Multiple sequence alignment - TraesCS2D01G089500

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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 TraesCS2D01G089500 chr2D 100.000 3897 0 0 1 3897 39499686 39503582 0.000000e+00 7197
1 TraesCS2D01G089500 chr2D 97.945 973 18 2 1 972 530335123 530334152 0.000000e+00 1685
2 TraesCS2D01G089500 chr2D 97.842 973 19 2 1 972 57128647 57127676 0.000000e+00 1679
3 TraesCS2D01G089500 chr2D 97.842 973 19 2 1 972 599703157 599704128 0.000000e+00 1679
4 TraesCS2D01G089500 chr4D 97.376 2896 48 9 1010 3897 123319042 123321917 0.000000e+00 4902
5 TraesCS2D01G089500 chr4D 97.449 980 22 3 1 978 379383406 379384384 0.000000e+00 1668
6 TraesCS2D01G089500 chrUn 97.272 2896 51 9 1010 3897 206782217 206785092 0.000000e+00 4885
7 TraesCS2D01G089500 chrUn 96.763 1946 38 7 1957 3897 345390133 345388208 0.000000e+00 3221
8 TraesCS2D01G089500 chr7A 96.994 2894 61 9 1010 3897 60262872 60265745 0.000000e+00 4839
9 TraesCS2D01G089500 chr1B 96.817 2890 62 11 1013 3897 672570527 672567663 0.000000e+00 4800
10 TraesCS2D01G089500 chr5A 96.750 2892 70 10 1013 3897 238848994 238846120 0.000000e+00 4798
11 TraesCS2D01G089500 chr2B 96.578 2893 70 9 1013 3897 391093290 391090419 0.000000e+00 4767
12 TraesCS2D01G089500 chr3B 96.508 2892 78 8 1013 3897 669796957 669794082 0.000000e+00 4759
13 TraesCS2D01G089500 chr3B 96.408 2895 80 8 1010 3897 483384272 483387149 0.000000e+00 4748
14 TraesCS2D01G089500 chr3D 96.441 2894 81 8 1010 3897 523766902 523769779 0.000000e+00 4754
15 TraesCS2D01G089500 chr3D 97.551 980 20 3 1 977 359638987 359638009 0.000000e+00 1674
16 TraesCS2D01G089500 chr4A 96.523 2847 80 5 1056 3897 246674330 246671498 0.000000e+00 4691
17 TraesCS2D01G089500 chr6D 97.252 2256 38 7 1650 3897 124501727 124503966 0.000000e+00 3801
18 TraesCS2D01G089500 chr6D 97.739 973 20 2 1 972 450882847 450883818 0.000000e+00 1674
19 TraesCS2D01G089500 chr6D 97.639 974 21 2 1 973 43013443 43012471 0.000000e+00 1670
20 TraesCS2D01G089500 chr6D 97.636 973 21 2 1 972 14711470 14710499 0.000000e+00 1668
21 TraesCS2D01G089500 chr6D 97.636 973 21 2 1 972 83145936 83146907 0.000000e+00 1668
22 TraesCS2D01G089500 chr6D 97.636 973 21 2 1 972 424659499 424658528 0.000000e+00 1668
23 TraesCS2D01G089500 chr6D 97.636 973 21 2 1 972 424666449 424665478 0.000000e+00 1668
24 TraesCS2D01G089500 chr7D 96.947 1441 23 6 2463 3897 203485007 203486432 0.000000e+00 2398
25 TraesCS2D01G089500 chr7D 97.842 973 19 2 1 972 262725292 262726263 0.000000e+00 1679
26 TraesCS2D01G089500 chr7D 97.741 974 20 2 1 973 430109605 430110577 0.000000e+00 1676
27 TraesCS2D01G089500 chr5D 98.043 971 17 2 1 970 385889835 385890804 0.000000e+00 1687
