Multiple sequence alignment - TraesCS5A01G149300

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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 TraesCS5A01G149300 chr5A 100.000 3035 0 0 1 3035 327091545 327094579 0.000000e+00 5605
1 TraesCS5A01G149300 chr5A 94.286 350 16 3 192 540 530205755 530205409 1.600000e-147 532
2 TraesCS5A01G149300 chr5A 89.315 365 16 15 321 665 634744193 634744554 1.290000e-118 436
3 TraesCS5A01G149300 chr5D 97.443 1408 33 2 782 2186 229352479 229351072 0.000000e+00 2398
4 TraesCS5A01G149300 chr5D 93.596 812 18 17 1 785 229353549 229352745 0.000000e+00 1181
5 TraesCS5A01G149300 chr5B 92.119 1675 72 15 606 2270 276251178 276252802 0.000000e+00 2307
6 TraesCS5A01G149300 chr5B 97.869 610 8 3 1 607 276250537 276251144 0.000000e+00 1050
7 TraesCS5A01G149300 chr1A 92.296 649 36 8 2395 3035 61394329 61394971 0.000000e+00 909
8 TraesCS5A01G149300 chr1A 87.273 495 19 17 192 665 7947086 7947557 2.680000e-145 525
9 TraesCS5A01G149300 chr1A 87.221 493 20 16 193 665 539851971 539851502 3.470000e-144 521
10 TraesCS5A01G149300 chr3B 91.641 658 31 7 2397 3035 527897544 527898196 0.000000e+00 889
11 TraesCS5A01G149300 chr3A 89.530 659 50 10 2395 3035 537516109 537515452 0.000000e+00 817
12 TraesCS5A01G149300 chr7B 88.725 612 36 10 2443 3035 105498303 105498900 0.000000e+00 717
13 TraesCS5A01G149300 chr7B 95.652 69 2 1 2395 2462 105481602 105481670 3.200000e-20 110
14 TraesCS5A01G149300 chr2A 89.980 489 24 16 197 665 110283087 110283570 2.590000e-170 608
15 TraesCS5A01G149300 chr2A 87.449 494 19 24 192 665 55077530 55077060 2.070000e-146 529
16 TraesCS5A01G149300 chr2A 86.235 494 25 16 192 665 599679135 599678665 2.100000e-136 496
17 TraesCS5A01G149300 chr7A 87.652 494 18 16 192 665 578433059 578432589 4.450000e-148 534
18 TraesCS5A01G149300 chr7A 86.842 494 21 17 192 665 493515282 493515751 2.090000e-141 512
19 TraesCS5A01G149300 chr6A 87.045 494 21 14 192 665 436390551 436391021 4.490000e-143 518
20 TraesCS5A01G149300 chr6A 80.368 489 77 14 2562 3035 329917857 329918341 1.340000e-93 353
21 TraesCS5A01G149300 chr6A 79.346 489 83 13 2562 3035 329929818 329930303 8.110000e-86 327
22 TraesCS5A01G149300 chr2B 84.104 541 62 11 2434 2952 488696446 488696984 4.520000e-138 501
23 TraesCS5A01G149300 chr6D 80.694 663 103 16 2395 3035 255100814 255100155 2.720000e-135 492
24 TraesCS5A01G149300 chr6B 84.914 464 34 8 2584 3035 2404500 2404061 1.290000e-118 436
25 TraesCS5A01G149300 chr6B 88.060 201 14 4 2398 2590 2406521 2406323 2.350000e-56 230


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 TraesCS5A01G149300 chr5A 327091545 327094579 3034 False 5605.0 5605 100.0000 1 3035 1 chr5A.!!$F1 3034
1 TraesCS5A01G149300 chr5D 229351072 229353549 2477 True 1789.5 2398 95.5195 1 2186 2 chr5D.!!$R1 2185
2 TraesCS5A01G149300 chr5B 276250537 276252802 2265 False 1678.5 2307 94.9940 1 2270 2 chr5B.!!$F1 2269
