0.00 31.76 2.52
1365 1412 4.033684 GTGCTCAAGCGATCAAAATCATC 58.966 43.478 0.00 0.00 45.83 2.92
1409 1474 6.460123 GGCCATGACAAATATTGTGTAGAAGG 60.460 42.308 0.00 0.00 45.52 3.46
1410 1475 6.319658 AGGCCATGACAAATATTGTGTAGAAG 59.680 38.462 5.01 0.00 45.52 2.85
1415 1480 7.422465 AAATAGGCCATGACAAATATTGTGT 57.578 32.000 5.01 0.00 45.52 3.72
1471 1536 1.009829 GCAGACGGCAAACCTATCAG 58.990 55.000 0.00 0.00 43.97 2.90
1522 1587 0.034380 AGAAGGCTGACATGCTGCAT 60.034 50.000 9.81 9.81 42.62 3.96
1525 1590 3.276857 ACAATAGAAGGCTGACATGCTG 58.723 45.455 0.00 0.00 0.00 4.41
1546 1614 3.119884 CGATGAAGCACCATACAAGCAAA 60.120 43.478 0.00 0.00 0.00 3.68
1561 1629 1.061131 GTGTCATTCGCCACGATGAAG 59.939 52.381 0.00 0.00 35.23 3.02
1588 1657 0.617413 AGAGCTCACACCTGGGAATG 59.383 55.000 17.77 0.00 0.00 2.67
1593 1662 2.027377 AGATCAAAGAGCTCACACCTGG 60.027 50.000 17.77 0.00 0.00 4.45
1660 1730 4.853007 CTTTCCTCCTCTCAACAATGGAT 58.147 43.478 0.00 0.00 0.00 3.41
1771 1841 1.347707 AGGAACTTCTCATCGTTGCCA 59.652 47.619 0.00 0.00 27.25 4.92
1998 2123 8.753497 AAAAGGTTATGGTCTTATGGAAGATC 57.247 34.615 0.00 0.00 43.58 2.75
1999 2124 8.971073 CAAAAAGGTTATGGTCTTATGGAAGAT 58.029 33.333 0.00 0.00 43.58 2.40
2000 2125 7.396055 CCAAAAAGGTTATGGTCTTATGGAAGA 59.604 37.037 0.00 0.00 39.47 2.87
2001 2126 7.547227 CCAAAAAGGTTATGGTCTTATGGAAG 58.453 38.462 0.00 0.00 34.61 3.46
2036 2162 9.545105 TTGTTCTTATTTCAAAATGCTCATTGT 57.455 25.926 0.00 0.00 0.00 2.71
2043 2169 8.337532 AGCAAGTTTGTTCTTATTTCAAAATGC 58.662 29.630 14.83 14.83 41.25 3.56
2195 2328 5.766150 AGACAAGATCCTTCGTCTGATAG 57.234 43.478 3.82 0.00 37.34 2.08
2203 2336 2.496070 TGGTACCAGACAAGATCCTTCG 59.504 50.000 11.60 0.00 0.00 3.79
2240 2373 2.083774 TGAAGGGCACGAATGATCAAC 58.916 47.619 0.00 0.00 0.00 3.18
2241 2374 2.290260 ACTGAAGGGCACGAATGATCAA 60.290 45.455 0.00 0.00 0.00 2.57
2494 2730 4.362279 CACAGGGAACAATGTGTTGAAAG 58.638 43.478 0.00 0.00 41.28 2.62
2521 2757 2.047655 CCAACACCGCGGCTCTTA 60.048 61.111 28.58 0.00 0.00 2.10
2571 2807 2.534757 GCATCGTTAAGTTCTCTACCGC 59.465 50.000 0.00 0.00 0.00 5.68
2872 3109 2.954684 CGGGGCTGTACTTGCAGGA 61.955 63.158 1.40 0.00 37.00 3.86
3131 3374 6.091849 TCAGCGATTCATCTCAAGAAGAAAAG 59.908 38.462 2.20 1.70 37.61 2.27
3133 3376 5.482006 TCAGCGATTCATCTCAAGAAGAAA 58.518 37.500 2.20 0.00 37.61 2.52
3142 3385 0.602372 GGGCCTCAGCGATTCATCTC 60.602 60.000 0.84 0.00 41.24 2.75
3166 3412 3.449018 CCAGAACAGCATACTACACCTCT 59.551 47.826 0.00 0.00 0.00 3.69
3169 3416 3.195825 AGTCCAGAACAGCATACTACACC 59.804 47.826 0.00 0.00 0.00 4.16
3291 3548 2.492881 TCGCACAACTTATCCGGACTTA 59.507 45.455 6.12 0.00 0.00 2.24
3382 3639 2.102578 GCAGCATTGGAAATACCCAGT 58.897 47.619 0.00 0.00 37.53 4.00
3406 3663 5.532406 AGTTGTTCCCATCCGAATCATATTG 59.468 40.000 0.00 0.00 0.00 1.90
3413 3670 2.305927 ACAGAGTTGTTCCCATCCGAAT 59.694 45.455 0.00 0.00 32.28 3.34
3448 3705 6.926313 TGATCATCATTGCAACAAGATCAAA 58.074 32.000 22.72 9.47 37.89 2.69
3449 3706 6.518208 TGATCATCATTGCAACAAGATCAA 57.482 33.333 22.72 12.79 37.89 2.57
3569 3826 5.812127 TGCACATGTATTACTAGCACAAGAG 59.188 40.000 0.00 0.00 0.00 2.85
3613 3872 2.814336 GGTGAAGTTCTCCATGGTGAAC 59.186 50.000 36.25 36.25 44.27 3.18
3667 3927 1.821759 CCCCACGTGCACACAAGAA 60.822 57.895 18.64 0.00 0.00 2.52
3669 3929 2.515991 ACCCCACGTGCACACAAG 60.516 61.111 18.64 2.44 0.00 3.16


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

AutoCloner maintained by Alex Coulton.