Multiple sequence alignment - TraesCS7B01G059200

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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 TraesCS7B01G059200 chr7B 100.000 2851 0 0 1 2851 61747323 61744473 0.000000e+00 5265.0
1 TraesCS7B01G059200 chr7B 89.479 1939 154 22 1 1901 61628991 61627065 0.000000e+00 2405.0
2 TraesCS7B01G059200 chr7B 81.897 116 19 2 1136 1249 425159128 425159243 2.340000e-16 97.1
3 TraesCS7B01G059200 chr7D 91.344 2657 167 24 1 2652 103333382 103330784 0.000000e+00 3574.0
4 TraesCS7B01G059200 chr7D 91.981 1908 133 9 1 1899 103212145 103210249 0.000000e+00 2658.0
5 TraesCS7B01G059200 chr7D 79.861 144 26 3 1136 1277 410522327 410522185 5.030000e-18 102.0
6 TraesCS7B01G059200 chr7D 88.312 77 7 1 2775 2851 103330697 103330623 1.090000e-14 91.6
7 TraesCS7B01G059200 chr7A 91.543 1880 137 11 1 1869 107917842 107915974 0.000000e+00 2571.0
8 TraesCS7B01G059200 chr7A 79.487 429 59 21 1998 2420 33534723 33534318 7.780000e-71 278.0
9 TraesCS7B01G059200 chr7A 77.865 384 58 18 2448 2806 276105674 276106055 2.230000e-51 213.0
10 TraesCS7B01G059200 chr5D 83.557 298 42 7 2507 2800 553862121 553861827 3.620000e-69 272.0
11 TraesCS7B01G059200 chr3A 82.595 316 45 8 2456 2764 730112056 730111744 1.300000e-68 270.0
12 TraesCS7B01G059200 chr3A 78.515 377 58 16 2454 2812 620752023 620751652 2.860000e-55 226.0
13 TraesCS7B01G059200 chr3A 80.519 308 44 13 2507 2807 235809798 235809500 3.700000e-54 222.0
14 TraesCS7B01G059200 chr2B 80.759 369 52 9 2455 2807 87830905 87830540 1.300000e-68 270.0
15 TraesCS7B01G059200 chr2B 81.588 277 49 2 2509 2783 441895626 441895902 7.950000e-56 228.0
16 TraesCS7B01G059200 chr2B 78.231 294 44 13 993 1284 152504411 152504686 1.360000e-38 171.0
17 TraesCS7B01G059200 chr1A 80.308 325 56 5 2489 2809 314613249 314612929 3.670000e-59 239.0
18 TraesCS7B01G059200 chr2A 78.125 288 47 11 993 1278 100627888 100627615 4.880000e-38 169.0
19 TraesCS7B01G059200 chr2D 78.846 260 43 8 1021 1278 100432360 100432609 6.320000e-37 165.0


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 TraesCS7B01G059200 chr7B 61744473 61747323 2850 True 5265.0 5265 100.000 1 2851 1 chr7B.!!$R2 2850
1 TraesCS7B01G059200 chr7B 61627065 61628991 1926 True 2405.0 2405 89.479 1 1901 1 chr7B.!!$R1 1900
2 TraesCS7B01G059200 chr7D 103210249 103212145 1896 True 2658.0 2658 91.981 1 1899 1 chr7D.!!$R1 1898
3 TraesCS7B01G059200 chr7D 103330623 103333382 2759 True 1832.8 3574 89.828 1 2851 2 chr7D.!!$R3 2850
4 TraesCS7B01G059200 chr7A 107915974 107917842 1868 True 2571.0 2571 91.543 1 1869 1 chr7A.!!$R2 1868

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
611 657 0.323629 ATGGCCTCGTTTTCTCCGAA 59.676 50.0 3.32 0.0 33.34 4.3 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2486 2554 0.254178 CATTGGTGGGAGGTGAGGAG 59.746 60.0 0.0 0.0 0.0 3.69 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