28 TraesCS2D01G089500 chr5D 97.837 971 19 2 1 970 233141507 233140538 0.000000e+00 1676
29 TraesCS2D01G089500 chr5D 97.739 973 20 2 1 972 389419082 389418111 0.000000e+00 1674
30 TraesCS2D01G089500 chr5D 97.739 973 20 2 1 972 389426031 389425060 0.000000e+00 1674
31 TraesCS2D01G089500 chr5D 97.739 973 20 2 1 972 540017765 540018736 0.000000e+00 1674
32 TraesCS2D01G089500 chr5D 97.739 973 20 2 1 972 544317748 544318719 0.000000e+00 1674
33 TraesCS2D01G089500 chr1D 97.748 977 20 2 1 976 340534596 340533621 0.000000e+00 1681
34 TraesCS2D01G089500 chr1D 97.333 975 23 3 1 974 420496808 420495836 0.000000e+00 1653
35 TraesCS2D01G089500 chr1D 97.234 976 24 3 1 975 362458414 362457441 0.000000e+00 1650
36 TraesCS2D01G089500 chr1D 97.134 977 26 2 1 976 410981515 410982490 0.000000e+00 1648
37 TraesCS2D01G089500 chr1D 96.951 984 24 5 1 980 159930180 159929199 0.000000e+00 1646
38 TraesCS2D01G089500 chr1D 97.131 976 26 2 1 975 482030013 482029039 0.000000e+00 1646
39 TraesCS2D01G089500 chr1A 91.720 314 9 2 3586 3897 402859872 402860170 1.670000e-113 420


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 TraesCS2D01G089500 chr2D 39499686 39503582 3896 False 7197 7197 100.000 1 3897 1 chr2D.!!$F1 3896
1 TraesCS2D01G089500 chr2D 530334152 530335123 971 True 1685 1685 97.945 1 972 1 chr2D.!!$R2 971
2 TraesCS2D01G089500 chr2D 57127676 57128647 971 True 1679 1679 97.842 1 972 1 chr2D.!!$R1 971
3 TraesCS2D01G089500 chr2D 599703157 599704128 971 False 1679 1679 97.842 1 972 1 chr2D.!!$F2 971
4 TraesCS2D01G089500 chr4D 123319042 123321917 2875 False 4902 4902 97.376 1010 3897 1 chr4D.!!$F1 2887
5 TraesCS2D01G089500 chr4D 379383406 379384384 978 False 1668 1668 97.449 1 978 1 chr4D.!!$F2 977
6 TraesCS2D01G089500 chrUn 206782217 206785092 2875 False 4885 4885 97.272 1010 3897 1 chrUn.!!$F1 2887
7 TraesCS2D01G089500 chrUn 345388208 345390133 1925 True 3221 3221 96.763 1957 3897 1 chrUn.!!$R1 1940
8 TraesCS2D01G089500 chr7A 60262872 60265745 2873 False 4839 4839 96.994 1010 3897 1 chr7A.!!$F1 2887
9 TraesCS2D01G089500 chr1B 672567663 672570527 2864 True 4800 4800 96.817 1013 3897 1 chr1B.!!$R1 2884
10 TraesCS2D01G089500 chr5A 238846120 238848994 2874 True 4798 4798 96.750 1013 3897 1 chr5A.!!$R1 2884
11 TraesCS2D01G089500 chr2B 391090419 391093290 2871 True 4767 4767 96.578 1013 3897 1 chr2B.!!$R1 2884
12 TraesCS2D01G089500 chr3B 669794082 669796957 2875 True 4759 4759 96.508 1013 3897 1 chr3B.!!$R1 2884
13 TraesCS2D01G089500 chr3B 483384272 483387149 2877 False 4748 4748 96.408 1010 3897 1 chr3B.!!$F1 2887
14 TraesCS2D01G089500 chr3D 523766902 523769779 2877 False 4754 4754 96.441 1010 3897 1 chr3D.!!$F1 2887
