Multiple sequence alignment - TraesCS4D01G120200

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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 TraesCS4D01G120200 chr4D 100.000 2918 0 0 1 2918 101391176 101388259 0.000000e+00 5389.0
1 TraesCS4D01G120200 chr4D 88.623 167 16 2 2537 2700 63224633 63224467 1.770000e-47 200.0
2 TraesCS4D01G120200 chr4A 92.605 2380 80 25 1 2337 474493149 474495475 0.000000e+00 3332.0
3 TraesCS4D01G120200 chr4A 88.690 168 17 2 2534 2700 660207510 660207344 1.370000e-48 204.0
4 TraesCS4D01G120200 chr4A 89.796 98 10 0 1562 1659 474494754 474494851 3.050000e-25 126.0
5 TraesCS4D01G120200 chr4B 94.444 1692 80 8 35 1717 144789281 144787595 0.000000e+00 2591.0
6 TraesCS4D01G120200 chr4B 93.515 879 33 6 1562 2419 144787690 144786815 0.000000e+00 1286.0
7 TraesCS4D01G120200 chr4B 82.734 139 22 2 1522 1659 144787670 144787533 3.950000e-24 122.0
8 TraesCS4D01G120200 chr6B 90.303 165 16 0 2536 2700 93571936 93572100 1.760000e-52 217.0
9 TraesCS4D01G120200 chr6B 100.000 29 0 0 2484 2512 146149409 146149437 1.000000e-03 54.7
10 TraesCS4D01G120200 chr6B 100.000 28 0 0 2483 2510 498526641 498526668 5.000000e-03 52.8
11 TraesCS4D01G120200 chr1D 91.447 152 13 0 2549 2700 42812896 42812745 2.950000e-50 209.0
12 TraesCS4D01G120200 chr2B 90.062 161 15 1 2538 2697 23888755 23888595 1.060000e-49 207.0
13 TraesCS4D01G120200 chr6D 88.957 163 18 0 2538 2700 460772180 460772342 4.930000e-48 202.0
14 TraesCS4D01G120200 chr6D 100.000 29 0 0 2484 2512 71537485 71537513 1.000000e-03 54.7
15 TraesCS4D01G120200 chrUn 89.024 164 15 2 2539 2700 243337285 243337447 1.770000e-47 200.0
16 TraesCS4D01G120200 chrUn 89.024 164 15 2 2539 2700 248708690 248708852 1.770000e-47 200.0
17 TraesCS4D01G120200 chrUn 89.474 57 6 0 2430 2486 234840935 234840879 4.030000e-09 73.1
18 TraesCS4D01G120200 chr3B 88.095 168 18 2 2537 2703 482668450 482668616 6.380000e-47 198.0
19 TraesCS4D01G120200 chr3B 94.118 34 2 0 2444 2477 808020257 808020290 5.000000e-03 52.8
20 TraesCS4D01G120200 chr1B 88.333 60 7 0 2427 2486 559338984 559339043 4.030000e-09 73.1
21 TraesCS4D01G120200 chr3A 86.567 67 5 2 2414 2476 126162423 126162357 1.450000e-08 71.3
22 TraesCS4D01G120200 chr7A 83.784 74 8 1 2417 2486 254896033 254896106 1.880000e-07 67.6
23 TraesCS4D01G120200 chr6A 87.719 57 7 0 2430 2486 614304736 614304680 1.880000e-07 67.6
24 TraesCS4D01G120200 chr6A 100.000 29 0 0 2484 2512 88080365 88080393 1.000000e-03 54.7
25 TraesCS4D01G120200 chr5D 87.719 57 7 0 2430 2486 54072005 54071949 1.880000e-07 67.6


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 TraesCS4D01G120200 chr4D 101388259 101391176 2917 True 5389 5389 100.0000 1 2918 1 chr4D.!!$R2 2917
1 TraesCS4D01G120200 chr4A 474493149 474495475 2326 False 1729 3332 91.2005 1 2337 2 chr4A.!!$F1 2336
2 TraesCS4D01G120200 chr4B 144786815 144789281 2466 True 1333 2591 90.2310 35 2419 3 chr4B.!!$R1 2384

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
796 817 0.179032 TTCACGCCTCCTTCTTTGCA 60.179 50.0 0.0 0.0 0.0 4.08 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2691 2802 0.036875 CCAAGGACAACACTCCCTCC 59.963 60.0 0.0 0.0 0.0 4.3 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
26 27 2.586914 GGGAAATACCGTCGGGCG 60.587 66.667 17.28 0.00 40.11 6.13
59 71 2.126031 GTCCCCGTCTCGCTGTTC 60.126 66.667 0.00 0.00 0.00 3.18
151 163 0.751277 TTACCCTCGCCGTTCCGATA 60.751 55.000 0.00 0.00 36.54 2.92
165 177 2.580276 GATACGTCGGGCCCACAA 59.420 61.111 24.92 10.32 0.00 3.33
260 278 2.936919 TGAGAACATGACCAGCTTGT 57.063 45.000 0.00 0.00 36.53 3.16
435 454 2.214920 CCCGGCTACCTACCCATCC 61.215 68.421 0.00 0.00 0.00 3.51
689 710 1.007038 TCGTAACTGACACACGGGC 60.007 57.895 0.00 0.00 36.37 6.13
793 814 0.951040 CGCTTCACGCCTCCTTCTTT 60.951 55.000 0.00 0.00 34.21 2.52
794 815 0.519077 GCTTCACGCCTCCTTCTTTG 59.481 55.000 0.00 0.00 0.00 2.77
795 816 0.519077 CTTCACGCCTCCTTCTTTGC 59.481 55.000 0.00 0.00 0.00 3.68
796 817 0.179032 TTCACGCCTCCTTCTTTGCA 60.179 50.000 0.00 0.00 0.00 4.08
798 819 1.961277 ACGCCTCCTTCTTTGCACG 60.961 57.895 0.00 0.00 0.00 5.34
799 820 2.563427 GCCTCCTTCTTTGCACGC 59.437 61.111 0.00 0.00 0.00 5.34
800 821 1.968540 GCCTCCTTCTTTGCACGCT 60.969 57.895 0.00 0.00 0.00 5.07
801 822 1.916697 GCCTCCTTCTTTGCACGCTC 61.917 60.000 0.00 0.00 0.00 5.03
802 823 0.321122 CCTCCTTCTTTGCACGCTCT 60.321 55.000 0.00 0.00 0.00 4.09
803 824 1.517242 CTCCTTCTTTGCACGCTCTT 58.483 50.000 0.00 0.00 0.00 2.85
979 1002 2.799176 GATGAAATCGGGGCTTGCT 58.201 52.632 0.00 0.00 31.13 3.91
982 1005 2.036256 AAATCGGGGCTTGCTGCT 59.964 55.556 0.00 0.00 42.39 4.24
1309 1332 3.087253 ATGATTGGTCCGCGGGGA 61.087 61.111 27.83 18.63 41.08 4.81