59 60 1.075482 CCCAATCCACCAGTGCAGT 59.925 57.895 0.00 0.00 0.00 4.40
71 73 2.414957 CCAGTGCAGTAACATCGTACGA 60.415 50.000 21.93 21.93 0.00 3.43
73 75 3.857665 CAGTGCAGTAACATCGTACGAAT 59.142 43.478 23.56 13.82 0.00 3.34
75 77 5.513849 CAGTGCAGTAACATCGTACGAATTA 59.486 40.000 23.56 19.54 0.00 1.40
76 78 5.514204 AGTGCAGTAACATCGTACGAATTAC 59.486 40.000 30.01 30.01 33.55 1.89
100 127 6.893784 TATATATGTACGTGCACGCGTGGG 62.894 50.000 37.47 16.86 45.33 4.61
160 200 2.630714 GCACAGATCGATCGTCGCG 61.631 63.158 19.33 0.00 40.21 5.87
234 280 3.939939 TGCTGGCAACCTCGCTGA 61.940 61.111 0.00 0.00 0.00 4.26
464 510 3.432782 GTCGTACGGTAAGATGTTCCTG 58.567 50.000 16.52 0.00 0.00 3.86
550 596 3.379445 CAGGACCGGGCTGTACGT 61.379 66.667 7.57 0.00 0.00 3.57
611 657 0.323629 ATGGCCTCGTTTTCTCCGAA 59.676 50.000 3.32 0.00 33.34 4.30
815 861 2.750637 ACCGCCGACGTGATCTCT 60.751 61.111 0.00 0.00 37.70 3.10
896 942 0.393944 TCCAGTACATCGCCGTCTCT 60.394 55.000 0.00 0.00 0.00 3.10
949 995 0.838987 TACCTCCCCACCAAGACCAC 60.839 60.000 0.00 0.00 0.00 4.16
951 997 2.856988 TCCCCACCAAGACCACCC 60.857 66.667 0.00 0.00 0.00 4.61
952 998 2.858974 CCCCACCAAGACCACCCT 60.859 66.667 0.00 0.00 0.00 4.34
953 999 2.436109 CCCACCAAGACCACCCTG 59.564 66.667 0.00 0.00 0.00 4.45
954 1000 2.282462 CCACCAAGACCACCCTGC 60.282 66.667 0.00 0.00 0.00 4.85
955 1001 2.669569 CACCAAGACCACCCTGCG 60.670 66.667 0.00 0.00 0.00 5.18
956 1002 3.953775 ACCAAGACCACCCTGCGG 61.954 66.667 0.00 0.00 0.00 5.69
1087 1133 1.078918 CTGATGCTCGAGGCCAACA 60.079 57.895 15.58 8.54 40.92 3.33
1206 1252 2.608988 CACCTCCTCACCTGGGCT 60.609 66.667 0.00 0.00 0.00 5.19
1224 1270 1.403814 CTATCTTCCTCCTCGGCACA 58.596 55.000 0.00 0.00 0.00 4.57
1272 1318 2.903404 GGAGGTCCTCCGAGAATGT 58.097 57.895 22.53 0.00 41.08 2.71
1340 1398 1.413077 GCTCGTAAGCCCCTGTCTATT 59.587 52.381 0.00 0.00 43.10 1.73
1345 1403 3.576982 CGTAAGCCCCTGTCTATTCCATA 59.423 47.826 0.00 0.00 0.00 2.74
1351 1409 6.091555 AGCCCCTGTCTATTCCATAATTCTA 58.908 40.000 0.00 0.00 0.00 2.10
1352 1410 6.214412 AGCCCCTGTCTATTCCATAATTCTAG 59.786 42.308 0.00 0.00 0.00 2.43
1354 1412 6.214412 CCCCTGTCTATTCCATAATTCTAGCT 59.786 42.308 0.00 0.00 0.00 3.32
1355 1413 7.400339 CCCCTGTCTATTCCATAATTCTAGCTA 59.600 40.741 0.00 0.00 0.00 3.32
1359 1417 9.712305 TGTCTATTCCATAATTCTAGCTAAAGC 57.288 33.333 0.00 0.00 42.49 3.51
1371 1429 2.739293 GCTAAAGCTCGTAATGCACC 57.261 50.000 0.00 0.00 38.21 5.01
1377 1437 1.369091 GCTCGTAATGCACCCCACAG 61.369 60.000 0.00 0.00 0.00 3.66
1388 1448 2.126307 CCCACAGCGACGAGTGAG 60.126 66.667 18.62 5.44 37.97 3.51
1409 1476 3.319405 AGACTCACTTCACTTGTGATCGT 59.681 43.478 4.18 2.90 42.57 3.73
1413 1480 3.802139 TCACTTCACTTGTGATCGTTGAC 59.198 43.478 4.18 0.00 39.23 3.18
1544 1611 1.070758 GGCACGATCACCATGATACCT 59.929 52.381 0.00 0.00 37.20 3.08
1655 1722 1.594194 CCAAGCACCCAAGCGCAATA 61.594 55.000 11.47 0.00 40.15 1.90
1703 1770 3.390521 ATCGGGCAGGACTTCGCA 61.391 61.111 0.00 0.00 0.00 5.10
