Multiple sequence alignment - TraesCS7B01G073000

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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 TraesCS7B01G073000 chr7B 100.000 2876 0 0 1 2876 81421201 81424076 0.000000e+00 5312.0
1 TraesCS7B01G073000 chr7D 89.247 2018 115 44 34 2015 119890328 119892279 0.000000e+00 2431.0
2 TraesCS7B01G073000 chr7D 88.718 780 45 25 2120 2876 119892459 119893218 0.000000e+00 913.0
3 TraesCS7B01G073000 chr7D 87.692 65 4 2 2025 2088 119892310 119892371 3.970000e-09 73.1
4 TraesCS7B01G073000 chr7A 88.872 1339 56 25 701 2015 124789608 124790877 0.000000e+00 1561.0
5 TraesCS7B01G073000 chr7A 88.747 782 43 20 2120 2876 124791042 124791803 0.000000e+00 915.0
6 TraesCS7B01G073000 chr3D 79.828 580 92 12 98 662 523657221 523657790 1.610000e-107 399.0
7 TraesCS7B01G073000 chr2B 77.664 685 115 14 23 675 184908810 184908132 1.620000e-102 383.0
8 TraesCS7B01G073000 chr2B 78.906 384 56 12 315 674 495331047 495330665 1.330000e-58 237.0
9 TraesCS7B01G073000 chr2D 79.566 553 94 10 24 573 425737988 425737452 7.520000e-101 377.0
10 TraesCS7B01G073000 chr2D 79.958 479 82 8 24 498 131314915 131314447 9.870000e-90 340.0
11 TraesCS7B01G073000 chr4D 78.173 591 108 15 6 584 464147777 464147196 9.800000e-95 357.0
12 TraesCS7B01G073000 chr2A 77.006 648 112 18 23 640 491531829 491531189 1.280000e-88 337.0
13 TraesCS7B01G073000 chr5D 84.014 294 37 5 10 303 134481684 134481401 1.020000e-69 274.0
14 TraesCS7B01G073000 chr1B 74.787 587 128 15 4 584 635975987 635975415 2.210000e-61 246.0
15 TraesCS7B01G073000 chr3B 75.671 559 94 22 22 562 429415105 429414571 1.030000e-59 241.0
16 TraesCS7B01G073000 chr5B 84.694 196 29 1 316 510 440202117 440201922 8.130000e-46 195.0
17 TraesCS7B01G073000 chr5B 78.947 266 39 12 331 584 631470866 631470606 6.380000e-37 165.0
18 TraesCS7B01G073000 chr5A 81.452 248 30 8 352 591 4993382 4993621 3.780000e-44 189.0
19 TraesCS7B01G073000 chr6D 78.644 295 42 15 315 594 464520189 464520477 2.950000e-40 176.0


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 TraesCS7B01G073000 chr7B 81421201 81424076 2875 False 5312.000000 5312 100.000000 1 2876 1 chr7B.!!$F1 2875
1 TraesCS7B01G073000 chr7D 119890328 119893218 2890 False 1139.033333 2431 88.552333 34 2876 3 chr7D.!!$F1 2842
2 TraesCS7B01G073000 chr7A 124789608 124791803 2195 False 1238.000000 1561 88.809500 701 2876 2 chr7A.!!$F1 2175
3 TraesCS7B01G073000 chr3D 523657221 523657790 569 False 399.000000 399 79.828000 98 662 1 chr3D.!!$F1 564
4 TraesCS7B01G073000 chr2B 184908132 184908810 678 True 383.000000 383 77.664000 23 675 1 chr2B.!!$R1 652
5 TraesCS7B01G073000 chr2D 425737452 425737988 536 True 377.000000 377 79.566000 24 573 1 chr2D.!!$R2 549