3 TraesCS5A01G149300 chr1A 61394329 61394971 642 False 909.0 909 92.2960 2395 3035 1 chr1A.!!$F2 640
4 TraesCS5A01G149300 chr3B 527897544 527898196 652 False 889.0 889 91.6410 2397 3035 1 chr3B.!!$F1 638
5 TraesCS5A01G149300 chr3A 537515452 537516109 657 True 817.0 817 89.5300 2395 3035 1 chr3A.!!$R1 640
6 TraesCS5A01G149300 chr7B 105498303 105498900 597 False 717.0 717 88.7250 2443 3035 1 chr7B.!!$F2 592
7 TraesCS5A01G149300 chr2B 488696446 488696984 538 False 501.0 501 84.1040 2434 2952 1 chr2B.!!$F1 518
8 TraesCS5A01G149300 chr6D 255100155 255100814 659 True 492.0 492 80.6940 2395 3035 1 chr6D.!!$R1 640
9 TraesCS5A01G149300 chr6B 2404061 2406521 2460 True 333.0 436 86.4870 2398 3035 2 chr6B.!!$R1 637

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
671 718 1.339151 ACTGGCAAGAGATTTCGGGAC 60.339 52.381 0.0 0.0 0.0 4.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2284 2617 0.032952 TTCGTCTCACGGGTTCCAAG 59.967 55.0 0.0 0.0 42.81 3.61 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
124 128 4.032217 GCCGATGCTTCATATCATAAGTCG 59.968 45.833 0.08 0.00 33.53 4.18
529 540 2.092212 CCTAGAATCATGGGCTGTGGTT 60.092 50.000 0.00 0.00 0.00 3.67
540 551 4.016444 TGGGCTGTGGTTTCTGAATATTC 58.984 43.478 8.60 8.60 0.00 1.75
601 612 1.814394 TGATGCAGCATGAGGTTGAAC 59.186 47.619 14.22 0.00 39.69 3.18
671 718 1.339151 ACTGGCAAGAGATTTCGGGAC 60.339 52.381 0.00 0.00 0.00 4.46
791 1121 5.890334 TGGCAAGTCAAGACTAAAAAGTTG 58.110 37.500 2.72 0.00 41.58 3.16
855 1186 2.382746 CCGATCACAGCCACACACG 61.383 63.158 0.00 0.00 0.00 4.49
1308 1641 2.697263 TGCATGCCCTCCCTCCAT 60.697 61.111 16.68 0.00 0.00 3.41
1620 1953 0.640768 CGTTCGACGAAATGCTCCTC 59.359 55.000 12.67 0.00 46.05 3.71
1997 2330 1.224075 CTGATATGTGCCAGCGAAGG 58.776 55.000 0.00 0.00 0.00 3.46
2104 2437 2.157738 GTTTCAGCTGCAGGTCAATCT 58.842 47.619 17.16 0.00 0.00 2.40
2156 2489 5.634020 GTCCACTGGATATTTAGATGTACGC 59.366 44.000 0.00 0.00 32.73 4.42
2270 2603 2.546789 GTGAAACTCCCAAAGTGGTACG 59.453 50.000 0.00 0.00 38.58 3.67
2271 2604 2.435069 TGAAACTCCCAAAGTGGTACGA 59.565 45.455 0.00 0.00 38.58 3.43
2272 2605 3.071892 TGAAACTCCCAAAGTGGTACGAT 59.928 43.478 0.00 0.00 38.58 3.73
2273 2606 2.762535 ACTCCCAAAGTGGTACGATG 57.237 50.000 0.00 0.00 36.65 3.84
2274 2607 1.278127 ACTCCCAAAGTGGTACGATGG 59.722 52.381 0.00 0.00 36.65 3.51
2275 2608 0.616371 TCCCAAAGTGGTACGATGGG 59.384 55.000 8.37 8.37 44.83 4.00
2276 2609 0.393808 CCCAAAGTGGTACGATGGGG 60.394 60.000 7.05 0.34 41.90 4.96
2277 2610 0.326927 CCAAAGTGGTACGATGGGGT 59.673 55.000 0.00 0.00 31.35 4.95
2278 2611 1.271707 CCAAAGTGGTACGATGGGGTT 60.272 52.381 0.00 0.00 31.35 4.11
2279 2612 1.810151 CAAAGTGGTACGATGGGGTTG 59.190 52.381 0.00 0.00 0.00 3.77
2280 2613 0.322187 AAGTGGTACGATGGGGTTGC 60.322 55.000 0.00 0.00 0.00 4.17
2281 2614 1.003112 GTGGTACGATGGGGTTGCA 60.003 57.895 0.00 0.00 0.00 4.08