1766 1833 2.655685 GAGTTCGAGATCGCGCCC 60.656 66.667 14.47 6.72 39.60 6.13
1856 1924 2.665165 CTCCTGGATCAGTAGAGCAGT 58.335 52.381 0.00 0.00 0.00 4.40
1881 1949 4.167268 CCTCTTTGAACGACTACTGCTAC 58.833 47.826 0.00 0.00 0.00 3.58
1910 1978 6.325804 AGAAGTATAAAATACACTAGCGGGGT 59.674 38.462 0.00 0.00 34.87 4.95
1957 2025 1.529865 GTTGCCCGTAGTTGTCTCAAC 59.470 52.381 4.69 4.69 0.00 3.18
1961 2029 2.685100 CCCGTAGTTGTCTCAACTTCC 58.315 52.381 18.02 9.94 0.00 3.46
2048 2116 2.894126 ACCCATGGTGAACGCAAAAATA 59.106 40.909 11.73 0.00 32.98 1.40
2078 2146 7.966246 TCCAAATCCATTCAAAACAGAATTG 57.034 32.000 0.00 0.00 36.13 2.32
2080 2148 7.874016 TCCAAATCCATTCAAAACAGAATTGAG 59.126 33.333 0.00 0.00 38.01 3.02
2109 2177 5.471797 TCAGAATTTTCCGTTGATGTAAGCA 59.528 36.000 0.00 0.00 0.00 3.91
2115 2183 2.546368 TCCGTTGATGTAAGCACACAAC 59.454 45.455 0.00 0.00 40.01 3.32
2135 2203 6.953743 CACAACTCTTACATTATTGTACGTGC 59.046 38.462 0.00 0.00 38.05 5.34
2150 2218 6.656314 TGTACGTGCTACCTGAATAATTTG 57.344 37.500 4.97 0.00 0.00 2.32
2185 2253 3.642705 CAAGAAGCACTACCTTTTTGCC 58.357 45.455 0.00 0.00 36.91 4.52
2196 2264 1.407989 CCTTTTTGCCAAAGCCACCAA 60.408 47.619 0.00 0.00 38.69 3.67
2209 2277 0.452987 CCACCAAATCAGCATCCGTG 59.547 55.000 0.00 0.00 0.00 4.94
2223 2291 8.803397 TCAGCATCCGTGTACTATATTATACT 57.197 34.615 0.00 0.00 0.00 2.12
2227 2295 8.456471 GCATCCGTGTACTATATTATACTGTCA 58.544 37.037 0.00 0.00 0.00 3.58
2274 2342 7.093112 ACCAAATCTATACTCAGAGCAGTTTCT 60.093 37.037 0.00 0.00 0.00 2.52
2276 2344 9.462174 CAAATCTATACTCAGAGCAGTTTCTAG 57.538 37.037 0.00 0.00 0.00 2.43
2308 2376 8.477256 CCAATAATTCTTTCATAGCCCTTTGAA 58.523 33.333 0.00 0.00 0.00 2.69
2340 2408 4.417426 ACCGGGGTGATTATGTAAGAAG 57.583 45.455 6.32 0.00 0.00 2.85
2343 2411 5.057149 CCGGGGTGATTATGTAAGAAGAAG 58.943 45.833 0.00 0.00 0.00 2.85
2429 2497 9.886132 CACTTCATATATCCTGAATGATGATGA 57.114 33.333 0.00 0.00 32.50 2.92
2442 2510 6.317893 TGAATGATGATGAATGTCTCAACTGG 59.682 38.462 0.00 0.00 37.67 4.00
2446 2514 6.888088 TGATGATGAATGTCTCAACTGGAATT 59.112 34.615 0.00 0.00 37.67 2.17
2479 2547 4.955335 TCTACTCTTAATGGGGGAGTTGA 58.045 43.478 0.00 0.00 40.29 3.18
2486 2554 5.602978 TCTTAATGGGGGAGTTGATAGTCTC 59.397 44.000 0.00 0.00 0.00 3.36
2487 2555 3.715648 ATGGGGGAGTTGATAGTCTCT 57.284 47.619 0.00 0.00 0.00 3.10
2496 2564 4.532834 AGTTGATAGTCTCTCCTCACCTC 58.467 47.826 0.00 0.00 0.00 3.85
2505 2573 0.254178 CTCCTCACCTCCCACCAATG 59.746 60.000 0.00 0.00 0.00 2.82
2535 2603 2.949451 CTCACGAGCATCTTACAGGT 57.051 50.000 0.00 0.00 0.00 4.00
2536 2604 2.803451 CTCACGAGCATCTTACAGGTC 58.197 52.381 0.00 0.00 0.00 3.85
2537 2605 2.164422 CTCACGAGCATCTTACAGGTCA 59.836 50.000 0.00 0.00 32.77 4.02
2547 2615 5.675575 GCATCTTACAGGTCATCTTTTGCTG 60.676 44.000 0.00 0.00 0.00 4.41
2554 2622 1.069022 GTCATCTTTTGCTGAAGCGCA 60.069 47.619 11.47 0.00 45.83 6.09