1500 1523 1.359848 CAGTCATGAAGTACACCGCC 58.640 55.000 0.00 0.00 0.00 6.13
2190 2295 0.663153 GGAGGTGTTGTCTTGTGTGC 59.337 55.000 0.00 0.00 0.00 4.57
2236 2341 2.124942 CCGAGAGAAAGGCTGCCC 60.125 66.667 16.57 0.00 0.00 5.36
2312 2420 1.068474 CGTTGTGGGAACGAGTGATC 58.932 55.000 0.68 0.00 45.64 2.92
2338 2447 3.862124 CGTGAGCCGTTTCTCCTG 58.138 61.111 0.00 0.00 32.22 3.86
2347 2456 4.142038 AGCCGTTTCTCCTGTGTTAAAAT 58.858 39.130 0.00 0.00 0.00 1.82
2348 2457 4.215613 AGCCGTTTCTCCTGTGTTAAAATC 59.784 41.667 0.00 0.00 0.00 2.17
2349 2458 4.215613 GCCGTTTCTCCTGTGTTAAAATCT 59.784 41.667 0.00 0.00 0.00 2.40
2350 2459 5.689819 CCGTTTCTCCTGTGTTAAAATCTG 58.310 41.667 0.00 0.00 0.00 2.90
2352 2461 5.468746 CGTTTCTCCTGTGTTAAAATCTGGA 59.531 40.000 0.00 0.00 0.00 3.86
2355 2464 7.510549 TTCTCCTGTGTTAAAATCTGGAAAG 57.489 36.000 0.00 0.00 0.00 2.62
2356 2465 6.601332 TCTCCTGTGTTAAAATCTGGAAAGT 58.399 36.000 0.00 0.00 0.00 2.66
2361 2471 9.280174 CCTGTGTTAAAATCTGGAAAGTTAGTA 57.720 33.333 0.00 0.00 0.00 1.82
2376 2486 4.403734 AGTTAGTAATGGTTTGGGTGTGG 58.596 43.478 0.00 0.00 0.00 4.17
2382 2492 5.841783 AGTAATGGTTTGGGTGTGGTAATTT 59.158 36.000 0.00 0.00 0.00 1.82
2383 2493 4.615588 ATGGTTTGGGTGTGGTAATTTG 57.384 40.909 0.00 0.00 0.00 2.32
2395 2505 7.598869 GGGTGTGGTAATTTGAAAAGAAATCTC 59.401 37.037 0.00 0.00 0.00 2.75
2419 2530 5.163764 CGGTGCAACATGTTTATGATGTACT 60.164 40.000 8.77 0.00 45.38 2.73
2420 2531 6.258160 GGTGCAACATGTTTATGATGTACTC 58.742 40.000 8.77 0.00 45.38 2.59
2421 2532 6.258160 GTGCAACATGTTTATGATGTACTCC 58.742 40.000 8.77 0.00 43.91 3.85
2422 2533 5.356751 TGCAACATGTTTATGATGTACTCCC 59.643 40.000 8.77 0.00 38.80 4.30
2423 2534 5.590259 GCAACATGTTTATGATGTACTCCCT 59.410 40.000 8.77 0.00 38.80 4.20
2424 2535 6.238484 GCAACATGTTTATGATGTACTCCCTC 60.238 42.308 8.77 0.00 38.80 4.30
2425 2536 5.930135 ACATGTTTATGATGTACTCCCTCC 58.070 41.667 0.00 0.00 37.73 4.30
2426 2537 5.428457 ACATGTTTATGATGTACTCCCTCCA 59.572 40.000 0.00 0.00 37.73 3.86
2427 2538 5.614324 TGTTTATGATGTACTCCCTCCAG 57.386 43.478 0.00 0.00 0.00 3.86
2428 2539 4.408921 TGTTTATGATGTACTCCCTCCAGG 59.591 45.833 0.00 0.00 0.00 4.45
2429 2540 4.552883 TTATGATGTACTCCCTCCAGGA 57.447 45.455 0.00 0.00 44.91 3.86
2430 2541 2.940514 TGATGTACTCCCTCCAGGAA 57.059 50.000 0.00 0.00 46.94 3.36
2431 2542 3.421394 TGATGTACTCCCTCCAGGAAT 57.579 47.619 0.00 0.00 46.94 3.01
2432 2543 4.552883 TGATGTACTCCCTCCAGGAATA 57.447 45.455 0.00 0.00 46.94 1.75
2433 2544 5.093236 TGATGTACTCCCTCCAGGAATAT 57.907 43.478 0.00 0.00 46.94 1.28
2434 2545 6.227624 TGATGTACTCCCTCCAGGAATATA 57.772 41.667 0.00 0.00 46.94 0.86
2435 2546 6.630131 TGATGTACTCCCTCCAGGAATATAA 58.370 40.000 0.00 0.00 46.94 0.98
2436 2547 6.726299 TGATGTACTCCCTCCAGGAATATAAG 59.274 42.308 0.00 0.00 46.94 1.73
2437 2548 6.289482 TGTACTCCCTCCAGGAATATAAGA 57.711 41.667 0.00 0.00 46.94 2.10
2438 2549 6.315714 TGTACTCCCTCCAGGAATATAAGAG 58.684 44.000 0.00 0.00 46.94 2.85
2439 2550 4.164204 ACTCCCTCCAGGAATATAAGAGC 58.836 47.826 0.00 0.00 46.94 4.09
2440 2551 4.163427 CTCCCTCCAGGAATATAAGAGCA 58.837 47.826 0.00 0.00 46.94 4.26
2441 2552 4.767908 TCCCTCCAGGAATATAAGAGCAT 58.232 43.478 0.00 0.00 43.78 3.79
2442 2553 5.915628 TCCCTCCAGGAATATAAGAGCATA 58.084 41.667 0.00 0.00 43.78 3.14
2443 2554 6.515779 TCCCTCCAGGAATATAAGAGCATAT 58.484 40.000 0.00 0.00 43.78 1.78
2444 2555 7.662083 TCCCTCCAGGAATATAAGAGCATATA 58.338 38.462 0.00 0.00 43.78 0.86
2445 2556 8.129001 TCCCTCCAGGAATATAAGAGCATATAA 58.871 37.037 0.00 0.00 43.78 0.98
2446 2557 8.772250 CCCTCCAGGAATATAAGAGCATATAAA 58.228 37.037 0.00 0.00 38.24 1.40
2508 2619 9.590451 TTTATATTTGTTTACAGAGGGAGTACG 57.410 33.333 0.00 0.00 0.00 3.67
2509 2620 4.942761 TTTGTTTACAGAGGGAGTACGT 57.057 40.909 0.00 0.00 0.00 3.57
2510 2621 3.928727 TGTTTACAGAGGGAGTACGTG 57.071 47.619 0.00 0.00 0.00 4.49
2511 2622 3.489355 TGTTTACAGAGGGAGTACGTGA 58.511 45.455 0.00 0.00 0.00 4.35
2512 2623 4.084287 TGTTTACAGAGGGAGTACGTGAT 58.916 43.478 0.00 0.00 0.00 3.06
2513 2624 4.082408 TGTTTACAGAGGGAGTACGTGATG 60.082 45.833 0.00 0.00 0.00 3.07
2514 2625 0.818296 ACAGAGGGAGTACGTGATGC 59.182 55.000 0.00 0.00 0.00 3.91
2515 2626 1.107114 CAGAGGGAGTACGTGATGCT 58.893 55.000 0.00 0.00 0.00 3.79
2516 2627 2.298610 CAGAGGGAGTACGTGATGCTA 58.701 52.381 0.00 0.00 0.00 3.49
2517 2628 2.033550 CAGAGGGAGTACGTGATGCTAC 59.966 54.545 0.00 0.00 0.00 3.58
2518 2629 2.092321 AGAGGGAGTACGTGATGCTACT 60.092 50.000 0.00 0.00 0.00 2.57
2519 2630 3.136077 AGAGGGAGTACGTGATGCTACTA 59.864 47.826 0.00 0.00 0.00 1.82
2520 2631 3.212685 AGGGAGTACGTGATGCTACTAC 58.787 50.000 0.00 0.00 0.00 2.73