2282 2615 0.606944 GTGGTACGATGGGGTTGCAA 60.607 55.000 0.00 0.00 0.00 4.08
2283 2616 0.110678 TGGTACGATGGGGTTGCAAA 59.889 50.000 0.00 0.00 0.00 3.68
2295 2628 2.889200 TTGCAAACTTGGAACCCGT 58.111 47.368 0.00 0.00 33.44 5.28
2296 2629 0.457851 TTGCAAACTTGGAACCCGTG 59.542 50.000 0.00 0.00 33.44 4.94
2297 2630 0.394488 TGCAAACTTGGAACCCGTGA 60.394 50.000 0.00 0.00 0.00 4.35
2298 2631 0.310854 GCAAACTTGGAACCCGTGAG 59.689 55.000 0.00 0.00 0.00 3.51
2299 2632 1.961793 CAAACTTGGAACCCGTGAGA 58.038 50.000 0.00 0.00 0.00 3.27
2300 2633 1.602377 CAAACTTGGAACCCGTGAGAC 59.398 52.381 0.00 0.00 0.00 3.36
2301 2634 0.249741 AACTTGGAACCCGTGAGACG 60.250 55.000 0.00 0.00 42.11 4.18
2302 2635 1.111116 ACTTGGAACCCGTGAGACGA 61.111 55.000 0.00 0.00 46.05 4.20
2303 2636 0.032952 CTTGGAACCCGTGAGACGAA 59.967 55.000 0.00 0.00 46.05 3.85
2304 2637 0.464870 TTGGAACCCGTGAGACGAAA 59.535 50.000 0.00 0.00 46.05 3.46
2305 2638 0.464870 TGGAACCCGTGAGACGAAAA 59.535 50.000 0.00 0.00 46.05 2.29
2306 2639 1.145803 GGAACCCGTGAGACGAAAAG 58.854 55.000 0.00 0.00 46.05 2.27
2307 2640 1.145803 GAACCCGTGAGACGAAAAGG 58.854 55.000 0.00 0.00 46.05 3.11
2308 2641 0.466963 AACCCGTGAGACGAAAAGGT 59.533 50.000 0.00 0.00 46.05 3.50
2309 2642 0.033090 ACCCGTGAGACGAAAAGGTC 59.967 55.000 0.00 0.00 46.05 3.85
2310 2643 0.032952 CCCGTGAGACGAAAAGGTCA 59.967 55.000 0.00 0.00 46.05 4.02
2311 2644 1.137513 CCGTGAGACGAAAAGGTCAC 58.862 55.000 0.00 0.00 46.05 3.67
2312 2645 1.537348 CCGTGAGACGAAAAGGTCACA 60.537 52.381 0.00 0.00 46.05 3.58
2313 2646 2.404215 CGTGAGACGAAAAGGTCACAT 58.596 47.619 0.00 0.00 46.05 3.21
2314 2647 2.155732 CGTGAGACGAAAAGGTCACATG 59.844 50.000 0.00 0.00 46.05 3.21
2315 2648 2.096218 GTGAGACGAAAAGGTCACATGC 60.096 50.000 0.00 0.00 39.20 4.06
2316 2649 1.464997 GAGACGAAAAGGTCACATGCC 59.535 52.381 0.00 0.00 39.42 4.40
2317 2650 1.202758 AGACGAAAAGGTCACATGCCA 60.203 47.619 0.00 0.00 39.42 4.92
2318 2651 1.606668 GACGAAAAGGTCACATGCCAA 59.393 47.619 0.00 0.00 36.91 4.52
2319 2652 2.228822 GACGAAAAGGTCACATGCCAAT 59.771 45.455 0.00 0.00 36.91 3.16
2320 2653 2.228822 ACGAAAAGGTCACATGCCAATC 59.771 45.455 0.00 0.00 0.00 2.67
2321 2654 2.228582 CGAAAAGGTCACATGCCAATCA 59.771 45.455 0.00 0.00 0.00 2.57
2322 2655 3.578688 GAAAAGGTCACATGCCAATCAC 58.421 45.455 0.00 0.00 0.00 3.06
2323 2656 2.291209 AAGGTCACATGCCAATCACA 57.709 45.000 0.00 0.00 0.00 3.58
2324 2657 1.830279 AGGTCACATGCCAATCACAG 58.170 50.000 0.00 0.00 0.00 3.66
2325 2658 0.171903 GGTCACATGCCAATCACAGC 59.828 55.000 0.00 0.00 0.00 4.40
2326 2659 1.171308 GTCACATGCCAATCACAGCT 58.829 50.000 0.00 0.00 0.00 4.24
2327 2660 1.131883 GTCACATGCCAATCACAGCTC 59.868 52.381 0.00 0.00 0.00 4.09
2328 2661 0.098200 CACATGCCAATCACAGCTCG 59.902 55.000 0.00 0.00 0.00 5.03
2329 2662 1.063649 CATGCCAATCACAGCTCGC 59.936 57.895 0.00 0.00 0.00 5.03
2330 2663 2.117156 ATGCCAATCACAGCTCGCC 61.117 57.895 0.00 0.00 0.00 5.54