6 TraesCS7B01G073000 chr4D 464147196 464147777 581 True 357.000000 357 78.173000 6 584 1 chr4D.!!$R1 578
7 TraesCS7B01G073000 chr2A 491531189 491531829 640 True 337.000000 337 77.006000 23 640 1 chr2A.!!$R1 617
8 TraesCS7B01G073000 chr1B 635975415 635975987 572 True 246.000000 246 74.787000 4 584 1 chr1B.!!$R1 580
9 TraesCS7B01G073000 chr3B 429414571 429415105 534 True 241.000000 241 75.671000 22 562 1 chr3B.!!$R1 540

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
806 867 0.034337 AAACCCGCAAGCGAACTAGA 59.966 50.0 16.97 0.0 42.83 2.43 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2477 2687 0.101579 TTGTGAAGCTCGACGACACA 59.898 50.0 13.2 13.2 37.4 3.72 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
19 20 3.001406 GGTGCCACTCCGGTAGGT 61.001 66.667 0.00 0.00 39.05 3.08
26 27 1.167851 CACTCCGGTAGGTCACGTAA 58.832 55.000 0.00 0.00 39.05 3.18
84 86 1.946984 AATCCTACCCGTCTGTCCAA 58.053 50.000 0.00 0.00 0.00 3.53
139 145 0.813610 CACTCGCAGTCCACCAACAA 60.814 55.000 0.00 0.00 0.00 2.83
144 155 2.151202 CGCAGTCCACCAACAATAGTT 58.849 47.619 0.00 0.00 38.88 2.24
155 166 0.485099 ACAATAGTTGCCAACCCCCA 59.515 50.000 3.45 0.00 0.00 4.96
363 393 2.758327 ACGCTGGGGACGCAGATA 60.758 61.111 18.98 0.00 0.00 1.98
421 451 2.158813 GGTTAGAATTGGATGCGGAGGA 60.159 50.000 0.00 0.00 0.00 3.71
474 507 4.029186 ACGCCGCGTAAGTCGACA 62.029 61.111 18.63 0.00 38.73 4.35
480 513 1.466866 CCGCGTAAGTCGACAAGATGA 60.467 52.381 19.50 0.00 42.86 2.92
562 610 0.108804 ATCGACGCCGTGAACATCTT 60.109 50.000 0.00 0.00 37.05 2.40
587 636 4.876125 ACGATGAATCATAGCTAGGTGTG 58.124 43.478 12.04 12.04 0.00 3.82
599 648 7.948447 TCATAGCTAGGTGTGGTAATACATAGT 59.052 37.037 17.25 0.00 35.12 2.12
601 650 7.052142 AGCTAGGTGTGGTAATACATAGTTC 57.948 40.000 0.00 0.00 35.12 3.01
645 705 7.502120 AATGAAATATGAAAGACTCGGATGG 57.498 36.000 0.00 0.00 0.00 3.51
662 722 6.987386 TCGGATGGAAAAGAGCAAATTTAAA 58.013 32.000 0.00 0.00 0.00 1.52
672 732 4.022329 AGAGCAAATTTAAAACCTGACCGG 60.022 41.667 0.00 0.00 39.35 5.28
696 756 4.347453 ACGCGTCGGTGGGTGTAC 62.347 66.667 5.58 0.00 33.30 2.90
806 867 0.034337 AAACCCGCAAGCGAACTAGA 59.966 50.000 16.97 0.00 42.83 2.43
812 873 0.666577 GCAAGCGAACTAGACACGGT 60.667 55.000 0.00 1.77 39.33 4.83
813 874 1.401931 GCAAGCGAACTAGACACGGTA 60.402 52.381 0.00 0.00 36.78 4.02
814 875 2.248487 CAAGCGAACTAGACACGGTAC 58.752 52.381 0.00 0.00 36.78 3.34
815 876 1.527034 AGCGAACTAGACACGGTACA 58.473 50.000 0.00 0.00 36.06 2.90
821 885 4.362279 GAACTAGACACGGTACAACACAA 58.638 43.478 0.00 0.00 0.00 3.33
854 918 3.812156 AAAAGTAGCCGTTGCCTTTTT 57.188 38.095 0.00 0.00 36.30 1.94
872 936 4.871933 TTTTTCCCCAAATCTCTCAAGC 57.128 40.909 0.00 0.00 0.00 4.01
873 937 3.814504 TTTCCCCAAATCTCTCAAGCT 57.185 42.857 0.00 0.00 0.00 3.74