2521 2632 3.117963 AGGGAGTACGTGATGCTACTACT 60.118 47.826 0.00 0.00 0.00 2.57
2522 2633 3.003482 GGGAGTACGTGATGCTACTACTG 59.997 52.174 0.00 0.00 0.00 2.74
2523 2634 3.626670 GGAGTACGTGATGCTACTACTGT 59.373 47.826 0.00 0.00 0.00 3.55
2524 2635 4.496010 GGAGTACGTGATGCTACTACTGTG 60.496 50.000 0.00 0.00 0.00 3.66
2525 2636 2.279582 ACGTGATGCTACTACTGTGC 57.720 50.000 0.00 0.00 0.00 4.57
2526 2637 1.819288 ACGTGATGCTACTACTGTGCT 59.181 47.619 0.00 0.00 0.00 4.40
2527 2638 2.188524 CGTGATGCTACTACTGTGCTG 58.811 52.381 0.00 0.00 0.00 4.41
2528 2639 1.929836 GTGATGCTACTACTGTGCTGC 59.070 52.381 0.00 0.00 0.00 5.25
2529 2640 1.550072 TGATGCTACTACTGTGCTGCA 59.450 47.619 0.00 0.00 34.68 4.41
2530 2641 2.169144 TGATGCTACTACTGTGCTGCAT 59.831 45.455 5.27 10.46 39.56 3.96
2531 2642 2.768253 TGCTACTACTGTGCTGCATT 57.232 45.000 5.27 0.00 0.00 3.56
2532 2643 2.349590 TGCTACTACTGTGCTGCATTG 58.650 47.619 5.27 4.39 0.00 2.82
2533 2644 2.289631 TGCTACTACTGTGCTGCATTGT 60.290 45.455 5.27 10.47 0.00 2.71
2534 2645 2.094894 GCTACTACTGTGCTGCATTGTG 59.905 50.000 5.27 5.90 0.00 3.33
2535 2646 0.877071 ACTACTGTGCTGCATTGTGC 59.123 50.000 5.27 0.00 45.29 4.57
2550 2661 5.810525 GCATTGTGCATATACTTTCTTCGT 58.189 37.500 0.00 0.00 44.26 3.85
2551 2662 6.258160 GCATTGTGCATATACTTTCTTCGTT 58.742 36.000 0.00 0.00 44.26 3.85
2552 2663 6.412072 GCATTGTGCATATACTTTCTTCGTTC 59.588 38.462 0.00 0.00 44.26 3.95
2553 2664 6.417191 TTGTGCATATACTTTCTTCGTTCC 57.583 37.500 0.00 0.00 0.00 3.62
2554 2665 5.730550 TGTGCATATACTTTCTTCGTTCCT 58.269 37.500 0.00 0.00 0.00 3.36
2555 2666 6.869695 TGTGCATATACTTTCTTCGTTCCTA 58.130 36.000 0.00 0.00 0.00 2.94
2556 2667 7.324935 TGTGCATATACTTTCTTCGTTCCTAA 58.675 34.615 0.00 0.00 0.00 2.69
2557 2668 7.820386 TGTGCATATACTTTCTTCGTTCCTAAA 59.180 33.333 0.00 0.00 0.00 1.85
2558 2669 8.827677 GTGCATATACTTTCTTCGTTCCTAAAT 58.172 33.333 0.00 0.00 0.00 1.40
2610 2721 9.317936 TGAACTACATATAGAGCAAAATGAGTG 57.682 33.333 0.00 0.00 32.23 3.51
2611 2722 9.534565 GAACTACATATAGAGCAAAATGAGTGA 57.465 33.333 0.00 0.00 32.23 3.41
2612 2723 9.890629 AACTACATATAGAGCAAAATGAGTGAA 57.109 29.630 0.00 0.00 32.23 3.18
2622 2733 9.678260 AGAGCAAAATGAGTGAATTTATACTCT 57.322 29.630 15.15 0.00 42.86 3.24
2664 2775 9.739276 ATATTCGTATGTGGTTCATAATGGAAT 57.261 29.630 0.00 0.00 40.21 3.01
2665 2776 7.490962 TTCGTATGTGGTTCATAATGGAATC 57.509 36.000 0.00 0.00 40.21 2.52
2666 2777 6.826668 TCGTATGTGGTTCATAATGGAATCT 58.173 36.000 0.00 0.00 40.21 2.40
2667 2778 6.929049 TCGTATGTGGTTCATAATGGAATCTC 59.071 38.462 0.00 0.00 40.21 2.75
2668 2779 6.931281 CGTATGTGGTTCATAATGGAATCTCT 59.069 38.462 0.00 0.00 40.21 3.10
2669 2780 8.088365 CGTATGTGGTTCATAATGGAATCTCTA 58.912 37.037 0.00 0.00 40.21 2.43
2670 2781 9.209175 GTATGTGGTTCATAATGGAATCTCTAC 57.791 37.037 0.00 0.00 40.21 2.59
2671 2782 7.194112 TGTGGTTCATAATGGAATCTCTACA 57.806 36.000 0.00 0.00 0.00 2.74
2672 2783 7.629157 TGTGGTTCATAATGGAATCTCTACAA 58.371 34.615 0.00 0.00 0.00 2.41
2673 2784 8.106462 TGTGGTTCATAATGGAATCTCTACAAA 58.894 33.333 0.00 0.00 0.00 2.83
2674 2785 8.616076 GTGGTTCATAATGGAATCTCTACAAAG 58.384 37.037 0.00 0.00 0.00 2.77
2675 2786 8.328758 TGGTTCATAATGGAATCTCTACAAAGT 58.671 33.333 0.00 0.00 0.00 2.66
2676 2787 8.831550 GGTTCATAATGGAATCTCTACAAAGTC 58.168 37.037 0.00 0.00 0.00 3.01
2677 2788 9.606631 GTTCATAATGGAATCTCTACAAAGTCT 57.393 33.333 0.00 0.00 0.00 3.24
2695 2806 9.379791 ACAAAGTCTTATATTTAGAAACGGAGG 57.620 33.333 0.00 0.00 0.00 4.30
2696 2807 8.827677 CAAAGTCTTATATTTAGAAACGGAGGG 58.172 37.037 0.00 0.00 0.00 4.30
2697 2808 7.909485 AGTCTTATATTTAGAAACGGAGGGA 57.091 36.000 0.00 0.00 0.00 4.20
2698 2809 7.953752 AGTCTTATATTTAGAAACGGAGGGAG 58.046 38.462 0.00 0.00 0.00 4.30
2699 2810 7.564292 AGTCTTATATTTAGAAACGGAGGGAGT 59.436 37.037 0.00 0.00 0.00 3.85
2700 2811 7.652507 GTCTTATATTTAGAAACGGAGGGAGTG 59.347 40.741 0.00 0.00 0.00 3.51
2701 2812 5.952347 ATATTTAGAAACGGAGGGAGTGT 57.048 39.130 0.00 0.00 0.00 3.55
2702 2813 4.635699 ATTTAGAAACGGAGGGAGTGTT 57.364 40.909 0.00 0.00 0.00 3.32
2703 2814 3.396260 TTAGAAACGGAGGGAGTGTTG 57.604 47.619 0.00 0.00 0.00 3.33
2704 2815 1.129058 AGAAACGGAGGGAGTGTTGT 58.871 50.000 0.00 0.00 0.00 3.32
2705 2816 1.070289 AGAAACGGAGGGAGTGTTGTC 59.930 52.381 0.00 0.00 0.00 3.18
2706 2817 0.108019 AAACGGAGGGAGTGTTGTCC 59.892 55.000 0.00 0.00 35.64 4.02
2707 2818 0.763223 AACGGAGGGAGTGTTGTCCT 60.763 55.000 0.00 0.00 36.75 3.85
2708 2819 0.763223 ACGGAGGGAGTGTTGTCCTT 60.763 55.000 0.00 0.00 36.75 3.36
2709 2820 0.320771 CGGAGGGAGTGTTGTCCTTG 60.321 60.000 0.00 0.00 36.75 3.61
2710 2821 0.036875 GGAGGGAGTGTTGTCCTTGG 59.963 60.000 0.00 0.00 36.75 3.61
2711 2822 0.606673 GAGGGAGTGTTGTCCTTGGC 60.607 60.000 0.00 0.00 36.75 4.52