2331 2664 3.869272 GCCAATCACAGCTCGCCG 61.869 66.667 0.00 0.00 0.00 6.46
2332 2665 2.434884 CCAATCACAGCTCGCCGT 60.435 61.111 0.00 0.00 0.00 5.68
2333 2666 2.034879 CCAATCACAGCTCGCCGTT 61.035 57.895 0.00 0.00 0.00 4.44
2334 2667 1.133253 CAATCACAGCTCGCCGTTG 59.867 57.895 0.00 0.00 0.00 4.10
2335 2668 2.034879 AATCACAGCTCGCCGTTGG 61.035 57.895 0.00 0.00 0.00 3.77
2349 2682 4.980805 TTGGCAGCCACGTCGGTC 62.981 66.667 15.89 0.00 36.97 4.79
2353 2686 3.991051 CAGCCACGTCGGTCCTGT 61.991 66.667 0.00 0.00 36.97 4.00
2354 2687 3.231736 AGCCACGTCGGTCCTGTT 61.232 61.111 0.00 0.00 36.97 3.16
2355 2688 2.280592 GCCACGTCGGTCCTGTTT 60.281 61.111 0.00 0.00 36.97 2.83
2356 2689 2.604174 GCCACGTCGGTCCTGTTTG 61.604 63.158 0.00 0.00 36.97 2.93
2357 2690 2.604174 CCACGTCGGTCCTGTTTGC 61.604 63.158 0.00 0.00 0.00 3.68
2358 2691 2.280592 ACGTCGGTCCTGTTTGCC 60.281 61.111 0.00 0.00 0.00 4.52
2359 2692 3.411351 CGTCGGTCCTGTTTGCCG 61.411 66.667 0.00 0.00 46.12 5.69
2364 2697 2.471255 GGTCCTGTTTGCCGATCTG 58.529 57.895 0.00 0.00 0.00 2.90
2365 2698 0.036388 GGTCCTGTTTGCCGATCTGA 60.036 55.000 0.00 0.00 0.00 3.27
2366 2699 1.079503 GTCCTGTTTGCCGATCTGAC 58.920 55.000 0.00 0.00 0.00 3.51
2367 2700 0.389817 TCCTGTTTGCCGATCTGACG 60.390 55.000 0.00 0.00 0.00 4.35
2368 2701 0.389817 CCTGTTTGCCGATCTGACGA 60.390 55.000 0.00 0.00 35.09 4.20
2369 2702 0.716108 CTGTTTGCCGATCTGACGAC 59.284 55.000 0.00 0.00 35.09 4.34
2370 2703 1.006825 TGTTTGCCGATCTGACGACG 61.007 55.000 0.00 0.00 35.09 5.12
2371 2704 1.007336 GTTTGCCGATCTGACGACGT 61.007 55.000 0.00 0.00 35.09 4.34
2372 2705 0.522626 TTTGCCGATCTGACGACGTA 59.477 50.000 0.00 0.00 35.09 3.57
2373 2706 0.098200 TTGCCGATCTGACGACGTAG 59.902 55.000 0.00 0.00 35.09 3.51
2387 2720 2.888834 ACGTAGTTAACACCCGTTGT 57.111 45.000 8.61 0.00 37.78 3.32
2388 2721 2.742774 ACGTAGTTAACACCCGTTGTC 58.257 47.619 8.61 0.00 37.78 3.18
2389 2722 2.100584 ACGTAGTTAACACCCGTTGTCA 59.899 45.455 8.61 0.00 37.78 3.58
2390 2723 3.122297 CGTAGTTAACACCCGTTGTCAA 58.878 45.455 8.61 0.00 37.51 3.18
2391 2724 3.555139 CGTAGTTAACACCCGTTGTCAAA 59.445 43.478 8.61 0.00 37.51 2.69
2392 2725 4.318263 CGTAGTTAACACCCGTTGTCAAAG 60.318 45.833 8.61 0.00 37.51 2.77
2393 2726 3.876341 AGTTAACACCCGTTGTCAAAGA 58.124 40.909 8.61 0.00 37.51 2.52
2408 2741 5.457140 TGTCAAAGAATTGCAACCGAATAC 58.543 37.500 0.00 0.00 36.45 1.89
2494 2832 2.158449 CAGTTCTCTGTCAAATCGGCAC 59.842 50.000 0.00 0.00 36.97 5.01
2520 2858 4.649267 TGTGGAATGGGATCACAAGTTA 57.351 40.909 0.00 0.00 38.30 2.24
2532 2870 7.091993 TGGGATCACAAGTTAGGGAATAATCTT 60.092 37.037 0.00 0.00 0.00 2.40
2604 4778 1.976474 CTAGGCTGCCCGGCAAAAA 60.976 57.895 16.57 0.00 38.41 1.94
2635 4809 2.437850 CTTGGAAAGCGTTGCATGC 58.562 52.632 11.82 11.82 36.98 4.06
2640 4814 0.804989 GAAAGCGTTGCATGCTACCT 59.195 50.000 23.51 18.41 40.06 3.08
2679 4853 1.141657 TGGCCCAGAGACATATCAAGC 59.858 52.381 0.00 0.00 0.00 4.01