2574 2642 3.530260 CATGTTGCCCGGCCCATC 61.530 66.667 7.03 0.00 0.00 3.51
2578 2646 4.424711 TTGCCCGGCCCATCTGAC 62.425 66.667 7.03 0.00 0.00 3.51
2588 2656 1.596603 CCCATCTGACGCATGCATTA 58.403 50.000 19.57 0.00 0.00 1.90
2596 2664 4.018649 TGACGCATGCATTAACTCAATG 57.981 40.909 19.57 0.00 45.87 2.82
2599 2667 4.665212 ACGCATGCATTAACTCAATGAAG 58.335 39.130 19.57 0.00 45.99 3.02
2601 2669 3.800506 GCATGCATTAACTCAATGAAGCC 59.199 43.478 14.21 0.00 45.99 4.35
2603 2671 3.342719 TGCATTAACTCAATGAAGCCGA 58.657 40.909 1.26 0.00 45.99 5.54
2620 2688 2.223947 GCCGACACTTTCCCAAAACAAT 60.224 45.455 0.00 0.00 0.00 2.71
2623 2691 3.796178 CGACACTTTCCCAAAACAATGTG 59.204 43.478 0.00 0.00 35.07 3.21
2684 2752 9.403583 TCTCAACTAAATCCAAACTTTACTTGT 57.596 29.630 0.00 0.00 0.00 3.16
2685 2753 9.665264 CTCAACTAAATCCAAACTTTACTTGTC 57.335 33.333 0.00 0.00 0.00 3.18
2686 2754 8.626526 TCAACTAAATCCAAACTTTACTTGTCC 58.373 33.333 0.00 0.00 0.00 4.02
2687 2755 8.630037 CAACTAAATCCAAACTTTACTTGTCCT 58.370 33.333 0.00 0.00 0.00 3.85
2688 2756 8.392372 ACTAAATCCAAACTTTACTTGTCCTC 57.608 34.615 0.00 0.00 0.00 3.71
2689 2757 8.218488 ACTAAATCCAAACTTTACTTGTCCTCT 58.782 33.333 0.00 0.00 0.00 3.69
2690 2758 7.511959 AAATCCAAACTTTACTTGTCCTCTC 57.488 36.000 0.00 0.00 0.00 3.20
2691 2759 4.969484 TCCAAACTTTACTTGTCCTCTCC 58.031 43.478 0.00 0.00 0.00 3.71
2692 2760 4.658901 TCCAAACTTTACTTGTCCTCTCCT 59.341 41.667 0.00 0.00 0.00 3.69
2693 2761 5.842328 TCCAAACTTTACTTGTCCTCTCCTA 59.158 40.000 0.00 0.00 0.00 2.94
2694 2762 5.932883 CCAAACTTTACTTGTCCTCTCCTAC 59.067 44.000 0.00 0.00 0.00 3.18
2695 2763 6.239629 CCAAACTTTACTTGTCCTCTCCTACT 60.240 42.308 0.00 0.00 0.00 2.57
2696 2764 6.593268 AACTTTACTTGTCCTCTCCTACTC 57.407 41.667 0.00 0.00 0.00 2.59
2697 2765 5.642165 ACTTTACTTGTCCTCTCCTACTCA 58.358 41.667 0.00 0.00 0.00 3.41
2698 2766 6.257586 ACTTTACTTGTCCTCTCCTACTCAT 58.742 40.000 0.00 0.00 0.00 2.90
2699 2767 7.411808 ACTTTACTTGTCCTCTCCTACTCATA 58.588 38.462 0.00 0.00 0.00 2.15
2700 2768 7.339976 ACTTTACTTGTCCTCTCCTACTCATAC 59.660 40.741 0.00 0.00 0.00 2.39
2701 2769 4.538738 ACTTGTCCTCTCCTACTCATACC 58.461 47.826 0.00 0.00 0.00 2.73
2702 2770 3.596940 TGTCCTCTCCTACTCATACCC 57.403 52.381 0.00 0.00 0.00 3.69
2703 2771 2.856864 TGTCCTCTCCTACTCATACCCA 59.143 50.000 0.00 0.00 0.00 4.51
2704 2772 3.271225 TGTCCTCTCCTACTCATACCCAA 59.729 47.826 0.00 0.00 0.00 4.12
2705 2773 4.264668 TGTCCTCTCCTACTCATACCCAAA 60.265 45.833 0.00 0.00 0.00 3.28
2706 2774 4.902448 GTCCTCTCCTACTCATACCCAAAT 59.098 45.833 0.00 0.00 0.00 2.32
2707 2775 5.011227 GTCCTCTCCTACTCATACCCAAATC 59.989 48.000 0.00 0.00 0.00 2.17
2708 2776 4.901849 CCTCTCCTACTCATACCCAAATCA 59.098 45.833 0.00 0.00 0.00 2.57
2709 2777 5.366768 CCTCTCCTACTCATACCCAAATCAA 59.633 44.000 0.00 0.00 0.00 2.57
2710 2778 6.126768 CCTCTCCTACTCATACCCAAATCAAA 60.127 42.308 0.00 0.00 0.00 2.69
2713 2781 8.998814 TCTCCTACTCATACCCAAATCAAATAA 58.001 33.333 0.00 0.00 0.00 1.40