15 TraesCS2D01G089500 chr3D 359638009 359638987 978 True 1674 1674 97.551 1 977 1 chr3D.!!$R1 976
16 TraesCS2D01G089500 chr4A 246671498 246674330 2832 True 4691 4691 96.523 1056 3897 1 chr4A.!!$R1 2841
17 TraesCS2D01G089500 chr6D 124501727 124503966 2239 False 3801 3801 97.252 1650 3897 1 chr6D.!!$F2 2247
18 TraesCS2D01G089500 chr6D 450882847 450883818 971 False 1674 1674 97.739 1 972 1 chr6D.!!$F3 971
19 TraesCS2D01G089500 chr6D 43012471 43013443 972 True 1670 1670 97.639 1 973 1 chr6D.!!$R2 972
20 TraesCS2D01G089500 chr6D 14710499 14711470 971 True 1668 1668 97.636 1 972 1 chr6D.!!$R1 971
21 TraesCS2D01G089500 chr6D 83145936 83146907 971 False 1668 1668 97.636 1 972 1 chr6D.!!$F1 971
22 TraesCS2D01G089500 chr6D 424658528 424659499 971 True 1668 1668 97.636 1 972 1 chr6D.!!$R3 971
23 TraesCS2D01G089500 chr6D 424665478 424666449 971 True 1668 1668 97.636 1 972 1 chr6D.!!$R4 971
24 TraesCS2D01G089500 chr7D 203485007 203486432 1425 False 2398 2398 96.947 2463 3897 1 chr7D.!!$F1 1434
25 TraesCS2D01G089500 chr7D 262725292 262726263 971 False 1679 1679 97.842 1 972 1 chr7D.!!$F2 971
26 TraesCS2D01G089500 chr7D 430109605 430110577 972 False 1676 1676 97.741 1 973 1 chr7D.!!$F3 972
27 TraesCS2D01G089500 chr5D 385889835 385890804 969 False 1687 1687 98.043 1 970 1 chr5D.!!$F1 969
28 TraesCS2D01G089500 chr5D 233140538 233141507 969 True 1676 1676 97.837 1 970 1 chr5D.!!$R1 969
29 TraesCS2D01G089500 chr5D 389418111 389419082 971 True 1674 1674 97.739 1 972 1 chr5D.!!$R2 971
30 TraesCS2D01G089500 chr5D 389425060 389426031 971 True 1674 1674 97.739 1 972 1 chr5D.!!$R3 971
31 TraesCS2D01G089500 chr5D 540017765 540018736 971 False 1674 1674 97.739 1 972 1 chr5D.!!$F2 971
32 TraesCS2D01G089500 chr5D 544317748 544318719 971 False 1674 1674 97.739 1 972 1 chr5D.!!$F3 971
33 TraesCS2D01G089500 chr1D 340533621 340534596 975 True 1681 1681 97.748 1 976 1 chr1D.!!$R2 975
34 TraesCS2D01G089500 chr1D 420495836 420496808 972 True 1653 1653 97.333 1 974 1 chr1D.!!$R4 973
35 TraesCS2D01G089500 chr1D 362457441 362458414 973 True 1650 1650 97.234 1 975 1 chr1D.!!$R3 974
36 TraesCS2D01G089500 chr1D 410981515 410982490 975 False 1648 1648 97.134 1 976 1 chr1D.!!$F1 975
37 TraesCS2D01G089500 chr1D 159929199 159930180 981 True 1646 1646 96.951 1 980 1 chr1D.!!$R1 979
38 TraesCS2D01G089500 chr1D 482029039 482030013 974 True 1646 1646 97.131 1 975 1 chr1D.!!$R5 974

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
840 843 1.141053 GGCTTACTAGGGACATGGTGG 59.859 57.143 0.0 0.0 0.00 4.61 F
1006 1009 0.326904 ATGAGTCTCCCCCATGAGCA 60.327 55.000 0.0 0.0 32.22 4.26 F
1418 1421 0.685097 CCAGAAACGGGGAGTTGAGA 59.315 55.000 0.0 0.0 43.37 3.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2351 2362 0.906775 GTAAGACCCCGGTGGAATCA 59.093 55.000 15.08 0.0 38.00 2.57 R