2883 5070 6.071952 GGACCAGAAACAAGAAAAGATGCATA 60.072 38.462 0.00 0.00 0.00 3.14
2941 5128 1.195115 AGGAGAAAGCTACGCCATGA 58.805 50.000 13.92 0.00 0.00 3.07
2986 5174 5.482175 ACCAGATTGCTACTTCTGTTAGAGT 59.518 40.000 0.00 0.00 38.12 3.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
142 146 0.824182 TAAACAACCACTTGCCCGGG 60.824 55.000 19.09 19.09 0.00 5.73
143 147 1.253100 ATAAACAACCACTTGCCCGG 58.747 50.000 0.00 0.00 0.00 5.73
144 148 3.181491 CCATATAAACAACCACTTGCCCG 60.181 47.826 0.00 0.00 0.00 6.13
145 149 3.132111 CCCATATAAACAACCACTTGCCC 59.868 47.826 0.00 0.00 0.00 5.36
146 150 3.430236 GCCCATATAAACAACCACTTGCC 60.430 47.826 0.00 0.00 0.00 4.52
406 417 7.765307 AGGAGAAACATGCATTACAACTTATG 58.235 34.615 0.00 0.00 0.00 1.90
427 438 0.911769 TGCCAGATACACCCAAGGAG 59.088 55.000 0.00 0.00 0.00 3.69
529 540 7.884877 ACAGAATTCCACACAGAATATTCAGAA 59.115 33.333 17.56 9.88 35.40 3.02
540 551 5.964958 AAACCATACAGAATTCCACACAG 57.035 39.130 0.65 0.00 0.00 3.66
671 718 6.171006 GCAAGTAAAATTTCATTTCATCGCG 58.829 36.000 0.00 0.00 0.00 5.87
733 780 5.186256 TGGTGAAATACAGGATGCCTTAA 57.814 39.130 0.00 0.00 42.53 1.85
734 781 4.853468 TGGTGAAATACAGGATGCCTTA 57.147 40.909 0.00 0.00 42.53 2.69
791 1121 4.024977 CCAAATGGCTTAAGCACAAAACAC 60.025 41.667 27.83 9.23 44.36 3.32
830 1161 2.027653 TGTGGCTGTGATCGGTCAATTA 60.028 45.455 0.00 0.00 36.25 1.40
855 1186 2.178890 CATTGCCGCTCCTCTCTGC 61.179 63.158 0.00 0.00 0.00 4.26
994 1327 2.280052 GGAGCAGCTCATCTCGCC 60.280 66.667 24.09 1.17 31.08 5.54
1499 1832 1.000731 CATCGGAGCCCATCTTCTCTC 59.999 57.143 0.00 0.00 0.00 3.20
1500 1833 1.047002 CATCGGAGCCCATCTTCTCT 58.953 55.000 0.00 0.00 0.00 3.10
1950 2283 4.131088 GTCGAGGCGTCCACTCCC 62.131 72.222 0.00 0.00 0.00 4.30
2187 2520 7.791029 AGCAATTAAACTCTTTCCCTCAAAAA 58.209 30.769 0.00 0.00 0.00 1.94
2188 2521 7.360113 AGCAATTAAACTCTTTCCCTCAAAA 57.640 32.000 0.00 0.00 0.00 2.44
2189 2522 6.976934 AGCAATTAAACTCTTTCCCTCAAA 57.023 33.333 0.00 0.00 0.00 2.69
2190 2523 6.976934 AAGCAATTAAACTCTTTCCCTCAA 57.023 33.333 0.00 0.00 0.00 3.02
2191 2524 6.323739 ACAAAGCAATTAAACTCTTTCCCTCA 59.676 34.615 0.00 0.00 0.00 3.86
2192 2525 6.642540 CACAAAGCAATTAAACTCTTTCCCTC 59.357 38.462 0.00 0.00 0.00 4.30
2193 2526 6.515832 CACAAAGCAATTAAACTCTTTCCCT 58.484 36.000 0.00 0.00 0.00 4.20
2194 2527 5.177511 GCACAAAGCAATTAAACTCTTTCCC 59.822 40.000 0.00 0.00 44.79 3.97
2195 2528 6.215477 GCACAAAGCAATTAAACTCTTTCC 57.785 37.500 0.00 0.00 44.79 3.13
2270 2603 1.337118 TCCAAGTTTGCAACCCCATC 58.663 50.000 0.00 0.00 0.00 3.51
2271 2604 1.416030 GTTCCAAGTTTGCAACCCCAT 59.584 47.619 0.00 0.00 0.00 4.00
2272 2605 0.827368 GTTCCAAGTTTGCAACCCCA 59.173 50.000 0.00 0.00 0.00 4.96
2273 2606 0.105964 GGTTCCAAGTTTGCAACCCC 59.894 55.000 6.45 0.00 33.42 4.95
2274 2607 3.678921 GGTTCCAAGTTTGCAACCC 57.321 52.632 6.45 0.00 33.42 4.11
2275 2608 0.249280 CGGGTTCCAAGTTTGCAACC 60.249 55.000 8.84 8.84 38.07 3.77