2758 2827 0.407528 TCAAAGTTGGCAGGCCCATA 59.592 50.000 8.02 0.00 44.89 2.74
2761 2830 0.630673 AAGTTGGCAGGCCCATATGA 59.369 50.000 8.02 0.00 44.89 2.15
2768 2837 1.751733 GCAGGCCCATATGATGTGTGT 60.752 52.381 3.65 0.00 0.00 3.72
2770 2839 1.565759 AGGCCCATATGATGTGTGTGT 59.434 47.619 3.65 0.00 0.00 3.72
2771 2840 1.677576 GGCCCATATGATGTGTGTGTG 59.322 52.381 3.65 0.00 0.00 3.82
2776 2845 4.142116 CCCATATGATGTGTGTGTGCATTT 60.142 41.667 3.65 0.00 0.00 2.32
2785 2854 6.595772 TGTGTGTGTGCATTTTTATTTTCC 57.404 33.333 0.00 0.00 0.00 3.13
2787 2856 6.478344 TGTGTGTGTGCATTTTTATTTTCCTC 59.522 34.615 0.00 0.00 0.00 3.71
2788 2857 6.701400 GTGTGTGTGCATTTTTATTTTCCTCT 59.299 34.615 0.00 0.00 0.00 3.69
2791 2860 8.063630 GTGTGTGCATTTTTATTTTCCTCTTTG 58.936 33.333 0.00 0.00 0.00 2.77
2793 2862 8.275632 GTGTGCATTTTTATTTTCCTCTTTGTC 58.724 33.333 0.00 0.00 0.00 3.18
2835 2926 9.793252 ATGACAAATCTATTATTTTGTGCTCAC 57.207 29.630 5.83 0.00 43.95 3.51
2848 2939 2.700371 TGTGCTCACCATACTATCAGGG 59.300 50.000 0.00 0.00 0.00 4.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
71 73 6.249893 CGCGTGCACGTACATATATAGTAATT 59.750 38.462 36.80 0.00 42.22 1.40
73 75 5.081394 CGCGTGCACGTACATATATAGTAA 58.919 41.667 36.80 0.00 42.22 2.24
75 77 3.058708 ACGCGTGCACGTACATATATAGT 60.059 43.478 36.80 18.61 46.19 2.12
76 78 3.297202 CACGCGTGCACGTACATATATAG 59.703 47.826 36.80 18.06 46.34 1.31
100 127 4.036380 TGATTGATCTGCTGATGATTGTGC 59.964 41.667 11.21 0.00 32.19 4.57
464 510 2.259511 GTGTACCCCGACCACGAC 59.740 66.667 0.00 0.00 42.66 4.34
489 535 2.335369 GAGGTCGCGGACGCATAT 59.665 61.111 17.35 0.00 42.06 1.78
550 596 4.011517 GCCCCGGGTTCGTCTTGA 62.012 66.667 21.85 0.00 33.95 3.02
593 639 0.320421 CTTCGGAGAAAACGAGGCCA 60.320 55.000 5.01 0.00 45.90 5.36
602 648 1.080974 GTCGTCGCCTTCGGAGAAA 60.081 57.895 0.00 0.00 45.90 2.52
763 809 4.077184 GCCCGACGTCATCCACCA 62.077 66.667 17.16 0.00 0.00 4.17
770 816 3.858868 GAACTGCTGCCCGACGTCA 62.859 63.158 17.16 0.00 0.00 4.35
815 861 4.351938 CTCCCGAACGCCGTGTGA 62.352 66.667 0.00 0.00 36.31 3.58
896 942 1.009903 CGCGGACGTTGTTGATGGTA 61.010 55.000 0.00 0.00 33.53 3.25
1068 1114 1.219124 GTTGGCCTCGAGCATCAGA 59.781 57.895 6.99 0.00 46.50 3.27
1137 1183 1.585668 GTCTTGCACTCGTCGATGATG 59.414 52.381 7.99 9.75 0.00 3.07
1186 1232 4.767255 CCAGGTGAGGAGGTGCGC 62.767 72.222 0.00 0.00 0.00 6.09
1206 1252 1.112113 GTGTGCCGAGGAGGAAGATA 58.888 55.000 0.00 0.00 45.00 1.98
1224 1270 3.925630 CTGCTGCCATTCGGGGTGT 62.926 63.158 0.00 0.00 37.04 4.16
1323 1369 1.760613 TGGAATAGACAGGGGCTTACG 59.239 52.381 0.00 0.00 0.00 3.18
1352 1410 1.330829 GGGTGCATTACGAGCTTTAGC 59.669 52.381 0.00 0.00 42.49 3.09
1354 1412 1.279558 TGGGGTGCATTACGAGCTTTA 59.720 47.619 0.00 0.00 0.00 1.85
1355 1413 0.037590 TGGGGTGCATTACGAGCTTT 59.962 50.000 0.00 0.00 0.00 3.51
1358 1416 1.369091 CTGTGGGGTGCATTACGAGC 61.369 60.000 0.00 0.00 0.00 5.03
1359 1417 1.369091 GCTGTGGGGTGCATTACGAG 61.369 60.000 0.00 0.00 0.00 4.18