2712 2823 1.966451 GGGAGTGTTGTCCTTGGCG 60.966 63.158 0.00 0.00 36.75 5.69
2713 2824 1.966451 GGAGTGTTGTCCTTGGCGG 60.966 63.158 0.00 0.00 33.30 6.13
2714 2825 2.594592 AGTGTTGTCCTTGGCGGC 60.595 61.111 0.00 0.00 0.00 6.53
2715 2826 4.025401 GTGTTGTCCTTGGCGGCG 62.025 66.667 0.51 0.51 0.00 6.46
2716 2827 4.243008 TGTTGTCCTTGGCGGCGA 62.243 61.111 12.98 0.14 0.00 5.54
2717 2828 3.723348 GTTGTCCTTGGCGGCGAC 61.723 66.667 12.98 9.31 0.00 5.19
2718 2829 3.936203 TTGTCCTTGGCGGCGACT 61.936 61.111 16.45 0.00 0.00 4.18
2719 2830 3.876589 TTGTCCTTGGCGGCGACTC 62.877 63.158 16.45 0.75 0.00 3.36
2730 2841 4.149970 GCGACTCGAGCGACGACT 62.150 66.667 26.02 1.45 46.45 4.18
2731 2842 2.020287 CGACTCGAGCGACGACTC 59.980 66.667 19.91 4.07 46.45 3.36
2732 2843 2.400402 GACTCGAGCGACGACTCC 59.600 66.667 13.61 0.00 46.45 3.85
2733 2844 3.098377 GACTCGAGCGACGACTCCC 62.098 68.421 13.61 0.00 46.45 4.30
2734 2845 3.125573 CTCGAGCGACGACTCCCA 61.126 66.667 0.00 0.00 46.45 4.37
2735 2846 3.384014 CTCGAGCGACGACTCCCAC 62.384 68.421 0.00 0.00 46.45 4.61
2736 2847 4.477975 CGAGCGACGACTCCCACC 62.478 72.222 0.00 0.00 45.77 4.61
2737 2848 4.477975 GAGCGACGACTCCCACCG 62.478 72.222 0.00 0.00 0.00 4.94
2744 2855 4.736896 GACTCCCACCGTCGCCAC 62.737 72.222 0.00 0.00 0.00 5.01
2746 2857 3.066190 CTCCCACCGTCGCCACTA 61.066 66.667 0.00 0.00 0.00 2.74
2747 2858 3.064987 CTCCCACCGTCGCCACTAG 62.065 68.421 0.00 0.00 0.00 2.57
2748 2859 4.814294 CCCACCGTCGCCACTAGC 62.814 72.222 0.00 0.00 38.52 3.42
2757 2868 2.280457 GCCACTAGCGCCTCCATC 60.280 66.667 2.29 0.00 0.00 3.51
2758 2869 2.423446 CCACTAGCGCCTCCATCC 59.577 66.667 2.29 0.00 0.00 3.51
2759 2870 2.136878 CCACTAGCGCCTCCATCCT 61.137 63.158 2.29 0.00 0.00 3.24
2760 2871 1.068753 CACTAGCGCCTCCATCCTG 59.931 63.158 2.29 0.00 0.00 3.86
2761 2872 2.030262 CTAGCGCCTCCATCCTGC 59.970 66.667 2.29 0.00 0.00 4.85
2762 2873 3.527775 CTAGCGCCTCCATCCTGCC 62.528 68.421 2.29 0.00 0.00 4.85
2764 2875 4.925861 GCGCCTCCATCCTGCCTC 62.926 72.222 0.00 0.00 0.00 4.70
2765 2876 4.247380 CGCCTCCATCCTGCCTCC 62.247 72.222 0.00 0.00 0.00 4.30
2766 2877 3.883549 GCCTCCATCCTGCCTCCC 61.884 72.222 0.00 0.00 0.00 4.30
2767 2878 3.174265 CCTCCATCCTGCCTCCCC 61.174 72.222 0.00 0.00 0.00 4.81
2768 2879 3.174265 CTCCATCCTGCCTCCCCC 61.174 72.222 0.00 0.00 0.00 5.40
2769 2880 3.710631 TCCATCCTGCCTCCCCCT 61.711 66.667 0.00 0.00 0.00 4.79
2770 2881 2.697644 CCATCCTGCCTCCCCCTT 60.698 66.667 0.00 0.00 0.00 3.95
2771 2882 2.761465 CCATCCTGCCTCCCCCTTC 61.761 68.421 0.00 0.00 0.00 3.46
2772 2883 1.695597 CATCCTGCCTCCCCCTTCT 60.696 63.158 0.00 0.00 0.00 2.85
2773 2884 1.085605 ATCCTGCCTCCCCCTTCTT 59.914 57.895 0.00 0.00 0.00 2.52
2774 2885 1.284841 ATCCTGCCTCCCCCTTCTTG 61.285 60.000 0.00 0.00 0.00 3.02
2775 2886 2.044551 CTGCCTCCCCCTTCTTGC 60.045 66.667 0.00 0.00 0.00 4.01
2776 2887 3.651980 CTGCCTCCCCCTTCTTGCC 62.652 68.421 0.00 0.00 0.00 4.52
2777 2888 4.803908 GCCTCCCCCTTCTTGCCG 62.804 72.222 0.00 0.00 0.00 5.69
2778 2889 4.803908 CCTCCCCCTTCTTGCCGC 62.804 72.222 0.00 0.00 0.00 6.53
2779 2890 4.803908 CTCCCCCTTCTTGCCGCC 62.804 72.222 0.00 0.00 0.00 6.13
2796 2907 4.514577 CACCGGCTAGGGTCGCAG 62.515 72.222 0.00 0.00 46.96 5.18
2802 2913 3.399181 CTAGGGTCGCAGGGGCAA 61.399 66.667 0.00 0.00 41.24 4.52
2803 2914 2.931105 TAGGGTCGCAGGGGCAAA 60.931 61.111 0.00 0.00 41.24 3.68
2804 2915 2.876368 CTAGGGTCGCAGGGGCAAAG 62.876 65.000 0.00 0.00 41.24 2.77
2816 2927 2.046314 GCAAAGCCCCTCGCACTA 60.046 61.111 0.00 0.00 41.38 2.74
2817 2928 2.399356 GCAAAGCCCCTCGCACTAC 61.399 63.158 0.00 0.00 41.38 2.73
2818 2929 1.003839 CAAAGCCCCTCGCACTACA 60.004 57.895 0.00 0.00 41.38 2.74
2819 2930 1.003718 AAAGCCCCTCGCACTACAC 60.004 57.895 0.00 0.00 41.38 2.90
2820 2931 2.781595 AAAGCCCCTCGCACTACACG 62.782 60.000 0.00 0.00 41.38 4.49
2821 2932 4.814294 GCCCCTCGCACTACACGG 62.814 72.222 0.00 0.00 37.47 4.94
2822 2933 3.379445 CCCCTCGCACTACACGGT 61.379 66.667 0.00 0.00 0.00 4.83
2823 2934 2.126071 CCCTCGCACTACACGGTG 60.126 66.667 6.58 6.58 39.91 4.94
2824 2935 2.126071 CCTCGCACTACACGGTGG 60.126 66.667 13.48 0.00 37.65 4.61
2825 2936 2.809601 CTCGCACTACACGGTGGC 60.810 66.667 13.48 5.10 37.65 5.01
2826 2937 4.710695 TCGCACTACACGGTGGCG 62.711 66.667 18.99 18.99 37.65 5.69
2828 2939 4.675029 GCACTACACGGTGGCGGT 62.675 66.667 13.48 5.20 37.65 5.68
2829 2940 2.736995 CACTACACGGTGGCGGTG 60.737 66.667 13.48 13.17 39.91 4.94
2830 2941 3.998672 ACTACACGGTGGCGGTGG 61.999 66.667 13.48 0.00 38.67 4.61
2831 2942 4.752879 CTACACGGTGGCGGTGGG 62.753 72.222 13.48 1.45 38.67 4.61
2842 2953 4.452733 CGGTGGGCGACTTCCTCC 62.453 72.222 0.00 0.00 35.27 4.30
2843 2954 3.003763 GGTGGGCGACTTCCTCCT 61.004 66.667 0.00 0.00 35.62 3.69