2276 2609 0.458260 ACGGGTTCCAAGTTTGCAAC 59.542 50.000 0.00 0.00 0.00 4.17
2277 2610 0.457851 CACGGGTTCCAAGTTTGCAA 59.542 50.000 0.00 0.00 0.00 4.08
2278 2611 0.394488 TCACGGGTTCCAAGTTTGCA 60.394 50.000 0.00 0.00 0.00 4.08
2279 2612 0.310854 CTCACGGGTTCCAAGTTTGC 59.689 55.000 0.00 0.00 0.00 3.68
2280 2613 1.602377 GTCTCACGGGTTCCAAGTTTG 59.398 52.381 0.00 0.00 0.00 2.93
2281 2614 1.808891 CGTCTCACGGGTTCCAAGTTT 60.809 52.381 0.00 0.00 38.08 2.66
2282 2615 0.249741 CGTCTCACGGGTTCCAAGTT 60.250 55.000 0.00 0.00 38.08 2.66
2283 2616 1.111116 TCGTCTCACGGGTTCCAAGT 61.111 55.000 0.00 0.00 42.81 3.16
2284 2617 0.032952 TTCGTCTCACGGGTTCCAAG 59.967 55.000 0.00 0.00 42.81 3.61
2285 2618 0.464870 TTTCGTCTCACGGGTTCCAA 59.535 50.000 0.00 0.00 42.81 3.53
2286 2619 0.464870 TTTTCGTCTCACGGGTTCCA 59.535 50.000 0.00 0.00 42.81 3.53
2287 2620 1.145803 CTTTTCGTCTCACGGGTTCC 58.854 55.000 0.00 0.00 42.81 3.62
2288 2621 1.145803 CCTTTTCGTCTCACGGGTTC 58.854 55.000 0.00 0.00 42.81 3.62
2289 2622 0.466963 ACCTTTTCGTCTCACGGGTT 59.533 50.000 0.00 0.00 42.81 4.11
2290 2623 0.033090 GACCTTTTCGTCTCACGGGT 59.967 55.000 0.00 0.00 42.81 5.28
2291 2624 0.032952 TGACCTTTTCGTCTCACGGG 59.967 55.000 0.00 0.00 42.81 5.28
2292 2625 1.137513 GTGACCTTTTCGTCTCACGG 58.862 55.000 0.00 0.00 42.81 4.94
2293 2626 1.847818 TGTGACCTTTTCGTCTCACG 58.152 50.000 0.00 0.00 44.19 4.35
2294 2627 2.096218 GCATGTGACCTTTTCGTCTCAC 60.096 50.000 0.00 0.00 38.63 3.51
2295 2628 2.143122 GCATGTGACCTTTTCGTCTCA 58.857 47.619 0.00 0.00 39.72 3.27
2296 2629 1.464997 GGCATGTGACCTTTTCGTCTC 59.535 52.381 0.00 0.00 33.70 3.36
2297 2630 1.202758 TGGCATGTGACCTTTTCGTCT 60.203 47.619 0.00 0.00 33.70 4.18
2298 2631 1.234821 TGGCATGTGACCTTTTCGTC 58.765 50.000 0.00 0.00 0.00 4.20
2299 2632 1.686355 TTGGCATGTGACCTTTTCGT 58.314 45.000 0.00 0.00 0.00 3.85
2300 2633 2.228582 TGATTGGCATGTGACCTTTTCG 59.771 45.455 0.00 0.00 0.00 3.46
2301 2634 3.005684 TGTGATTGGCATGTGACCTTTTC 59.994 43.478 0.00 0.00 0.00 2.29
2302 2635 2.964464 TGTGATTGGCATGTGACCTTTT 59.036 40.909 0.00 0.00 0.00 2.27
2303 2636 2.559668 CTGTGATTGGCATGTGACCTTT 59.440 45.455 0.00 0.00 0.00 3.11
2304 2637 2.165167 CTGTGATTGGCATGTGACCTT 58.835 47.619 0.00 0.00 0.00 3.50
2305 2638 1.830279 CTGTGATTGGCATGTGACCT 58.170 50.000 0.00 0.00 0.00 3.85
2306 2639 0.171903 GCTGTGATTGGCATGTGACC 59.828 55.000 0.00 0.00 0.00 4.02
2307 2640 1.131883 GAGCTGTGATTGGCATGTGAC 59.868 52.381 0.00 0.00 0.00 3.67
2308 2641 1.456296 GAGCTGTGATTGGCATGTGA 58.544 50.000 0.00 0.00 0.00 3.58
2309 2642 0.098200 CGAGCTGTGATTGGCATGTG 59.902 55.000 0.00 0.00 0.00 3.21
2310 2643 1.651240 GCGAGCTGTGATTGGCATGT 61.651 55.000 0.00 0.00 0.00 3.21
2311 2644 1.063649 GCGAGCTGTGATTGGCATG 59.936 57.895 0.00 0.00 0.00 4.06
2312 2645 2.117156 GGCGAGCTGTGATTGGCAT 61.117 57.895 0.00 0.00 0.00 4.40
2313 2646 2.747460 GGCGAGCTGTGATTGGCA 60.747 61.111 0.00 0.00 0.00 4.92