1360 1418 1.376683 GCTGTGGGGTGCATTACGA 60.377 57.895 0.00 0.00 0.00 3.43
1361 1419 2.749865 CGCTGTGGGGTGCATTACG 61.750 63.158 0.00 0.00 0.00 3.18
1362 1420 1.376683 TCGCTGTGGGGTGCATTAC 60.377 57.895 0.00 0.00 0.00 1.89
1363 1421 1.376683 GTCGCTGTGGGGTGCATTA 60.377 57.895 0.00 0.00 0.00 1.90
1364 1422 2.672996 GTCGCTGTGGGGTGCATT 60.673 61.111 0.00 0.00 0.00 3.56
1371 1429 2.126307 CTCACTCGTCGCTGTGGG 60.126 66.667 14.85 9.94 35.15 4.61
1409 1476 0.948623 CCATTGTCGTCTGCCGTCAA 60.949 55.000 0.00 0.00 45.83 3.18
1413 1480 3.027170 GCACCATTGTCGTCTGCCG 62.027 63.158 0.00 0.00 38.13 5.69
1475 1542 4.147449 TCCGCCATCGTCTGCCTG 62.147 66.667 0.00 0.00 0.00 4.85
1703 1770 2.439156 GCCTTCGCCTCCAGCATT 60.439 61.111 0.00 0.00 44.04 3.56
1758 1825 4.547905 CACGTACTCGGGCGCGAT 62.548 66.667 26.78 17.82 41.85 4.58
1786 1853 2.258591 GCAGCGTCAGGAACTCGA 59.741 61.111 0.00 0.00 34.60 4.04
1856 1924 3.390135 CAGTAGTCGTTCAAAGAGGCAA 58.610 45.455 0.00 0.00 0.00 4.52
1881 1949 9.395707 CCGCTAGTGTATTTTATACTTCTACTG 57.604 37.037 1.99 0.00 32.20 2.74
1892 1960 3.106054 TCCACCCCGCTAGTGTATTTTA 58.894 45.455 1.99 0.00 33.20 1.52
1943 2011 1.719780 GCGGAAGTTGAGACAACTACG 59.280 52.381 23.58 23.58 35.37 3.51
1944 2012 3.027974 AGCGGAAGTTGAGACAACTAC 57.972 47.619 15.77 11.53 0.00 2.73
1957 2025 6.537301 TGTCCAATACACTATTTAAGCGGAAG 59.463 38.462 0.00 0.00 31.43 3.46
1961 2029 8.394877 TGAATTGTCCAATACACTATTTAAGCG 58.605 33.333 0.00 0.00 38.00 4.68
2006 2074 6.015350 TGGGTACAAACAACAAAAGACAGAAA 60.015 34.615 0.00 0.00 0.00 2.52
2007 2075 5.477291 TGGGTACAAACAACAAAAGACAGAA 59.523 36.000 0.00 0.00 0.00 3.02
2008 2076 5.010933 TGGGTACAAACAACAAAAGACAGA 58.989 37.500 0.00 0.00 0.00 3.41
2009 2077 5.317733 TGGGTACAAACAACAAAAGACAG 57.682 39.130 0.00 0.00 0.00 3.51
2010 2078 5.394663 CCATGGGTACAAACAACAAAAGACA 60.395 40.000 2.85 0.00 0.00 3.41
2011 2079 5.047188 CCATGGGTACAAACAACAAAAGAC 58.953 41.667 2.85 0.00 0.00 3.01
2048 2116 3.558608 TTGAATGGATTTGGAAGGGGT 57.441 42.857 0.00 0.00 0.00 4.95
2078 2146 3.336138 ACGGAAAATTCTGAGTCCCTC 57.664 47.619 8.91 0.00 37.03 4.30
2080 2148 3.408634 TCAACGGAAAATTCTGAGTCCC 58.591 45.455 8.91 0.00 37.03 4.46
2088 2156 5.342259 GTGTGCTTACATCAACGGAAAATTC 59.658 40.000 0.00 0.00 0.00 2.17
2096 2164 3.494626 AGAGTTGTGTGCTTACATCAACG 59.505 43.478 14.21 0.00 42.67 4.10
2109 2177 7.359765 GCACGTACAATAATGTAAGAGTTGTGT 60.360 37.037 10.35 0.00 43.41 3.72
2115 2183 7.167635 CAGGTAGCACGTACAATAATGTAAGAG 59.832 40.741 10.35 4.32 43.41 2.85
2125 2193 7.551262 TCAAATTATTCAGGTAGCACGTACAAT 59.449 33.333 0.00 0.00 32.62 2.71
2150 2218 3.756069 GCTTCTTGCACTTGATGACATC 58.244 45.455 8.59 8.59 42.31 3.06
2185 2253 2.613691 GATGCTGATTTGGTGGCTTTG 58.386 47.619 0.00 0.00 0.00 2.77
2243 2311 7.661968 TGCTCTGAGTATAGATTTGGTGATAC 58.338 38.462 6.53 0.00 0.00 2.24
2276 2344 8.951243 GGGCTATGAAAGAATTATTGGACTATC 58.049 37.037 0.00 0.00 0.00 2.08