2844 2955 2.593956 GGTGGGCGACTTCCTCCTT 61.594 63.158 0.00 0.00 35.62 3.36
2845 2956 1.079057 GTGGGCGACTTCCTCCTTC 60.079 63.158 0.00 0.00 0.00 3.46
2846 2957 2.291043 TGGGCGACTTCCTCCTTCC 61.291 63.158 0.00 0.00 0.00 3.46
2847 2958 2.585153 GGCGACTTCCTCCTTCCC 59.415 66.667 0.00 0.00 0.00 3.97
2848 2959 1.990614 GGCGACTTCCTCCTTCCCT 60.991 63.158 0.00 0.00 0.00 4.20
2849 2960 1.518302 GCGACTTCCTCCTTCCCTC 59.482 63.158 0.00 0.00 0.00 4.30
2850 2961 0.973496 GCGACTTCCTCCTTCCCTCT 60.973 60.000 0.00 0.00 0.00 3.69
2851 2962 1.107945 CGACTTCCTCCTTCCCTCTC 58.892 60.000 0.00 0.00 0.00 3.20
2852 2963 1.491668 GACTTCCTCCTTCCCTCTCC 58.508 60.000 0.00 0.00 0.00 3.71
2853 2964 1.007842 GACTTCCTCCTTCCCTCTCCT 59.992 57.143 0.00 0.00 0.00 3.69
2854 2965 1.007842 ACTTCCTCCTTCCCTCTCCTC 59.992 57.143 0.00 0.00 0.00 3.71
2855 2966 0.340208 TTCCTCCTTCCCTCTCCTCC 59.660 60.000 0.00 0.00 0.00 4.30
2856 2967 1.074850 CCTCCTTCCCTCTCCTCCC 60.075 68.421 0.00 0.00 0.00 4.30
2857 2968 1.074850 CTCCTTCCCTCTCCTCCCC 60.075 68.421 0.00 0.00 0.00 4.81
2858 2969 1.550374 TCCTTCCCTCTCCTCCCCT 60.550 63.158 0.00 0.00 0.00 4.79
2859 2970 1.074850 CCTTCCCTCTCCTCCCCTC 60.075 68.421 0.00 0.00 0.00 4.30
2860 2971 1.706575 CTTCCCTCTCCTCCCCTCA 59.293 63.158 0.00 0.00 0.00 3.86
2861 2972 0.267356 CTTCCCTCTCCTCCCCTCAT 59.733 60.000 0.00 0.00 0.00 2.90
2862 2973 0.030705 TTCCCTCTCCTCCCCTCATG 60.031 60.000 0.00 0.00 0.00 3.07
2863 2974 2.146061 CCCTCTCCTCCCCTCATGC 61.146 68.421 0.00 0.00 0.00 4.06
2864 2975 2.146061 CCTCTCCTCCCCTCATGCC 61.146 68.421 0.00 0.00 0.00 4.40
2865 2976 1.074623 CTCTCCTCCCCTCATGCCT 60.075 63.158 0.00 0.00 0.00 4.75
2866 2977 0.693767 CTCTCCTCCCCTCATGCCTT 60.694 60.000 0.00 0.00 0.00 4.35
2867 2978 0.984961 TCTCCTCCCCTCATGCCTTG 60.985 60.000 0.00 0.00 0.00 3.61
2868 2979 1.992519 CTCCTCCCCTCATGCCTTGG 61.993 65.000 0.00 0.00 0.00 3.61
2869 2980 2.123982 CTCCCCTCATGCCTTGGC 60.124 66.667 4.43 4.43 0.00 4.52
2870 2981 2.614969 TCCCCTCATGCCTTGGCT 60.615 61.111 13.18 0.00 0.00 4.75
2871 2982 2.441532 CCCCTCATGCCTTGGCTG 60.442 66.667 13.18 8.63 0.00 4.85
2872 2983 3.145551 CCCTCATGCCTTGGCTGC 61.146 66.667 13.18 0.00 0.00 5.25
2873 2984 3.515286 CCTCATGCCTTGGCTGCG 61.515 66.667 13.18 4.11 0.00 5.18
2874 2985 3.515286 CTCATGCCTTGGCTGCGG 61.515 66.667 13.18 0.00 0.00 5.69
2899 3010 3.264897 CCCGAATCCGCGAGCTTG 61.265 66.667 8.23 0.00 0.00 4.01
2900 3011 3.929948 CCGAATCCGCGAGCTTGC 61.930 66.667 16.57 16.57 0.00 4.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
59 71 0.667993 TTTTCTTGCTTGGCTCACCG 59.332 50.000 0.00 0.00 39.70 4.94
151 163 1.546589 TAGATTTGTGGGCCCGACGT 61.547 55.000 19.37 0.99 0.00 4.34
165 177 2.830923 CGCCTGGGATGAGAGATAGATT 59.169 50.000 0.00 0.00 0.00 2.40
277 296 2.119029 GGGGCACTGGGCGTATTTC 61.119 63.158 0.00 0.00 46.16 2.17
503 522 3.560278 GATACGCAACGTGCCCCG 61.560 66.667 2.35 0.00 41.12 5.73
515 534 0.099259 TACAACCACCTCGCGATACG 59.901 55.000 10.36 2.40 45.62 3.06
525 545 4.700700 AGCGGTAAATATCTACAACCACC 58.299 43.478 0.00 0.00 0.00 4.61
668 689 1.405461 CCGTGTGTCAGTTACGACAG 58.595 55.000 9.48 1.19 46.23 3.51
803 824 4.342665 GGTGGAATGGGTGAAGTGTAAAAA 59.657 41.667 0.00 0.00 0.00 1.94
1233 1256 2.747855 GCCGCCCTCAACCTCTTG 60.748 66.667 0.00 0.00 0.00 3.02
1350 1373 3.211963 GCCGCATACTTGCCCCAG 61.212 66.667 0.00 0.00 46.57 4.45
1487 1510 2.203877 AGGGGGCGGTGTACTTCA 60.204 61.111 0.00 0.00 0.00 3.02
1488 1511 2.582978 GAGGGGGCGGTGTACTTC 59.417 66.667 0.00 0.00 0.00 3.01
1788 1886 1.518367 TCAGGTTGTTCAGGGAGGTT 58.482 50.000 0.00 0.00 0.00 3.50
1947 2052 6.272822 ACTGTTCTCTTTCAAAAAGTTGCT 57.727 33.333 0.00 0.00 34.50 3.91
1985 2090 3.866327 GCAGACTCCCGAGAAATAAAGTC 59.134 47.826 0.00 0.00 34.69 3.01
2236 2341 1.601171 CAGCTCCTGTCCCCTCAAG 59.399 63.158 0.00 0.00 0.00 3.02
2286 2394 2.867975 CTCGTTCCCACAACGTAAAACT 59.132 45.455 6.76 0.00 43.47 2.66
2312 2420 3.620428 CGGCTCACGTGCATAGCG 61.620 66.667 18.20 11.54 37.11 4.26
2333 2441 6.884280 ACTTTCCAGATTTTAACACAGGAG 57.116 37.500 0.00 0.00 0.00 3.69
2334 2442 7.996644 ACTAACTTTCCAGATTTTAACACAGGA 59.003 33.333 0.00 0.00 0.00 3.86
2347 2456 6.007703 CCCAAACCATTACTAACTTTCCAGA 58.992 40.000 0.00 0.00 0.00 3.86
2348 2457 5.773176 ACCCAAACCATTACTAACTTTCCAG 59.227 40.000 0.00 0.00 0.00 3.86
2349 2458 5.536916 CACCCAAACCATTACTAACTTTCCA 59.463 40.000 0.00 0.00 0.00 3.53
2350 2459 5.537295 ACACCCAAACCATTACTAACTTTCC 59.463 40.000 0.00 0.00 0.00 3.13
2352 2461 5.303333 CCACACCCAAACCATTACTAACTTT 59.697 40.000 0.00 0.00 0.00 2.66
2355 2464 4.146564 ACCACACCCAAACCATTACTAAC 58.853 43.478 0.00 0.00 0.00 2.34
2356 2465 4.456662 ACCACACCCAAACCATTACTAA 57.543 40.909 0.00 0.00 0.00 2.24