2437 2448 1.172180 CCCGCAAAAAGCTCTCCACA 61.172 55.000 0.00 0.0 42.61 4.17 R
3194 3205 1.410882 GGCTTGTCTTCCTATCGCTCT 59.589 52.381 0.00 0.0 0.00 4.09 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
72 73 1.960689 CCGGGACTCCAAACAACATTT 59.039 47.619 0.00 0.00 0.00 2.32
233 234 2.040544 GCTCCCACATGTTCCACGG 61.041 63.158 0.00 0.00 0.00 4.94
302 303 7.287466 CCCATATACAATTCCCTTTGTCAATCA 59.713 37.037 0.00 0.00 40.25 2.57
555 558 5.918608 AGATACCTGTAGTGCACCTTTATG 58.081 41.667 14.63 0.52 0.00 1.90
667 670 9.809096 TGATACTTGACATTAGAAAAGCTCTAG 57.191 33.333 0.00 0.00 37.93 2.43
668 671 6.976636 ACTTGACATTAGAAAAGCTCTAGC 57.023 37.500 0.00 0.00 37.93 3.42
669 672 6.467677 ACTTGACATTAGAAAAGCTCTAGCA 58.532 36.000 4.54 0.00 45.16 3.49
677 680 5.948992 AGAAAAGCTCTAGCAAAACGAAT 57.051 34.783 4.54 0.00 45.16 3.34
695 698 5.348986 ACGAATTACACGATCTTGTGCTAT 58.651 37.500 14.69 3.43 43.74 2.97
840 843 1.141053 GGCTTACTAGGGACATGGTGG 59.859 57.143 0.00 0.00 0.00 4.61
897 900 9.288576 TCCTATCAATACAATTTTAGCATGGAG 57.711 33.333 0.00 0.00 0.00 3.86
977 980 8.848474 TCTAGGGCATATTTCTAACAAATAGC 57.152 34.615 0.00 0.00 0.00 2.97
980 983 5.240844 GGGCATATTTCTAACAAATAGCGGT 59.759 40.000 0.00 0.00 0.00 5.68
981 984 6.371389 GGCATATTTCTAACAAATAGCGGTC 58.629 40.000 0.00 0.00 0.00 4.79
982 985 6.371389 GCATATTTCTAACAAATAGCGGTCC 58.629 40.000 0.00 0.00 0.00 4.46
983 986 6.204882 GCATATTTCTAACAAATAGCGGTCCT 59.795 38.462 0.00 0.00 0.00 3.85
984 987 7.386848 GCATATTTCTAACAAATAGCGGTCCTA 59.613 37.037 0.00 0.00 0.00 2.94
985 988 8.709646 CATATTTCTAACAAATAGCGGTCCTAC 58.290 37.037 0.00 0.00 0.00 3.18
986 989 5.664294 TTCTAACAAATAGCGGTCCTACA 57.336 39.130 0.00 0.00 0.00 2.74
987 990 5.664294 TCTAACAAATAGCGGTCCTACAA 57.336 39.130 0.00 0.00 0.00 2.41
988 991 6.229936 TCTAACAAATAGCGGTCCTACAAT 57.770 37.500 0.00 0.00 0.00 2.71
989 992 6.046593 TCTAACAAATAGCGGTCCTACAATG 58.953 40.000 0.00 0.00 0.00 2.82
990 993 4.481368 ACAAATAGCGGTCCTACAATGA 57.519 40.909 0.00 0.00 0.00 2.57
991 994 4.442706 ACAAATAGCGGTCCTACAATGAG 58.557 43.478 0.00 0.00 0.00 2.90
992 995 4.081087 ACAAATAGCGGTCCTACAATGAGT 60.081 41.667 0.00 0.00 0.00 3.41
993 996 4.323553 AATAGCGGTCCTACAATGAGTC 57.676 45.455 0.00 0.00 0.00 3.36
994 997 1.853963 AGCGGTCCTACAATGAGTCT 58.146 50.000 0.00 0.00 0.00 3.24
995 998 1.751924 AGCGGTCCTACAATGAGTCTC 59.248 52.381 0.00 0.00 0.00 3.36
996 999 1.202428 GCGGTCCTACAATGAGTCTCC 60.202 57.143 0.00 0.00 0.00 3.71
997 1000 1.409427 CGGTCCTACAATGAGTCTCCC 59.591 57.143 0.00 0.00 0.00 4.30
998 1001 1.763545 GGTCCTACAATGAGTCTCCCC 59.236 57.143 0.00 0.00 0.00 4.81