874 938 2.795231 TCCCCAAATCTCTCAAGCTG 57.205 50.000 0.00 0.00 0.00 4.24
875 939 1.101331 CCCCAAATCTCTCAAGCTGC 58.899 55.000 0.00 0.00 0.00 5.25
876 940 1.101331 CCCAAATCTCTCAAGCTGCC 58.899 55.000 0.00 0.00 0.00 4.85
877 941 1.615116 CCCAAATCTCTCAAGCTGCCA 60.615 52.381 0.00 0.00 0.00 4.92
878 942 1.743958 CCAAATCTCTCAAGCTGCCAG 59.256 52.381 0.00 0.00 0.00 4.85
879 943 1.132643 CAAATCTCTCAAGCTGCCAGC 59.867 52.381 9.13 9.13 42.84 4.85
880 944 0.394080 AATCTCTCAAGCTGCCAGCC 60.394 55.000 14.25 0.00 43.77 4.85
881 945 2.590391 ATCTCTCAAGCTGCCAGCCG 62.590 60.000 14.25 5.11 43.77 5.52
882 946 3.306595 CTCTCAAGCTGCCAGCCGA 62.307 63.158 14.25 9.67 43.77 5.54
883 947 2.818714 CTCAAGCTGCCAGCCGAG 60.819 66.667 14.25 15.65 43.77 4.63
884 948 3.306595 CTCAAGCTGCCAGCCGAGA 62.307 63.158 22.84 13.68 43.77 4.04
885 949 3.123620 CAAGCTGCCAGCCGAGAC 61.124 66.667 14.25 0.00 43.77 3.36
886 950 4.749310 AAGCTGCCAGCCGAGACG 62.749 66.667 14.25 0.00 43.77 4.18
897 961 3.518998 CGAGACGGCGAGACCCAT 61.519 66.667 16.62 0.00 33.26 4.00
898 962 2.184830 CGAGACGGCGAGACCCATA 61.185 63.158 16.62 0.00 33.26 2.74
930 998 0.529119 CTATTACGCGCTCCCGGTTT 60.529 55.000 5.73 0.00 34.32 3.27
931 999 0.528249 TATTACGCGCTCCCGGTTTC 60.528 55.000 5.73 0.00 34.32 2.78
932 1000 2.510064 ATTACGCGCTCCCGGTTTCA 62.510 55.000 5.73 0.00 34.32 2.69
933 1001 2.712325 TTACGCGCTCCCGGTTTCAA 62.712 55.000 5.73 0.00 34.32 2.69
934 1002 2.712325 TACGCGCTCCCGGTTTCAAA 62.712 55.000 5.73 0.00 34.32 2.69
935 1003 2.254350 GCGCTCCCGGTTTCAAAC 59.746 61.111 0.00 0.00 34.32 2.93
936 1004 2.554272 CGCTCCCGGTTTCAAACG 59.446 61.111 0.00 0.00 0.00 3.60
977 1045 0.820482 AAACGAACCACCCCCGAAAG 60.820 55.000 0.00 0.00 0.00 2.62
1009 1081 3.254024 AAATCCACCGCCGCAGAGT 62.254 57.895 0.00 0.00 0.00 3.24
1119 1192 1.348594 GCGCGCTTCATGGTACTTC 59.651 57.895 26.67 0.00 0.00 3.01
1161 1234 0.826715 TCTCCGCCTCTTTCCATCTG 59.173 55.000 0.00 0.00 0.00 2.90
1199 1272 2.179427 GATTGGGTTTCCTTCCTTGGG 58.821 52.381 0.00 0.00 0.00 4.12
1200 1273 0.471022 TTGGGTTTCCTTCCTTGGGC 60.471 55.000 0.00 0.00 0.00 5.36
1230 1303 1.977594 CTTCGCCCGATTTCCGTTGG 61.978 60.000 0.00 0.00 36.31 3.77
1246 1325 0.944386 TTGGTTTTGACTCTCTGCGC 59.056 50.000 0.00 0.00 0.00 6.09
1324 1403 4.327885 GGATGACGACGAGGATGC 57.672 61.111 0.00 0.00 0.00 3.91
1474 1558 1.131826 CGTTCGTTGCGGTTGGATC 59.868 57.895 0.00 0.00 0.00 3.36
1483 1567 0.165944 GCGGTTGGATCGAACTTGTG 59.834 55.000 18.49 8.77 0.00 3.33
1513 1597 5.414765 GGAAACGAAATTGATGTCCTACCTT 59.585 40.000 0.00 0.00 0.00 3.50
1514 1598 6.403309 GGAAACGAAATTGATGTCCTACCTTC 60.403 42.308 0.00 0.00 0.00 3.46
1515 1599 4.514401 ACGAAATTGATGTCCTACCTTCC 58.486 43.478 0.00 0.00 0.00 3.46
1516 1600 4.225267 ACGAAATTGATGTCCTACCTTCCT 59.775 41.667 0.00 0.00 0.00 3.36