2361 2471 4.656112 TCAAATTACCACACCCAAACCATT 59.344 37.500 0.00 0.00 0.00 3.16
2376 2486 6.861055 TGCACCGAGATTTCTTTTCAAATTAC 59.139 34.615 0.00 0.00 0.00 1.89
2382 2492 3.629855 TGTTGCACCGAGATTTCTTTTCA 59.370 39.130 0.00 0.00 0.00 2.69
2383 2493 4.223320 TGTTGCACCGAGATTTCTTTTC 57.777 40.909 0.00 0.00 0.00 2.29
2395 2505 4.095410 ACATCATAAACATGTTGCACCG 57.905 40.909 12.82 2.43 29.75 4.94
2419 2530 4.213531 TGCTCTTATATTCCTGGAGGGA 57.786 45.455 0.00 0.00 43.41 4.20
2420 2531 6.821616 ATATGCTCTTATATTCCTGGAGGG 57.178 41.667 0.00 0.00 35.41 4.30
2482 2593 9.590451 CGTACTCCCTCTGTAAACAAATATAAA 57.410 33.333 0.00 0.00 0.00 1.40
2483 2594 8.752187 ACGTACTCCCTCTGTAAACAAATATAA 58.248 33.333 0.00 0.00 0.00 0.98
2484 2595 8.192774 CACGTACTCCCTCTGTAAACAAATATA 58.807 37.037 0.00 0.00 0.00 0.86
2485 2596 7.039882 CACGTACTCCCTCTGTAAACAAATAT 58.960 38.462 0.00 0.00 0.00 1.28
2486 2597 6.209192 TCACGTACTCCCTCTGTAAACAAATA 59.791 38.462 0.00 0.00 0.00 1.40
2487 2598 5.011329 TCACGTACTCCCTCTGTAAACAAAT 59.989 40.000 0.00 0.00 0.00 2.32
2488 2599 4.341806 TCACGTACTCCCTCTGTAAACAAA 59.658 41.667 0.00 0.00 0.00 2.83
2489 2600 3.890756 TCACGTACTCCCTCTGTAAACAA 59.109 43.478 0.00 0.00 0.00 2.83
2490 2601 3.489355 TCACGTACTCCCTCTGTAAACA 58.511 45.455 0.00 0.00 0.00 2.83
2491 2602 4.421948 CATCACGTACTCCCTCTGTAAAC 58.578 47.826 0.00 0.00 0.00 2.01
2492 2603 3.119245 GCATCACGTACTCCCTCTGTAAA 60.119 47.826 0.00 0.00 0.00 2.01
2493 2604 2.426024 GCATCACGTACTCCCTCTGTAA 59.574 50.000 0.00 0.00 0.00 2.41
2494 2605 2.022195 GCATCACGTACTCCCTCTGTA 58.978 52.381 0.00 0.00 0.00 2.74
2495 2606 0.818296 GCATCACGTACTCCCTCTGT 59.182 55.000 0.00 0.00 0.00 3.41
2496 2607 1.107114 AGCATCACGTACTCCCTCTG 58.893 55.000 0.00 0.00 0.00 3.35
2497 2608 2.092321 AGTAGCATCACGTACTCCCTCT 60.092 50.000 0.00 0.00 0.00 3.69
2498 2609 2.299521 AGTAGCATCACGTACTCCCTC 58.700 52.381 0.00 0.00 0.00 4.30
2499 2610 2.438800 AGTAGCATCACGTACTCCCT 57.561 50.000 0.00 0.00 0.00 4.20
2500 2611 3.003482 CAGTAGTAGCATCACGTACTCCC 59.997 52.174 0.00 0.00 31.79 4.30
2501 2612 3.626670 ACAGTAGTAGCATCACGTACTCC 59.373 47.826 0.00 0.00 31.79 3.85
2502 2613 4.589252 CACAGTAGTAGCATCACGTACTC 58.411 47.826 0.00 0.00 31.79 2.59
2503 2614 3.181499 GCACAGTAGTAGCATCACGTACT 60.181 47.826 0.00 0.00 33.92 2.73
2504 2615 3.106672 GCACAGTAGTAGCATCACGTAC 58.893 50.000 0.00 0.00 0.00 3.67
2505 2616 3.014623 AGCACAGTAGTAGCATCACGTA 58.985 45.455 0.00 0.00 0.00 3.57
2506 2617 1.819288 AGCACAGTAGTAGCATCACGT 59.181 47.619 0.00 0.00 0.00 4.49
2507 2618 2.188524 CAGCACAGTAGTAGCATCACG 58.811 52.381 0.00 0.00 0.00 4.35
2508 2619 1.929836 GCAGCACAGTAGTAGCATCAC 59.070 52.381 0.00 0.00 0.00 3.06
2509 2620 1.550072 TGCAGCACAGTAGTAGCATCA 59.450 47.619 0.00 0.00 0.00 3.07
2510 2621 2.299993 TGCAGCACAGTAGTAGCATC 57.700 50.000 0.00 0.00 0.00 3.91
2511 2622 2.941064 CAATGCAGCACAGTAGTAGCAT 59.059 45.455 0.00 0.00 39.82 3.79
2512 2623 2.289631 ACAATGCAGCACAGTAGTAGCA 60.290 45.455 0.00 0.00 34.95 3.49
2513 2624 2.094894 CACAATGCAGCACAGTAGTAGC 59.905 50.000 0.00 0.00 0.00 3.58
2514 2625 2.094894 GCACAATGCAGCACAGTAGTAG 59.905 50.000 0.00 0.00 44.26 2.57
2515 2626 2.076100 GCACAATGCAGCACAGTAGTA 58.924 47.619 0.00 0.00 44.26 1.82
2516 2627 0.877071 GCACAATGCAGCACAGTAGT 59.123 50.000 0.00 0.00 44.26 2.73
2517 2628 3.689224 GCACAATGCAGCACAGTAG 57.311 52.632 0.00 0.00 44.26 2.57
2527 2638 5.810525 ACGAAGAAAGTATATGCACAATGC 58.189 37.500 0.00 0.00 45.29 3.56
2528 2639 6.907212 GGAACGAAGAAAGTATATGCACAATG 59.093 38.462 0.00 0.00 0.00 2.82
2529 2640 6.823689 AGGAACGAAGAAAGTATATGCACAAT 59.176 34.615 0.00 0.00 0.00 2.71
2530 2641 6.170506 AGGAACGAAGAAAGTATATGCACAA 58.829 36.000 0.00 0.00 0.00 3.33
2531 2642 5.730550 AGGAACGAAGAAAGTATATGCACA 58.269 37.500 0.00 0.00 0.00 4.57
2532 2643 7.766219 TTAGGAACGAAGAAAGTATATGCAC 57.234 36.000 0.00 0.00 0.00 4.57
2533 2644 8.958119 ATTTAGGAACGAAGAAAGTATATGCA 57.042 30.769 0.00 0.00 0.00 3.96
2584 2695 9.317936 CACTCATTTTGCTCTATATGTAGTTCA 57.682 33.333 0.00 0.00 0.00 3.18
2585 2696 9.534565 TCACTCATTTTGCTCTATATGTAGTTC 57.465 33.333 0.00 0.00 0.00 3.01
2586 2697 9.890629 TTCACTCATTTTGCTCTATATGTAGTT 57.109 29.630 0.00 0.00 0.00 2.24
2596 2707 9.678260 AGAGTATAAATTCACTCATTTTGCTCT 57.322 29.630 13.99 0.00 42.99 4.09
2638 2749 9.739276 ATTCCATTATGAACCACATACGAATAT 57.261 29.630 0.00 0.00 40.62 1.28
2639 2750 9.214957 GATTCCATTATGAACCACATACGAATA 57.785 33.333 0.00 0.00 40.62 1.75
2640 2751 7.939039 AGATTCCATTATGAACCACATACGAAT 59.061 33.333 0.00 0.00 40.62 3.34
2641 2752 7.279615 AGATTCCATTATGAACCACATACGAA 58.720 34.615 0.00 0.00 40.62 3.85