2314 2647 3.869272 CGGCGAGCTGTGATTGGC 61.869 66.667 0.00 0.00 0.00 4.52
2315 2648 2.034879 AACGGCGAGCTGTGATTGG 61.035 57.895 16.62 0.00 35.44 3.16
2316 2649 1.133253 CAACGGCGAGCTGTGATTG 59.867 57.895 16.62 0.17 35.44 2.67
2317 2650 2.034879 CCAACGGCGAGCTGTGATT 61.035 57.895 16.62 0.00 35.44 2.57
2318 2651 2.434884 CCAACGGCGAGCTGTGAT 60.435 61.111 16.62 0.00 35.44 3.06
2332 2665 4.980805 GACCGACGTGGCTGCCAA 62.981 66.667 25.23 4.66 43.94 4.52
2336 2669 2.989055 AAACAGGACCGACGTGGCTG 62.989 60.000 0.00 0.00 43.94 4.85
2337 2670 2.803817 AAACAGGACCGACGTGGCT 61.804 57.895 0.00 0.00 43.94 4.75
2338 2671 2.280592 AAACAGGACCGACGTGGC 60.281 61.111 0.00 0.00 43.94 5.01
2339 2672 2.604174 GCAAACAGGACCGACGTGG 61.604 63.158 0.00 0.00 46.41 4.94
2340 2673 2.604174 GGCAAACAGGACCGACGTG 61.604 63.158 0.00 0.00 39.84 4.49
2341 2674 2.280592 GGCAAACAGGACCGACGT 60.281 61.111 0.00 0.00 0.00 4.34
2346 2679 0.036388 TCAGATCGGCAAACAGGACC 60.036 55.000 0.00 0.00 0.00 4.46
2347 2680 1.079503 GTCAGATCGGCAAACAGGAC 58.920 55.000 0.00 0.00 0.00 3.85
2348 2681 0.389817 CGTCAGATCGGCAAACAGGA 60.390 55.000 0.00 0.00 0.00 3.86
2349 2682 0.389817 TCGTCAGATCGGCAAACAGG 60.390 55.000 0.00 0.00 0.00 4.00
2350 2683 0.716108 GTCGTCAGATCGGCAAACAG 59.284 55.000 0.00 0.00 35.41 3.16
2351 2684 1.006825 CGTCGTCAGATCGGCAAACA 61.007 55.000 0.00 0.00 35.00 2.83
2352 2685 1.007336 ACGTCGTCAGATCGGCAAAC 61.007 55.000 0.00 0.00 35.00 2.93
2353 2686 0.522626 TACGTCGTCAGATCGGCAAA 59.477 50.000 0.00 0.00 35.00 3.68
2354 2687 0.098200 CTACGTCGTCAGATCGGCAA 59.902 55.000 0.00 0.00 35.00 4.52
2355 2688 1.022982 ACTACGTCGTCAGATCGGCA 61.023 55.000 0.00 0.00 35.00 5.69
2356 2689 0.098376 AACTACGTCGTCAGATCGGC 59.902 55.000 0.00 0.00 0.00 5.54
2357 2690 3.181517 TGTTAACTACGTCGTCAGATCGG 60.182 47.826 0.00 0.00 0.00 4.18
2358 2691 3.777680 GTGTTAACTACGTCGTCAGATCG 59.222 47.826 0.00 0.00 0.00 3.69
2359 2692 4.094212 GGTGTTAACTACGTCGTCAGATC 58.906 47.826 0.00 0.00 0.00 2.75
2360 2693 3.119708 GGGTGTTAACTACGTCGTCAGAT 60.120 47.826 0.00 0.00 0.00 2.90
2361 2694 2.226437 GGGTGTTAACTACGTCGTCAGA 59.774 50.000 0.00 0.00 0.00 3.27
2362 2695 2.589014 GGGTGTTAACTACGTCGTCAG 58.411 52.381 0.00 0.66 0.00 3.51
2363 2696 1.069296 CGGGTGTTAACTACGTCGTCA 60.069 52.381 0.00 0.00 0.00 4.35
2364 2697 1.069227 ACGGGTGTTAACTACGTCGTC 60.069 52.381 0.00 0.00 35.87 4.20
2365 2698 0.951558 ACGGGTGTTAACTACGTCGT 59.048 50.000 14.04 2.21 35.87 4.34
2366 2699 1.715519 CAACGGGTGTTAACTACGTCG 59.284 52.381 18.06 15.98 38.34 5.12
2367 2700 2.726241 GACAACGGGTGTTAACTACGTC 59.274 50.000 18.06 9.01 41.96 4.34
2368 2701 2.100584 TGACAACGGGTGTTAACTACGT 59.899 45.455 0.00 14.04 41.96 3.57
2369 2702 2.741612 TGACAACGGGTGTTAACTACG 58.258 47.619 0.00 10.75 41.96 3.51
2370 2703 4.810491 TCTTTGACAACGGGTGTTAACTAC 59.190 41.667 2.54 3.63 41.96 2.73
2371 2704 5.021033 TCTTTGACAACGGGTGTTAACTA 57.979 39.130 2.54 0.00 41.96 2.24