1517 1601 4.811557 CGAAATTGATGTCCTACCTTCCTC 59.188 45.833 0.00 0.00 0.00 3.71
1518 1602 5.395768 CGAAATTGATGTCCTACCTTCCTCT 60.396 44.000 0.00 0.00 0.00 3.69
1519 1603 5.622346 AATTGATGTCCTACCTTCCTCTC 57.378 43.478 0.00 0.00 0.00 3.20
1520 1604 4.338795 TTGATGTCCTACCTTCCTCTCT 57.661 45.455 0.00 0.00 0.00 3.10
1545 1629 2.006888 CTCTCTCTCTCTGTCGGTGAC 58.993 57.143 0.00 0.00 0.00 3.67
1570 1654 1.224075 GTCGTATCAGATCGACGGGA 58.776 55.000 15.20 0.00 44.70 5.14
1833 1933 1.537202 GATGTCTCGGCTGCAGTTTTT 59.463 47.619 16.64 0.00 0.00 1.94
1862 1965 8.506140 TTCCTTGCGTACGTACAATAATATAC 57.494 34.615 24.50 0.00 0.00 1.47
2002 2105 1.173043 TTTGGGATGCTACTTTGGCG 58.827 50.000 0.00 0.00 0.00 5.69
2005 2108 0.947244 GGGATGCTACTTTGGCGATG 59.053 55.000 0.00 0.00 0.00 3.84
2098 2223 7.925703 TTATCTCATCGATTTTAACGGAGAC 57.074 36.000 10.49 0.00 33.61 3.36
2099 2224 5.319140 TCTCATCGATTTTAACGGAGACA 57.681 39.130 0.00 0.00 0.00 3.41
2101 2226 6.160684 TCTCATCGATTTTAACGGAGACAAA 58.839 36.000 0.00 0.00 0.00 2.83
2135 2316 2.726681 CGATAAAAACCCTTTGACCGCG 60.727 50.000 0.00 0.00 0.00 6.46
2137 2318 1.668101 AAAAACCCTTTGACCGCGCA 61.668 50.000 8.75 0.00 0.00 6.09
2171 2352 2.653726 ACACTCTGAATGCACCACAAA 58.346 42.857 0.00 0.00 0.00 2.83
2181 2362 0.318614 GCACCACAAACATGAACCCG 60.319 55.000 0.00 0.00 0.00 5.28
2186 2367 1.081509 CAAACATGAACCCGCCACG 60.082 57.895 0.00 0.00 0.00 4.94
2197 2378 1.449601 CCGCCACGCCTCTACATTT 60.450 57.895 0.00 0.00 0.00 2.32
2213 2394 6.081356 TCTACATTTCAAAGGAAACCCCAAT 58.919 36.000 0.00 0.00 45.22 3.16
2216 2397 7.328404 ACATTTCAAAGGAAACCCCAATAAT 57.672 32.000 0.00 0.00 45.22 1.28
2222 2403 6.211785 TCAAAGGAAACCCCAATAATAACACC 59.788 38.462 0.00 0.00 37.41 4.16
2224 2405 5.020795 AGGAAACCCCAATAATAACACCAC 58.979 41.667 0.00 0.00 37.41 4.16
2235 2416 2.410785 TAACACCACGACTGAAGACG 57.589 50.000 0.73 0.73 38.99 4.18
2254 2435 0.250553 GACGGACACCACCAAATCCA 60.251 55.000 0.00 0.00 0.00 3.41
2255 2436 0.404040 ACGGACACCACCAAATCCAT 59.596 50.000 0.00 0.00 0.00 3.41
2256 2437 1.631388 ACGGACACCACCAAATCCATA 59.369 47.619 0.00 0.00 0.00 2.74
2257 2438 2.288666 CGGACACCACCAAATCCATAG 58.711 52.381 0.00 0.00 0.00 2.23
2293 2493 2.649312 TGGAGAACATTTCCCTCATGGT 59.351 45.455 0.00 0.00 33.62 3.55
2334 2539 8.698973 TGTCAAAATCTGGGATACAACTAAAA 57.301 30.769 0.00 0.00 39.74 1.52
2335 2540 9.308000 TGTCAAAATCTGGGATACAACTAAAAT 57.692 29.630 0.00 0.00 39.74 1.82
2401 2611 6.365153 TGTTACAACAAAGGCTATACGAGGC 61.365 44.000 0.00 0.00 42.71 4.70
2441 2651 1.529244 AGCTCAAGCCGCCAGTTTT 60.529 52.632 0.00 0.00 43.38 2.43
2477 2687 9.781425 ACCATATCTAAGATCTTGACCTCATAT 57.219 33.333 18.47 7.32 0.00 1.78
2504 2714 0.027194 CGAGCTTCACAATGCCATCG 59.973 55.000 0.00 0.00 0.00 3.84