2642 2753 6.826668 AGATTCCATTATGAACCACATACGA 58.173 36.000 0.00 0.00 40.62 3.43
2643 2754 6.931281 AGAGATTCCATTATGAACCACATACG 59.069 38.462 0.00 0.00 40.62 3.06
2644 2755 9.209175 GTAGAGATTCCATTATGAACCACATAC 57.791 37.037 0.00 0.00 40.62 2.39
2645 2756 8.933653 TGTAGAGATTCCATTATGAACCACATA 58.066 33.333 0.00 0.00 40.07 2.29
2646 2757 7.805163 TGTAGAGATTCCATTATGAACCACAT 58.195 34.615 0.00 0.00 42.39 3.21
2647 2758 7.194112 TGTAGAGATTCCATTATGAACCACA 57.806 36.000 0.00 0.00 0.00 4.17
2648 2759 8.506168 TTTGTAGAGATTCCATTATGAACCAC 57.494 34.615 0.00 0.00 0.00 4.16
2649 2760 8.328758 ACTTTGTAGAGATTCCATTATGAACCA 58.671 33.333 0.00 0.00 0.00 3.67
2650 2761 8.738645 ACTTTGTAGAGATTCCATTATGAACC 57.261 34.615 0.00 0.00 0.00 3.62
2651 2762 9.606631 AGACTTTGTAGAGATTCCATTATGAAC 57.393 33.333 0.00 0.00 0.00 3.18
2669 2780 9.379791 CCTCCGTTTCTAAATATAAGACTTTGT 57.620 33.333 0.00 0.00 0.00 2.83
2670 2781 8.827677 CCCTCCGTTTCTAAATATAAGACTTTG 58.172 37.037 0.00 0.00 0.00 2.77
2671 2782 8.765517 TCCCTCCGTTTCTAAATATAAGACTTT 58.234 33.333 0.00 0.00 0.00 2.66
2672 2783 8.315220 TCCCTCCGTTTCTAAATATAAGACTT 57.685 34.615 0.00 0.00 0.00 3.01
2673 2784 7.564292 ACTCCCTCCGTTTCTAAATATAAGACT 59.436 37.037 0.00 0.00 0.00 3.24
2674 2785 7.652507 CACTCCCTCCGTTTCTAAATATAAGAC 59.347 40.741 0.00 0.00 0.00 3.01
2675 2786 7.343833 ACACTCCCTCCGTTTCTAAATATAAGA 59.656 37.037 0.00 0.00 0.00 2.10
2676 2787 7.498443 ACACTCCCTCCGTTTCTAAATATAAG 58.502 38.462 0.00 0.00 0.00 1.73
2677 2788 7.427989 ACACTCCCTCCGTTTCTAAATATAA 57.572 36.000 0.00 0.00 0.00 0.98
2678 2789 7.093201 ACAACACTCCCTCCGTTTCTAAATATA 60.093 37.037 0.00 0.00 0.00 0.86
2679 2790 5.952347 ACACTCCCTCCGTTTCTAAATAT 57.048 39.130 0.00 0.00 0.00 1.28
2680 2791 5.012354 ACAACACTCCCTCCGTTTCTAAATA 59.988 40.000 0.00 0.00 0.00 1.40
2681 2792 4.202430 ACAACACTCCCTCCGTTTCTAAAT 60.202 41.667 0.00 0.00 0.00 1.40
2682 2793 3.135167 ACAACACTCCCTCCGTTTCTAAA 59.865 43.478 0.00 0.00 0.00 1.85
2683 2794 2.701951 ACAACACTCCCTCCGTTTCTAA 59.298 45.455 0.00 0.00 0.00 2.10
2684 2795 2.298163 GACAACACTCCCTCCGTTTCTA 59.702 50.000 0.00 0.00 0.00 2.10
2685 2796 1.070289 GACAACACTCCCTCCGTTTCT 59.930 52.381 0.00 0.00 0.00 2.52
2686 2797 1.509703 GACAACACTCCCTCCGTTTC 58.490 55.000 0.00 0.00 0.00 2.78
2687 2798 0.108019 GGACAACACTCCCTCCGTTT 59.892 55.000 0.00 0.00 0.00 3.60
2688 2799 0.763223 AGGACAACACTCCCTCCGTT 60.763 55.000 0.00 0.00 0.00 4.44
2689 2800 0.763223 AAGGACAACACTCCCTCCGT 60.763 55.000 0.00 0.00 0.00 4.69
2690 2801 0.320771 CAAGGACAACACTCCCTCCG 60.321 60.000 0.00 0.00 0.00 4.63
2691 2802 0.036875 CCAAGGACAACACTCCCTCC 59.963 60.000 0.00 0.00 0.00 4.30
2692 2803 0.606673 GCCAAGGACAACACTCCCTC 60.607 60.000 0.00 0.00 0.00 4.30
2693 2804 1.456287 GCCAAGGACAACACTCCCT 59.544 57.895 0.00 0.00 0.00 4.20
2694 2805 1.966451 CGCCAAGGACAACACTCCC 60.966 63.158 0.00 0.00 0.00 4.30
2695 2806 1.966451 CCGCCAAGGACAACACTCC 60.966 63.158 0.00 0.00 45.00 3.85
2696 2807 2.617274 GCCGCCAAGGACAACACTC 61.617 63.158 0.00 0.00 45.00 3.51
2697 2808 2.594592 GCCGCCAAGGACAACACT 60.595 61.111 0.00 0.00 45.00 3.55
2698 2809 4.025401 CGCCGCCAAGGACAACAC 62.025 66.667 0.00 0.00 45.00 3.32
2699 2810 4.243008 TCGCCGCCAAGGACAACA 62.243 61.111 0.00 0.00 45.00 3.33
2700 2811 3.723348 GTCGCCGCCAAGGACAAC 61.723 66.667 0.00 0.00 45.00 3.32
2701 2812 3.876589 GAGTCGCCGCCAAGGACAA 62.877 63.158 0.00 0.00 45.00 3.18
2702 2813 4.373116 GAGTCGCCGCCAAGGACA 62.373 66.667 0.00 0.00 45.00 4.02
2718 2829 3.429141 GTGGGAGTCGTCGCTCGA 61.429 66.667 9.52 0.00 46.83 4.04
2719 2830 4.477975 GGTGGGAGTCGTCGCTCG 62.478 72.222 9.52 0.00 36.58 5.03
2720 2831 4.477975 CGGTGGGAGTCGTCGCTC 62.478 72.222 7.80 7.80 36.58 5.03
2722 2833 4.773117 GACGGTGGGAGTCGTCGC 62.773 72.222 0.00 0.00 44.55 5.19
2727 2838 4.736896 GTGGCGACGGTGGGAGTC 62.737 72.222 0.00 0.00 35.41 3.36
2728 2839 3.873679 TAGTGGCGACGGTGGGAGT 62.874 63.158 0.00 0.00 0.00 3.85
2729 2840 3.064987 CTAGTGGCGACGGTGGGAG 62.065 68.421 0.00 0.00 0.00 4.30
2730 2841 3.066190 CTAGTGGCGACGGTGGGA 61.066 66.667 0.00 0.00 0.00 4.37
2731 2842 4.814294 GCTAGTGGCGACGGTGGG 62.814 72.222 0.00 0.00 0.00 4.61
2740 2851 2.280457 GATGGAGGCGCTAGTGGC 60.280 66.667 21.43 21.43 37.64 5.01
2741 2852 2.136878 AGGATGGAGGCGCTAGTGG 61.137 63.158 7.64 0.00 0.00 4.00
2742 2853 1.068753 CAGGATGGAGGCGCTAGTG 59.931 63.158 7.64 0.00 0.00 2.74
2743 2854 2.801631 GCAGGATGGAGGCGCTAGT 61.802 63.158 7.64 0.00 35.86 2.57
2744 2855 2.030262 GCAGGATGGAGGCGCTAG 59.970 66.667 7.64 0.00 35.86 3.42
2745 2856 3.550431 GGCAGGATGGAGGCGCTA 61.550 66.667 7.64 0.00 35.86 4.26
2747 2858 4.925861 GAGGCAGGATGGAGGCGC 62.926 72.222 0.00 0.00 35.86 6.53
2748 2859 4.247380 GGAGGCAGGATGGAGGCG 62.247 72.222 0.00 0.00 35.86 5.52