2321 2389 5.914033 TCTTCTTCTTACATAATCACCCCG 58.086 41.667 0.00 0.00 0.00 5.73
2394 2462 7.938490 TTCAGGATATATGAAGTGCTATTTGCA 59.062 33.333 0.00 0.00 39.41 4.08
2395 2463 7.912056 TCAGGATATATGAAGTGCTATTTGC 57.088 36.000 0.00 0.00 43.25 3.68
2399 2467 9.833917 CATCATTCAGGATATATGAAGTGCTAT 57.166 33.333 8.38 0.00 39.86 2.97
2400 2468 9.039165 TCATCATTCAGGATATATGAAGTGCTA 57.961 33.333 8.38 0.00 39.86 3.49
2401 2469 7.914859 TCATCATTCAGGATATATGAAGTGCT 58.085 34.615 8.38 0.00 39.86 4.40
2462 2530 5.538877 AGACTATCAACTCCCCCATTAAGA 58.461 41.667 0.00 0.00 0.00 2.10
2464 2532 5.538877 AGAGACTATCAACTCCCCCATTAA 58.461 41.667 0.00 0.00 34.13 1.40
2472 2540 3.634910 GGTGAGGAGAGACTATCAACTCC 59.365 52.174 0.00 0.00 46.28 3.85
2479 2547 2.091555 GTGGGAGGTGAGGAGAGACTAT 60.092 54.545 0.00 0.00 0.00 2.12
2486 2554 0.254178 CATTGGTGGGAGGTGAGGAG 59.746 60.000 0.00 0.00 0.00 3.69
2487 2555 1.852157 GCATTGGTGGGAGGTGAGGA 61.852 60.000 0.00 0.00 0.00 3.71
2496 2564 3.674997 AGCGTAATATAGCATTGGTGGG 58.325 45.455 0.00 0.00 35.48 4.61
2524 2592 5.645067 TCAGCAAAAGATGACCTGTAAGATG 59.355 40.000 0.00 0.00 34.07 2.90
2525 2593 5.809001 TCAGCAAAAGATGACCTGTAAGAT 58.191 37.500 0.00 0.00 34.07 2.40
2532 2600 1.808945 CGCTTCAGCAAAAGATGACCT 59.191 47.619 0.00 0.00 42.21 3.85
2533 2601 1.730446 GCGCTTCAGCAAAAGATGACC 60.730 52.381 0.00 0.00 42.21 4.02
2534 2602 1.069022 TGCGCTTCAGCAAAAGATGAC 60.069 47.619 9.73 0.00 45.06 3.06
2535 2603 1.237533 TGCGCTTCAGCAAAAGATGA 58.762 45.000 9.73 0.00 45.06 2.92
2536 2604 3.778969 TGCGCTTCAGCAAAAGATG 57.221 47.368 9.73 0.00 45.06 2.90
2547 2615 2.505557 GCAACATGGCTGCGCTTC 60.506 61.111 9.73 0.00 0.00 3.86
2565 2633 4.552365 ATGCGTCAGATGGGCCGG 62.552 66.667 0.00 0.00 0.00 6.13
2574 2642 3.745332 TTGAGTTAATGCATGCGTCAG 57.255 42.857 13.95 0.00 0.00 3.51
2578 2646 3.484649 GCTTCATTGAGTTAATGCATGCG 59.515 43.478 14.09 0.00 44.69 4.73
2588 2656 2.550830 AGTGTCGGCTTCATTGAGTT 57.449 45.000 0.00 0.00 0.00 3.01
2596 2664 1.314730 TTTGGGAAAGTGTCGGCTTC 58.685 50.000 0.00 0.00 0.00 3.86
2599 2667 0.741915 TGTTTTGGGAAAGTGTCGGC 59.258 50.000 0.00 0.00 0.00 5.54
2601 2669 3.796178 CACATTGTTTTGGGAAAGTGTCG 59.204 43.478 0.00 0.00 0.00 4.35
2603 2671 5.358922 CATCACATTGTTTTGGGAAAGTGT 58.641 37.500 0.00 0.00 31.59 3.55
2620 2688 7.393841 TGATTTGAATGAGTAATGCATCACA 57.606 32.000 2.05 0.46 0.00 3.58
2623 2691 9.745880 AGATTTGATTTGAATGAGTAATGCATC 57.254 29.630 0.00 0.00 0.00 3.91
2658 2726 9.403583 ACAAGTAAAGTTTGGATTTAGTTGAGA 57.596 29.630 22.97 0.00 46.73 3.27
2659 2727 9.665264 GACAAGTAAAGTTTGGATTTAGTTGAG 57.335 33.333 22.97 7.14 46.73 3.02
2660 2728 8.626526 GGACAAGTAAAGTTTGGATTTAGTTGA 58.373 33.333 22.97 0.00 46.73 3.18
2662 2730 8.762481 AGGACAAGTAAAGTTTGGATTTAGTT 57.238 30.769 0.00 0.00 36.61 2.24
2663 2731 8.218488 AGAGGACAAGTAAAGTTTGGATTTAGT 58.782 33.333 0.00 0.00 0.00 2.24
2664 2732 8.622948 AGAGGACAAGTAAAGTTTGGATTTAG 57.377 34.615 0.00 0.00 0.00 1.85