2540 2750 8.713708 TTCCTATAAGTTTTCCAACAAATCCA 57.286 30.769 0.00 0.00 35.05 3.41
2573 2783 4.451435 CCATTCATGATCTTGATCCTGTCG 59.549 45.833 11.72 5.83 0.00 4.35
2612 2822 1.309499 CCTCGAGCTCAGTCGGAAGT 61.309 60.000 15.40 0.00 40.49 3.01
2639 2849 3.055458 TCACAATATCTCCGTTGCCTGAA 60.055 43.478 0.00 0.00 0.00 3.02
2682 2892 3.960102 AGTTCCATCCTGCAAGTTCAAAA 59.040 39.130 0.00 0.00 0.00 2.44
2689 2899 3.118542 CCTGCAAGTTCAAAAGTTCAGC 58.881 45.455 0.00 0.00 0.00 4.26
2698 2908 4.404507 TCAAAAGTTCAGCGTAATCAGC 57.595 40.909 0.00 0.00 0.00 4.26
2704 2914 0.526310 TCAGCGTAATCAGCAGAGCG 60.526 55.000 0.00 0.00 37.01 5.03
2705 2915 1.880340 AGCGTAATCAGCAGAGCGC 60.880 57.895 14.34 14.34 40.85 5.92
2707 2917 1.695893 GCGTAATCAGCAGAGCGCAA 61.696 55.000 11.47 0.00 46.13 4.85
2710 2920 2.208431 GTAATCAGCAGAGCGCAAGAT 58.792 47.619 11.47 0.00 46.13 2.40
2712 2922 2.609427 ATCAGCAGAGCGCAAGATAA 57.391 45.000 11.47 0.00 46.13 1.75
2714 2924 2.698803 TCAGCAGAGCGCAAGATAAAA 58.301 42.857 11.47 0.00 46.13 1.52
2715 2925 3.073678 TCAGCAGAGCGCAAGATAAAAA 58.926 40.909 11.47 0.00 46.13 1.94
2716 2926 3.691118 TCAGCAGAGCGCAAGATAAAAAT 59.309 39.130 11.47 0.00 46.13 1.82
2729 2939 9.726034 CGCAAGATAAAAATAAACAATTCACAC 57.274 29.630 0.00 0.00 43.02 3.82
2747 2957 0.036010 ACGGACATCTTGGAAGCCAG 60.036 55.000 0.00 0.00 33.81 4.85
2760 2970 2.588314 GCCAGCGATGCTCTCCAG 60.588 66.667 0.00 0.00 36.40 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 3.000819 CCTACCGGAGTGGCACCA 61.001 66.667 15.27 0.00 43.94 4.17
2 3 3.001406 ACCTACCGGAGTGGCACC 61.001 66.667 15.27 5.76 43.94 5.01
15 16 1.684983 GGCTAGGCATTACGTGACCTA 59.315 52.381 12.16 2.95 36.01 3.08
16 17 0.464452 GGCTAGGCATTACGTGACCT 59.536 55.000 12.16 1.74 36.01 3.85
19 20 1.440060 CGGGCTAGGCATTACGTGA 59.560 57.895 19.14 0.00 0.00 4.35
84 86 1.522569 CGGGCGAGAGGAGGAAATT 59.477 57.895 0.00 0.00 0.00 1.82
105 111 2.746277 GTGGAAAGTGGCGGCGAT 60.746 61.111 12.98 0.00 0.00 4.58
139 145 0.610785 CGTTGGGGGTTGGCAACTAT 60.611 55.000 27.77 0.00 37.61 2.12
155 166 2.990967 TCCTTACCCGACGGCGTT 60.991 61.111 16.19 0.00 35.23 4.84
283 294 2.023888 CCTCCTTCTCCTCCAAGTCCTA 60.024 54.545 0.00 0.00 0.00 2.94
363 393 0.460987 GCCTGCTACTTCGTCTGCAT 60.461 55.000 0.00 0.00 34.79 3.96
465 495 2.096980 ACGCGATCATCTTGTCGACTTA 59.903 45.455 15.93 3.92 40.11 2.24
474 507 5.358160 TCTCATCCATATACGCGATCATCTT 59.642 40.000 15.93 0.00 0.00 2.40
480 513 4.017126 TCCTTCTCATCCATATACGCGAT 58.983 43.478 15.93 4.50 0.00 4.58
562 610 5.069119 ACACCTAGCTATGATTCATCGTCAA 59.931 40.000 1.55 0.00 0.00 3.18
645 705 7.306574 CGGTCAGGTTTTAAATTTGCTCTTTTC 60.307 37.037 0.00 0.00 0.00 2.29
678 738 4.041917 TACACCCACCGACGCGTC 62.042 66.667 28.96 28.96 0.00 5.19
685 745 3.045492 GGCAACGTACACCCACCG 61.045 66.667 0.00 0.00 0.00 4.94