999 1002 1.763545 GTCCTACAATGAGTCTCCCCC 59.236 57.143 0.00 0.00 0.00 5.40
1000 1003 1.364678 TCCTACAATGAGTCTCCCCCA 59.635 52.381 0.00 0.00 0.00 4.96
1001 1004 2.022035 TCCTACAATGAGTCTCCCCCAT 60.022 50.000 0.00 0.00 0.00 4.00
1002 1005 2.105477 CCTACAATGAGTCTCCCCCATG 59.895 54.545 0.00 0.00 0.00 3.66
1003 1006 1.971149 ACAATGAGTCTCCCCCATGA 58.029 50.000 0.00 0.00 0.00 3.07
1004 1007 1.842562 ACAATGAGTCTCCCCCATGAG 59.157 52.381 0.00 0.00 0.00 2.90
1005 1008 0.842635 AATGAGTCTCCCCCATGAGC 59.157 55.000 0.00 0.00 32.22 4.26
1006 1009 0.326904 ATGAGTCTCCCCCATGAGCA 60.327 55.000 0.00 0.00 32.22 4.26
1007 1010 0.326904 TGAGTCTCCCCCATGAGCAT 60.327 55.000 0.00 0.00 32.22 3.79
1008 1011 0.842635 GAGTCTCCCCCATGAGCATT 59.157 55.000 0.00 0.00 32.22 3.56
1009 1012 1.213926 GAGTCTCCCCCATGAGCATTT 59.786 52.381 0.00 0.00 32.22 2.32
1010 1013 1.642762 AGTCTCCCCCATGAGCATTTT 59.357 47.619 0.00 0.00 32.22 1.82
1011 1014 2.043526 AGTCTCCCCCATGAGCATTTTT 59.956 45.455 0.00 0.00 32.22 1.94
1054 1057 9.142014 TCTTCCTCATTCTTATTTTGGTTTTCA 57.858 29.630 0.00 0.00 0.00 2.69
1223 1226 6.894339 TGCTCTATTATACTCAATGGACGA 57.106 37.500 0.00 0.00 0.00 4.20
1313 1316 3.686016 ACGAGGGTGATTTAAGTGCAAT 58.314 40.909 0.00 0.00 0.00 3.56
1360 1363 1.115467 CTGGCTTACCGGTCATCTCT 58.885 55.000 12.40 0.00 39.70 3.10
1368 1371 1.123077 CCGGTCATCTCTCATTCCCA 58.877 55.000 0.00 0.00 0.00 4.37
1418 1421 0.685097 CCAGAAACGGGGAGTTGAGA 59.315 55.000 0.00 0.00 43.37 3.27
1437 1440 4.171243 TGAGATGGTTAGACCTATACCCCA 59.829 45.833 0.00 0.00 39.58 4.96
1624 1627 2.983898 ACAACTTTGGACCTAAGGGCTA 59.016 45.455 18.23 0.00 35.63 3.93
1816 1819 2.188994 GCGCTTCTGCTCCTCCAT 59.811 61.111 0.00 0.00 36.97 3.41
2004 2011 1.076332 CTGGAACGTGGGAATTCGAC 58.924 55.000 0.00 0.00 0.00 4.20
2085 2096 2.932569 TTAGATCTACGGGCCGGCCA 62.933 60.000 44.46 26.47 37.98 5.36
2283 2294 3.071023 TGAACATTGTCTTCCTCGGTTCT 59.929 43.478 0.00 0.00 35.45 3.01
2351 2362 2.486727 GCCTATTAGTAAGCGGGCCTTT 60.487 50.000 0.84 0.00 34.95 3.11
2377 2388 2.768492 CCGGGGTCTTACGGTCTCG 61.768 68.421 0.00 0.00 44.85 4.04
2530 2541 7.876936 TGAGTATTCGGACTATAACAGTTCT 57.123 36.000 0.00 0.00 37.72 3.01
2626 2637 9.871238 TTATTAGAAGTTGACAATAGAGTGGTC 57.129 33.333 0.00 0.00 0.00 4.02
2631 2642 4.765856 AGTTGACAATAGAGTGGTCGTACT 59.234 41.667 0.00 0.00 34.32 2.73
2796 2807 1.693606 TGGTCAGTGCAGTGAGATTCA 59.306 47.619 24.49 16.31 0.00 2.57
3194 3205 4.822685 TTTAAGGCCGACCACTACATAA 57.177 40.909 0.00 0.00 39.06 1.90
3208 3219 5.473846 CCACTACATAAGAGCGATAGGAAGA 59.526 44.000 0.00 0.00 0.00 2.87
3445 3457 0.403655 TGATGTACCAGCCAAGCCAA 59.596 50.000 0.00 0.00 0.00 4.52
3521 3535 9.768662 AAAGAGAGTTTGTATTTGCAAATGAAT 57.231 25.926 30.43 14.87 40.01 2.57