2372 2705 3.876341 TCTTTGACAACGGGTGTTAACT 58.124 40.909 2.54 0.00 41.96 2.24
2373 2706 4.619437 TTCTTTGACAACGGGTGTTAAC 57.381 40.909 2.54 0.00 41.96 2.01
2374 2707 5.583495 CAATTCTTTGACAACGGGTGTTAA 58.417 37.500 0.00 0.00 41.96 2.01
2375 2708 4.498345 GCAATTCTTTGACAACGGGTGTTA 60.498 41.667 0.00 0.00 41.96 2.41
2376 2709 3.736740 GCAATTCTTTGACAACGGGTGTT 60.737 43.478 0.00 0.00 41.96 3.32
2377 2710 2.223711 GCAATTCTTTGACAACGGGTGT 60.224 45.455 0.00 0.00 45.74 4.16
2378 2711 2.223688 TGCAATTCTTTGACAACGGGTG 60.224 45.455 0.00 0.00 34.60 4.61
2379 2712 2.028130 TGCAATTCTTTGACAACGGGT 58.972 42.857 0.00 0.00 34.60 5.28
2380 2713 2.791383 TGCAATTCTTTGACAACGGG 57.209 45.000 0.00 0.00 34.60 5.28
2381 2714 2.794350 GGTTGCAATTCTTTGACAACGG 59.206 45.455 0.59 0.00 43.28 4.44
2382 2715 2.467305 CGGTTGCAATTCTTTGACAACG 59.533 45.455 0.59 0.00 43.28 4.10
2383 2716 3.701241 TCGGTTGCAATTCTTTGACAAC 58.299 40.909 0.59 13.02 42.56 3.32
2384 2717 4.377839 TTCGGTTGCAATTCTTTGACAA 57.622 36.364 0.59 0.00 34.60 3.18
2385 2718 4.582701 ATTCGGTTGCAATTCTTTGACA 57.417 36.364 0.59 0.00 34.60 3.58
2386 2719 5.699839 AGTATTCGGTTGCAATTCTTTGAC 58.300 37.500 0.59 0.00 34.60 3.18
2387 2720 5.957842 AGTATTCGGTTGCAATTCTTTGA 57.042 34.783 0.59 0.00 34.60 2.69
2388 2721 5.739161 GCTAGTATTCGGTTGCAATTCTTTG 59.261 40.000 0.59 0.00 35.85 2.77
2389 2722 5.648092 AGCTAGTATTCGGTTGCAATTCTTT 59.352 36.000 0.59 0.00 0.00 2.52
2390 2723 5.186198 AGCTAGTATTCGGTTGCAATTCTT 58.814 37.500 0.59 0.00 0.00 2.52
2391 2724 4.770795 AGCTAGTATTCGGTTGCAATTCT 58.229 39.130 0.59 0.00 0.00 2.40
2392 2725 6.787085 ATAGCTAGTATTCGGTTGCAATTC 57.213 37.500 0.59 0.00 0.00 2.17
2393 2726 6.649557 GGTATAGCTAGTATTCGGTTGCAATT 59.350 38.462 0.59 0.00 0.00 2.32
2408 2741 7.806960 GTCGTAGTTTGGTAATGGTATAGCTAG 59.193 40.741 0.00 0.00 0.00 3.42
2494 2832 4.155063 TGTGATCCCATTCCACATAGTG 57.845 45.455 0.00 0.00 36.07 2.74
2520 2858 4.837093 TGACCAACGAAGATTATTCCCT 57.163 40.909 0.00 0.00 0.00 4.20
2532 2870 0.958091 CTTGGCCATTTGACCAACGA 59.042 50.000 6.09 0.00 40.98 3.85
2604 4778 5.010012 ACGCTTTCCAAGTGAAAATTCTGAT 59.990 36.000 4.09 0.00 42.25 2.90
2635 4809 3.610040 TGACACCACATGCTAAGGTAG 57.390 47.619 0.00 0.00 33.49 3.18
2640 4814 3.305950 GCCAAATTGACACCACATGCTAA 60.306 43.478 0.00 0.00 0.00 3.09
2679 4853 3.443045 GGGGCATTGCGGTGACAG 61.443 66.667 1.91 0.00 0.00 3.51
2835 5022 3.277715 TCATTTCATGTTGCGGCATCTA 58.722 40.909 2.28 0.00 0.00 1.98
2860 5047 5.796424 ATGCATCTTTTCTTGTTTCTGGT 57.204 34.783 0.00 0.00 0.00 4.00
2883 5070 4.250464 CAGCAGGTCATTGCAATCATTTT 58.750 39.130 9.53 0.00 46.47 1.82
2941 5128 5.420739 TGGTTAGCAGTTTGAACCTTTTCTT 59.579 36.000 4.77 0.00 42.65 2.52
2986 5174 4.527038 AGCAGTGTAGTTAGCTGTAAGGAA 59.473 41.667 0.00 0.00 35.72 3.36


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

AutoCloner maintained by Alex Coulton.