806 867 1.658994 CTGGTTGTGTTGTACCGTGT 58.341 50.000 0.00 0.00 37.23 4.49
812 873 1.894756 GCGGGCTGGTTGTGTTGTA 60.895 57.895 0.00 0.00 0.00 2.41
813 874 3.216292 GCGGGCTGGTTGTGTTGT 61.216 61.111 0.00 0.00 0.00 3.32
814 875 3.215568 TGCGGGCTGGTTGTGTTG 61.216 61.111 0.00 0.00 0.00 3.33
815 876 3.216292 GTGCGGGCTGGTTGTGTT 61.216 61.111 0.00 0.00 0.00 3.32
821 885 0.466555 TACTTTTTGTGCGGGCTGGT 60.467 50.000 0.00 0.00 0.00 4.00
854 918 2.881403 GCAGCTTGAGAGATTTGGGGAA 60.881 50.000 0.00 0.00 0.00 3.97
855 919 1.340405 GCAGCTTGAGAGATTTGGGGA 60.340 52.381 0.00 0.00 0.00 4.81
869 933 4.749310 CGTCTCGGCTGGCAGCTT 62.749 66.667 35.73 0.00 41.99 3.74
880 944 2.184830 TATGGGTCTCGCCGTCTCG 61.185 63.158 0.00 0.00 38.44 4.04
881 945 1.359475 GTATGGGTCTCGCCGTCTC 59.641 63.158 0.00 0.00 38.44 3.36
882 946 2.125961 GGTATGGGTCTCGCCGTCT 61.126 63.158 0.00 0.00 38.44 4.18
883 947 1.745320 ATGGTATGGGTCTCGCCGTC 61.745 60.000 0.00 0.00 38.44 4.79
884 948 0.468585 TATGGTATGGGTCTCGCCGT 60.469 55.000 0.00 0.00 38.44 5.68
885 949 0.677288 TTATGGTATGGGTCTCGCCG 59.323 55.000 0.00 0.00 38.44 6.46
886 950 2.158871 TGTTTATGGTATGGGTCTCGCC 60.159 50.000 0.00 0.00 0.00 5.54
887 951 3.188159 TGTTTATGGTATGGGTCTCGC 57.812 47.619 0.00 0.00 0.00 5.03
888 952 3.560068 GCTTGTTTATGGTATGGGTCTCG 59.440 47.826 0.00 0.00 0.00 4.04
889 953 3.883489 GGCTTGTTTATGGTATGGGTCTC 59.117 47.826 0.00 0.00 0.00 3.36
890 954 3.527665 AGGCTTGTTTATGGTATGGGTCT 59.472 43.478 0.00 0.00 0.00 3.85
891 955 3.898482 AGGCTTGTTTATGGTATGGGTC 58.102 45.455 0.00 0.00 0.00 4.46
892 956 5.663158 ATAGGCTTGTTTATGGTATGGGT 57.337 39.130 0.00 0.00 0.00 4.51
893 957 6.148811 CGTAATAGGCTTGTTTATGGTATGGG 59.851 42.308 0.00 0.00 0.00 4.00
894 958 6.348213 GCGTAATAGGCTTGTTTATGGTATGG 60.348 42.308 0.00 0.00 0.00 2.74
895 959 6.599437 GCGTAATAGGCTTGTTTATGGTATG 58.401 40.000 0.00 0.00 0.00 2.39
896 960 5.407387 CGCGTAATAGGCTTGTTTATGGTAT 59.593 40.000 0.00 0.00 0.00 2.73
897 961 4.746115 CGCGTAATAGGCTTGTTTATGGTA 59.254 41.667 0.00 0.00 0.00 3.25
898 962 3.558418 CGCGTAATAGGCTTGTTTATGGT 59.442 43.478 0.00 0.00 0.00 3.55
930 998 1.096416 GTGGTGGTTTGACCGTTTGA 58.904 50.000 0.00 0.00 42.58 2.69
931 999 0.248296 CGTGGTGGTTTGACCGTTTG 60.248 55.000 0.00 0.00 42.58 2.93
932 1000 1.378124 CCGTGGTGGTTTGACCGTTT 61.378 55.000 0.00 0.00 42.58 3.60
933 1001 1.820481 CCGTGGTGGTTTGACCGTT 60.820 57.895 0.00 0.00 42.58 4.44
934 1002 2.203098 CCGTGGTGGTTTGACCGT 60.203 61.111 0.00 0.00 42.58 4.83
935 1003 1.096386 TTTCCGTGGTGGTTTGACCG 61.096 55.000 0.00 0.00 42.58 4.79
936 1004 1.066454 CTTTTCCGTGGTGGTTTGACC 59.934 52.381 0.00 0.00 39.52 4.02
937 1005 1.066454 CCTTTTCCGTGGTGGTTTGAC 59.934 52.381 0.00 0.00 39.52 3.18
979 1047 2.440247 GGATTTGGCACGGGGGAG 60.440 66.667 0.00 0.00 0.00 4.30