3608 3623 3.181450 CCTTCGCCCCTTATCTCTTCATT 60.181 47.826 0.00 0.00 0.00 2.57
3662 3677 6.928348 TTAGAATCTTGTTGACCCTACTCA 57.072 37.500 0.00 0.00 0.00 3.41
3738 3755 1.002857 AATTGGGTTCTCTCTGGGGG 58.997 55.000 0.00 0.00 0.00 5.40
3776 3793 1.889170 GCACCCTCTCTTCCTTTTTGG 59.111 52.381 0.00 0.00 37.10 3.28
3782 3799 3.829026 CCTCTCTTCCTTTTTGGGAAAGG 59.171 47.826 10.55 10.55 43.74 3.11
3880 3900 0.618458 AGGCGAAGGGCATTCTGTTA 59.382 50.000 10.42 0.00 46.16 2.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
72 73 6.317312 AGGGAATAGATATACGTGGTTACCA 58.683 40.000 0.00 0.00 0.00 3.25
233 234 3.126831 GTGGTTCATCCGATGAGATCAC 58.873 50.000 10.91 14.86 40.94 3.06
302 303 4.694339 GAATCTCGGGCAAGTAACATACT 58.306 43.478 0.00 0.00 41.73 2.12
488 491 2.860735 CACGAATCGAGACTGGGATTTC 59.139 50.000 10.55 0.00 33.25 2.17
555 558 1.228033 ACAACGTAACTGGGTGGCC 60.228 57.895 0.00 0.00 0.00 5.36
666 669 5.049680 ACAAGATCGTGTAATTCGTTTTGCT 60.050 36.000 12.88 0.00 0.00 3.91
667 670 5.058008 CACAAGATCGTGTAATTCGTTTTGC 59.942 40.000 14.10 0.00 32.00 3.68
668 671 5.058008 GCACAAGATCGTGTAATTCGTTTTG 59.942 40.000 14.10 0.00 39.19 2.44
669 672 5.049680 AGCACAAGATCGTGTAATTCGTTTT 60.050 36.000 14.10 0.00 39.19 2.43
677 680 4.123497 AGCATAGCACAAGATCGTGTAA 57.877 40.909 14.10 3.82 39.19 2.41
695 698 2.026262 GGACAAGACCCAATCCTAAGCA 60.026 50.000 0.00 0.00 0.00 3.91
977 980 1.409427 GGGAGACTCATTGTAGGACCG 59.591 57.143 4.53 0.00 0.00 4.79
980 983 1.364678 TGGGGGAGACTCATTGTAGGA 59.635 52.381 4.53 0.00 0.00 2.94
981 984 1.879575 TGGGGGAGACTCATTGTAGG 58.120 55.000 4.53 0.00 0.00 3.18
982 985 3.041211 TCATGGGGGAGACTCATTGTAG 58.959 50.000 4.53 0.00 0.00 2.74
983 986 3.041211 CTCATGGGGGAGACTCATTGTA 58.959 50.000 4.53 0.00 37.05 2.41
984 987 1.842562 CTCATGGGGGAGACTCATTGT 59.157 52.381 4.53 0.00 37.05 2.71
985 988 1.476471 GCTCATGGGGGAGACTCATTG 60.476 57.143 4.53 0.00 37.05 2.82
986 989 0.842635 GCTCATGGGGGAGACTCATT 59.157 55.000 4.53 0.00 37.05 2.57
987 990 0.326904 TGCTCATGGGGGAGACTCAT 60.327 55.000 4.53 0.00 37.05 2.90
988 991 0.326904 ATGCTCATGGGGGAGACTCA 60.327 55.000 4.53 0.00 37.05 3.41
989 992 0.842635 AATGCTCATGGGGGAGACTC 59.157 55.000 0.00 0.00 37.05 3.36
990 993 1.302907 AAATGCTCATGGGGGAGACT 58.697 50.000 0.00 0.00 37.05 3.24
991 994 2.149973 AAAATGCTCATGGGGGAGAC 57.850 50.000 0.00 0.00 37.05 3.36
992 995 2.042842 TGAAAAATGCTCATGGGGGAGA 59.957 45.455 0.00 0.00 37.05 3.71
993 996 2.459644 TGAAAAATGCTCATGGGGGAG 58.540 47.619 0.00 0.00 37.97 4.30
994 997 2.619697 TGAAAAATGCTCATGGGGGA 57.380 45.000 0.00 0.00 0.00 4.81
995 998 2.767394 TGATGAAAAATGCTCATGGGGG 59.233 45.455 0.00 0.00 33.63 5.40
996 999 3.735820 CGTGATGAAAAATGCTCATGGGG 60.736 47.826 0.00 0.00 33.63 4.96