2665 2733 7.664318 GGAGAGGACAAGTAAAGTTTGGATTTA 59.336 37.037 0.00 0.00 0.00 1.40
2666 2734 6.490381 GGAGAGGACAAGTAAAGTTTGGATTT 59.510 38.462 0.00 0.00 0.00 2.17
2667 2735 6.004574 GGAGAGGACAAGTAAAGTTTGGATT 58.995 40.000 0.00 0.00 0.00 3.01
2668 2736 5.310857 AGGAGAGGACAAGTAAAGTTTGGAT 59.689 40.000 0.00 0.00 0.00 3.41
2669 2737 4.658901 AGGAGAGGACAAGTAAAGTTTGGA 59.341 41.667 0.00 0.00 0.00 3.53
2670 2738 4.974399 AGGAGAGGACAAGTAAAGTTTGG 58.026 43.478 0.00 0.00 0.00 3.28
2671 2739 6.760291 AGTAGGAGAGGACAAGTAAAGTTTG 58.240 40.000 0.00 0.00 0.00 2.93
2672 2740 6.553852 TGAGTAGGAGAGGACAAGTAAAGTTT 59.446 38.462 0.00 0.00 0.00 2.66
2673 2741 6.075984 TGAGTAGGAGAGGACAAGTAAAGTT 58.924 40.000 0.00 0.00 0.00 2.66
2674 2742 5.642165 TGAGTAGGAGAGGACAAGTAAAGT 58.358 41.667 0.00 0.00 0.00 2.66
2675 2743 6.783708 ATGAGTAGGAGAGGACAAGTAAAG 57.216 41.667 0.00 0.00 0.00 1.85
2676 2744 6.606395 GGTATGAGTAGGAGAGGACAAGTAAA 59.394 42.308 0.00 0.00 0.00 2.01
2677 2745 6.127793 GGTATGAGTAGGAGAGGACAAGTAA 58.872 44.000 0.00 0.00 0.00 2.24
2678 2746 5.398809 GGGTATGAGTAGGAGAGGACAAGTA 60.399 48.000 0.00 0.00 0.00 2.24
2679 2747 4.538738 GGTATGAGTAGGAGAGGACAAGT 58.461 47.826 0.00 0.00 0.00 3.16
2680 2748 3.892588 GGGTATGAGTAGGAGAGGACAAG 59.107 52.174 0.00 0.00 0.00 3.16
2681 2749 3.271225 TGGGTATGAGTAGGAGAGGACAA 59.729 47.826 0.00 0.00 0.00 3.18
2682 2750 2.856864 TGGGTATGAGTAGGAGAGGACA 59.143 50.000 0.00 0.00 0.00 4.02
2683 2751 3.596940 TGGGTATGAGTAGGAGAGGAC 57.403 52.381 0.00 0.00 0.00 3.85
2684 2752 4.620086 TTTGGGTATGAGTAGGAGAGGA 57.380 45.455 0.00 0.00 0.00 3.71
2685 2753 4.901849 TGATTTGGGTATGAGTAGGAGAGG 59.098 45.833 0.00 0.00 0.00 3.69
2686 2754 6.485830 TTGATTTGGGTATGAGTAGGAGAG 57.514 41.667 0.00 0.00 0.00 3.20
2687 2755 6.884472 TTTGATTTGGGTATGAGTAGGAGA 57.116 37.500 0.00 0.00 0.00 3.71
2688 2756 9.627123 TTTATTTGATTTGGGTATGAGTAGGAG 57.373 33.333 0.00 0.00 0.00 3.69
2689 2757 9.983024 TTTTATTTGATTTGGGTATGAGTAGGA 57.017 29.630 0.00 0.00 0.00 2.94
2735 2803 2.110578 GGGCCTGCCAACTTTGATTAT 58.889 47.619 10.86 0.00 37.98 1.28
2744 2812 0.963962 CATCATATGGGCCTGCCAAC 59.036 55.000 10.86 0.00 37.98 3.77
2745 2813 0.557238 ACATCATATGGGCCTGCCAA 59.443 50.000 10.86 0.00 37.98 4.52
2749 2818 1.951602 CACACACATCATATGGGCCTG 59.048 52.381 4.53 0.00 37.11 4.85
2750 2819 1.565759 ACACACACATCATATGGGCCT 59.434 47.619 4.53 0.00 37.11 5.19
2758 2827 7.966246 AAATAAAAATGCACACACACATCAT 57.034 28.000 0.00 0.00 0.00 2.45
2761 2830 6.991531 AGGAAAATAAAAATGCACACACACAT 59.008 30.769 0.00 0.00 0.00 3.21
2768 2837 8.203485 AGACAAAGAGGAAAATAAAAATGCACA 58.797 29.630 0.00 0.00 0.00 4.57
2770 2839 9.044150 CAAGACAAAGAGGAAAATAAAAATGCA 57.956 29.630 0.00 0.00 0.00 3.96
2771 2840 9.045223 ACAAGACAAAGAGGAAAATAAAAATGC 57.955 29.630 0.00 0.00 0.00 3.56


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

AutoCloner maintained by Alex Coulton.