980 1048 3.260888 TGGATTTGGCACGGGGGA 61.261 61.111 0.00 0.00 0.00 4.81
1009 1081 6.561519 AGATCTTTTTCGGATCCTTCCTTA 57.438 37.500 10.75 0.00 40.07 2.69
1065 1138 1.500783 CCCCTTTTGCTCTCTCCCCA 61.501 60.000 0.00 0.00 0.00 4.96
1119 1192 0.948678 GGGAGGAGATCTCGAGTTCG 59.051 60.000 16.46 0.00 43.34 3.95
1200 1273 1.811679 GGGCGAAGAGAAGCGGAAG 60.812 63.158 0.00 0.00 0.00 3.46
1230 1303 0.110464 GCAGCGCAGAGAGTCAAAAC 60.110 55.000 11.47 0.00 0.00 2.43
1257 1336 2.554893 GCTCCTCGACCTTATCCTACAG 59.445 54.545 0.00 0.00 0.00 2.74
1306 1385 1.658717 GCATCCTCGTCGTCATCCG 60.659 63.158 0.00 0.00 38.13 4.18
1474 1558 3.060138 TCGTTTCCGATTTCACAAGTTCG 60.060 43.478 0.00 0.00 38.40 3.95
1483 1567 5.511729 GGACATCAATTTCGTTTCCGATTTC 59.488 40.000 0.00 0.00 43.80 2.17
1496 1580 5.728741 AGAGAGGAAGGTAGGACATCAATTT 59.271 40.000 0.00 0.00 0.00 1.82
1513 1597 4.078922 AGAGAGAGAGAGAGAGAGAGAGGA 60.079 50.000 0.00 0.00 0.00 3.71
1514 1598 4.039004 CAGAGAGAGAGAGAGAGAGAGAGG 59.961 54.167 0.00 0.00 0.00 3.69
1515 1599 4.648762 ACAGAGAGAGAGAGAGAGAGAGAG 59.351 50.000 0.00 0.00 0.00 3.20
1516 1600 4.614475 ACAGAGAGAGAGAGAGAGAGAGA 58.386 47.826 0.00 0.00 0.00 3.10
1517 1601 4.498850 CGACAGAGAGAGAGAGAGAGAGAG 60.499 54.167 0.00 0.00 0.00 3.20
1518 1602 3.381590 CGACAGAGAGAGAGAGAGAGAGA 59.618 52.174 0.00 0.00 0.00 3.10
1519 1603 3.491619 CCGACAGAGAGAGAGAGAGAGAG 60.492 56.522 0.00 0.00 0.00 3.20
1520 1604 2.430694 CCGACAGAGAGAGAGAGAGAGA 59.569 54.545 0.00 0.00 0.00 3.10
1545 1629 3.060978 TCGATCTGATACGACCAAACG 57.939 47.619 7.70 0.00 39.31 3.60
1833 1933 1.612950 TGTACGTACGCAAGGAAAGGA 59.387 47.619 20.18 0.00 46.39 3.36
1862 1965 4.434330 GCAAAGTCGTAAAGAACAGATCGG 60.434 45.833 0.00 0.00 0.00 4.18
1918 2021 5.410132 CGTATCCCATTTGTACACAAGAACA 59.590 40.000 0.00 0.00 37.15 3.18
2015 2118 8.765488 AGATCATTCTCTTCTATCAAGTGAGA 57.235 34.615 0.00 0.00 34.30 3.27
2076 2201 5.902681 TGTCTCCGTTAAAATCGATGAGAT 58.097 37.500 11.22 0.00 42.43 2.75
2077 2202 5.319140 TGTCTCCGTTAAAATCGATGAGA 57.681 39.130 0.00 1.69 0.00 3.27
2106 2231 7.148069 GGTCAAAGGGTTTTTATCGATGAGATT 60.148 37.037 8.54 0.00 40.66 2.40
2108 2233 5.646360 GGTCAAAGGGTTTTTATCGATGAGA 59.354 40.000 8.54 0.00 0.00 3.27
2109 2234 5.447279 CGGTCAAAGGGTTTTTATCGATGAG 60.447 44.000 8.54 0.00 0.00 2.90
2111 2236 4.658071 CGGTCAAAGGGTTTTTATCGATG 58.342 43.478 8.54 0.00 0.00 3.84
2112 2237 3.128068 GCGGTCAAAGGGTTTTTATCGAT 59.872 43.478 2.16 2.16 0.00 3.59
2113 2238 2.485038 GCGGTCAAAGGGTTTTTATCGA 59.515 45.455 0.00 0.00 0.00 3.59
2115 2240 2.858839 CGCGGTCAAAGGGTTTTTATC 58.141 47.619 0.00 0.00 0.00 1.75
2118 2243 1.066752 GCGCGGTCAAAGGGTTTTT 59.933 52.632 8.83 0.00 0.00 1.94
2147 2328 2.358898 GTGGTGCATTCAGAGTGTTTGT 59.641 45.455 0.00 0.00 0.00 2.83