997 1000 3.129113 TCGTGATGAAAAATGCTCATGGG 59.871 43.478 0.00 0.00 33.63 4.00
998 1001 4.359971 TCGTGATGAAAAATGCTCATGG 57.640 40.909 0.00 0.00 33.63 3.66
999 1002 7.582352 AGATATCGTGATGAAAAATGCTCATG 58.418 34.615 0.00 0.00 33.63 3.07
1000 1003 7.741027 AGATATCGTGATGAAAAATGCTCAT 57.259 32.000 0.00 0.00 36.21 2.90
1001 1004 7.558161 AAGATATCGTGATGAAAAATGCTCA 57.442 32.000 0.00 0.00 0.00 4.26
1002 1005 8.847444 AAAAGATATCGTGATGAAAAATGCTC 57.153 30.769 0.00 0.00 0.00 4.26
1003 1006 9.294030 GAAAAAGATATCGTGATGAAAAATGCT 57.706 29.630 0.00 0.00 0.00 3.79
1004 1007 9.294030 AGAAAAAGATATCGTGATGAAAAATGC 57.706 29.630 0.00 0.00 0.00 3.56
1007 1010 9.840427 GGAAGAAAAAGATATCGTGATGAAAAA 57.160 29.630 0.00 0.00 0.00 1.94
1008 1011 9.231297 AGGAAGAAAAAGATATCGTGATGAAAA 57.769 29.630 0.00 0.00 0.00 2.29
1009 1012 8.792830 AGGAAGAAAAAGATATCGTGATGAAA 57.207 30.769 0.00 0.00 0.00 2.69
1010 1013 8.040727 TGAGGAAGAAAAAGATATCGTGATGAA 58.959 33.333 0.00 0.00 0.00 2.57
1011 1014 7.555965 TGAGGAAGAAAAAGATATCGTGATGA 58.444 34.615 0.00 0.00 0.00 2.92
1054 1057 2.210116 GCGAACCAACATCCGTGATAT 58.790 47.619 0.00 0.00 0.00 1.63
1223 1226 7.249715 AGTAATGGCTGGATCTACTAATACCT 58.750 38.462 0.00 0.00 0.00 3.08
1313 1316 1.798283 CGAACCACCGGTACATTTCA 58.202 50.000 6.87 0.00 33.12 2.69
1360 1363 1.676529 GTCTCTCGACGATGGGAATGA 59.323 52.381 0.00 0.00 0.00 2.57
1368 1371 5.883503 AGTTCTTTTAGTCTCTCGACGAT 57.116 39.130 0.00 0.00 44.93 3.73
1418 1421 6.610830 CATTTTGGGGTATAGGTCTAACCAT 58.389 40.000 0.00 0.00 41.95 3.55
1816 1819 2.261671 GCAAGAACGGCTCCTCGA 59.738 61.111 0.00 0.00 0.00 4.04
2085 2096 5.579753 AGATTCCCTATGCTCATGTGAAT 57.420 39.130 0.00 0.00 0.00 2.57
2283 2294 4.215908 CCCTACCTACATCAGTGAAGCTA 58.784 47.826 0.00 0.00 0.00 3.32
2351 2362 0.906775 GTAAGACCCCGGTGGAATCA 59.093 55.000 15.08 0.00 38.00 2.57
2437 2448 1.172180 CCCGCAAAAAGCTCTCCACA 61.172 55.000 0.00 0.00 42.61 4.17
2493 2504 4.141801 CCGAATACTCATAAGGTTGGGTCA 60.142 45.833 0.00 0.00 31.31 4.02
2530 2541 6.318396 TGTCAAAAGTGAGTGATTGTTCATCA 59.682 34.615 0.00 0.00 35.32 3.07
2539 2550 7.375834 TCGTATAACTGTCAAAAGTGAGTGAT 58.624 34.615 0.00 0.00 33.27 3.06
2626 2637 4.733887 CGTAGATGAGTTTTGGCTAGTACG 59.266 45.833 0.00 0.00 0.00 3.67
2631 2642 6.459670 TCATACGTAGATGAGTTTTGGCTA 57.540 37.500 0.08 0.00 32.05 3.93
2796 2807 4.275936 GCGTAAAGGCATGATTAGTTCCAT 59.724 41.667 0.00 0.00 0.00 3.41
3194 3205 1.410882 GGCTTGTCTTCCTATCGCTCT 59.589 52.381 0.00 0.00 0.00 4.09
3208 3219 2.037641 GCCTTTCCTTTTGATGGCTTGT 59.962 45.455 0.00 0.00 38.90 3.16
3608 3623 1.135603 CAAGTGACGGAACCGACGATA 60.136 52.381 20.14 0.00 42.83 2.92


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

AutoCloner maintained by Alex Coulton.