2148 2329 2.358582 TGTGGTGCATTCAGAGTGTTTG 59.641 45.455 0.00 0.00 0.00 2.93
2149 2330 2.653726 TGTGGTGCATTCAGAGTGTTT 58.346 42.857 0.00 0.00 0.00 2.83
2150 2331 2.346766 TGTGGTGCATTCAGAGTGTT 57.653 45.000 0.00 0.00 0.00 3.32
2181 2362 1.448985 TTGAAATGTAGAGGCGTGGC 58.551 50.000 0.00 0.00 0.00 5.01
2186 2367 4.082190 GGGTTTCCTTTGAAATGTAGAGGC 60.082 45.833 0.00 0.00 42.20 4.70
2197 2378 6.211785 GGTGTTATTATTGGGGTTTCCTTTGA 59.788 38.462 0.00 0.00 36.20 2.69
2213 2394 4.216042 TCGTCTTCAGTCGTGGTGTTATTA 59.784 41.667 0.00 0.00 0.00 0.98
2216 2397 1.948834 TCGTCTTCAGTCGTGGTGTTA 59.051 47.619 0.00 0.00 0.00 2.41
2222 2403 0.725118 GTCCGTCGTCTTCAGTCGTG 60.725 60.000 0.00 0.00 0.00 4.35
2224 2405 0.725118 GTGTCCGTCGTCTTCAGTCG 60.725 60.000 0.00 0.00 0.00 4.18
2235 2416 0.250553 TGGATTTGGTGGTGTCCGTC 60.251 55.000 0.00 0.00 33.39 4.79
2396 2606 5.113383 TGTATATTTGTAACCTGTGCCTCG 58.887 41.667 0.00 0.00 0.00 4.63
2401 2611 6.767902 AGCTGGATGTATATTTGTAACCTGTG 59.232 38.462 0.00 0.00 0.00 3.66
2441 2651 7.520798 AGATCTTAGATATGGTGATTTTGGCA 58.479 34.615 0.00 0.00 0.00 4.92
2477 2687 0.101579 TTGTGAAGCTCGACGACACA 59.898 50.000 13.20 13.20 37.40 3.72
2504 2714 7.440556 GGAAAACTTATAGGAATAGACGGTTCC 59.559 40.741 4.31 4.31 44.39 3.62
2540 2750 3.711704 AGATCATGAATGGTACCTTCCGT 59.288 43.478 14.36 0.00 0.00 4.69
2612 2822 3.735820 GCAACGGAGATATTGTGACGGTA 60.736 47.826 0.00 0.00 0.00 4.02
2624 2834 0.250513 GGTCTTCAGGCAACGGAGAT 59.749 55.000 0.00 0.00 43.33 2.75
2639 2849 2.111043 CGTGTGGCACTTGGGTCT 59.889 61.111 19.83 0.00 31.34 3.85
2682 2892 2.886081 CTCTGCTGATTACGCTGAACT 58.114 47.619 0.00 0.00 35.42 3.01
2689 2899 0.299895 CTTGCGCTCTGCTGATTACG 59.700 55.000 9.73 0.36 46.63 3.18
2698 2908 7.795431 TTGTTTATTTTTATCTTGCGCTCTG 57.205 32.000 9.73 0.00 0.00 3.35
2704 2914 9.726034 CGTGTGAATTGTTTATTTTTATCTTGC 57.274 29.630 0.00 0.00 0.00 4.01
2707 2917 9.620660 GTCCGTGTGAATTGTTTATTTTTATCT 57.379 29.630 0.00 0.00 0.00 1.98
2710 2920 9.400638 GATGTCCGTGTGAATTGTTTATTTTTA 57.599 29.630 0.00 0.00 0.00 1.52
2712 2922 7.657336 AGATGTCCGTGTGAATTGTTTATTTT 58.343 30.769 0.00 0.00 0.00 1.82
2714 2924 6.817765 AGATGTCCGTGTGAATTGTTTATT 57.182 33.333 0.00 0.00 0.00 1.40
2715 2925 6.349280 CCAAGATGTCCGTGTGAATTGTTTAT 60.349 38.462 0.00 0.00 0.00 1.40
2716 2926 5.049060 CCAAGATGTCCGTGTGAATTGTTTA 60.049 40.000 0.00 0.00 0.00 2.01
2729 2939 1.372087 GCTGGCTTCCAAGATGTCCG 61.372 60.000 0.00 0.00 30.80 4.79
2747 2957 1.520342 GTGTCCTGGAGAGCATCGC 60.520 63.158 0.00 0.00 42.67 4.58
2760 2970 0.328258 AGTGCTTGGGGTATGTGTCC 59.672 55.000 0.00 0.00 0.00 4.02
2852 3062 3.322466 AGGTGGCGAGGGTGAAGG 61.322 66.667 0.00 0.00 0.00 3.46


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

AutoCloner maintained by Alex Coulton.