2749 2860 3.883549 GGGAGGCAGGATGGAGGC 61.884 72.222 0.00 0.00 35.86 4.70
2750 2861 3.174265 GGGGAGGCAGGATGGAGG 61.174 72.222 0.00 0.00 35.86 4.30
2751 2862 3.174265 GGGGGAGGCAGGATGGAG 61.174 72.222 0.00 0.00 35.86 3.86
2752 2863 3.287954 AAGGGGGAGGCAGGATGGA 62.288 63.158 0.00 0.00 35.86 3.41
2753 2864 2.697644 AAGGGGGAGGCAGGATGG 60.698 66.667 0.00 0.00 35.86 3.51
2754 2865 1.284841 AAGAAGGGGGAGGCAGGATG 61.285 60.000 0.00 0.00 40.87 3.51
2755 2866 1.085605 AAGAAGGGGGAGGCAGGAT 59.914 57.895 0.00 0.00 0.00 3.24
2756 2867 1.925455 CAAGAAGGGGGAGGCAGGA 60.925 63.158 0.00 0.00 0.00 3.86
2757 2868 2.679716 CAAGAAGGGGGAGGCAGG 59.320 66.667 0.00 0.00 0.00 4.85
2758 2869 2.044551 GCAAGAAGGGGGAGGCAG 60.045 66.667 0.00 0.00 0.00 4.85
2759 2870 3.661648 GGCAAGAAGGGGGAGGCA 61.662 66.667 0.00 0.00 0.00 4.75
2760 2871 4.803908 CGGCAAGAAGGGGGAGGC 62.804 72.222 0.00 0.00 0.00 4.70
2761 2872 4.803908 GCGGCAAGAAGGGGGAGG 62.804 72.222 0.00 0.00 0.00 4.30
2762 2873 4.803908 GGCGGCAAGAAGGGGGAG 62.804 72.222 3.07 0.00 0.00 4.30
2779 2890 4.514577 CTGCGACCCTAGCCGGTG 62.515 72.222 1.90 0.00 35.79 4.94
2785 2896 2.876368 CTTTGCCCCTGCGACCCTAG 62.876 65.000 0.00 0.00 41.78 3.02
2786 2897 2.931105 TTTGCCCCTGCGACCCTA 60.931 61.111 0.00 0.00 41.78 3.53
2787 2898 4.351054 CTTTGCCCCTGCGACCCT 62.351 66.667 0.00 0.00 41.78 4.34
2799 2910 2.046314 TAGTGCGAGGGGCTTTGC 60.046 61.111 0.00 0.00 44.05 3.68
2800 2911 1.003839 TGTAGTGCGAGGGGCTTTG 60.004 57.895 0.00 0.00 44.05 2.77
2801 2912 1.003718 GTGTAGTGCGAGGGGCTTT 60.004 57.895 0.00 0.00 44.05 3.51
2802 2913 2.663196 GTGTAGTGCGAGGGGCTT 59.337 61.111 0.00 0.00 44.05 4.35
2803 2914 3.760035 CGTGTAGTGCGAGGGGCT 61.760 66.667 0.00 0.00 44.05 5.19
2804 2915 4.814294 CCGTGTAGTGCGAGGGGC 62.814 72.222 0.00 0.00 43.96 5.80
2805 2916 3.379445 ACCGTGTAGTGCGAGGGG 61.379 66.667 0.00 0.00 0.00 4.79
2806 2917 2.126071 CACCGTGTAGTGCGAGGG 60.126 66.667 0.00 0.00 0.00 4.30
2807 2918 2.126071 CCACCGTGTAGTGCGAGG 60.126 66.667 0.00 0.00 36.38 4.63
2808 2919 2.809601 GCCACCGTGTAGTGCGAG 60.810 66.667 0.00 0.00 36.38 5.03
2809 2920 4.710695 CGCCACCGTGTAGTGCGA 62.711 66.667 12.76 0.00 38.60 5.10
2811 2922 4.675029 ACCGCCACCGTGTAGTGC 62.675 66.667 0.00 0.00 36.38 4.40
2812 2923 2.736995 CACCGCCACCGTGTAGTG 60.737 66.667 0.00 0.00 37.51 2.74
2813 2924 3.998672 CCACCGCCACCGTGTAGT 61.999 66.667 0.00 0.00 0.00 2.73
2814 2925 4.752879 CCCACCGCCACCGTGTAG 62.753 72.222 0.00 0.00 0.00 2.74
2825 2936 4.452733 GGAGGAAGTCGCCCACCG 62.453 72.222 0.00 0.00 38.61 4.94
2826 2937 2.523453 GAAGGAGGAAGTCGCCCACC 62.523 65.000 0.00 0.00 35.80 4.61
2827 2938 1.079057 GAAGGAGGAAGTCGCCCAC 60.079 63.158 0.00 0.00 35.80 4.61
2828 2939 2.291043 GGAAGGAGGAAGTCGCCCA 61.291 63.158 0.00 0.00 35.80 5.36
2829 2940 2.585153 GGAAGGAGGAAGTCGCCC 59.415 66.667 0.00 0.00 35.80 6.13
2830 2941 1.962321 GAGGGAAGGAGGAAGTCGCC 61.962 65.000 0.00 0.00 35.38 5.54
2831 2942 0.973496 AGAGGGAAGGAGGAAGTCGC 60.973 60.000 0.00 0.00 0.00 5.19
2832 2943 1.107945 GAGAGGGAAGGAGGAAGTCG 58.892 60.000 0.00 0.00 0.00 4.18
2833 2944 1.007842 AGGAGAGGGAAGGAGGAAGTC 59.992 57.143 0.00 0.00 0.00 3.01
2834 2945 1.007842 GAGGAGAGGGAAGGAGGAAGT 59.992 57.143 0.00 0.00 0.00 3.01
2835 2946 1.691163 GGAGGAGAGGGAAGGAGGAAG 60.691 61.905 0.00 0.00 0.00 3.46
2836 2947 0.340208 GGAGGAGAGGGAAGGAGGAA 59.660 60.000 0.00 0.00 0.00 3.36
2837 2948 1.595058 GGGAGGAGAGGGAAGGAGGA 61.595 65.000 0.00 0.00 0.00 3.71
2838 2949 1.074850 GGGAGGAGAGGGAAGGAGG 60.075 68.421 0.00 0.00 0.00 4.30
2839 2950 1.074850 GGGGAGGAGAGGGAAGGAG 60.075 68.421 0.00 0.00 0.00 3.69
2840 2951 1.550374 AGGGGAGGAGAGGGAAGGA 60.550 63.158 0.00 0.00 0.00 3.36
2841 2952 1.074850 GAGGGGAGGAGAGGGAAGG 60.075 68.421 0.00 0.00 0.00 3.46
2842 2953 0.267356 ATGAGGGGAGGAGAGGGAAG 59.733 60.000 0.00 0.00 0.00 3.46
2843 2954 0.030705 CATGAGGGGAGGAGAGGGAA 60.031 60.000 0.00 0.00 0.00 3.97
2844 2955 1.628727 CATGAGGGGAGGAGAGGGA 59.371 63.158 0.00 0.00 0.00 4.20
2845 2956 2.146061 GCATGAGGGGAGGAGAGGG 61.146 68.421 0.00 0.00 0.00 4.30
2846 2957 2.146061 GGCATGAGGGGAGGAGAGG 61.146 68.421 0.00 0.00 0.00 3.69
2847 2958 0.693767 AAGGCATGAGGGGAGGAGAG 60.694 60.000 0.00 0.00 0.00 3.20
2848 2959 0.984961 CAAGGCATGAGGGGAGGAGA 60.985 60.000 0.00 0.00 0.00 3.71
2849 2960 1.530771 CAAGGCATGAGGGGAGGAG 59.469 63.158 0.00 0.00 0.00 3.69
2850 2961 2.002977 CCAAGGCATGAGGGGAGGA 61.003 63.158 0.00 0.00 0.00 3.71
2851 2962 2.599597 CCAAGGCATGAGGGGAGG 59.400 66.667 0.00 0.00 0.00 4.30
2852 2963 2.123982 GCCAAGGCATGAGGGGAG 60.124 66.667 6.14 0.00 41.49 4.30
2853 2964 2.614969 AGCCAAGGCATGAGGGGA 60.615 61.111 14.40 0.00 44.88 4.81
2854 2965 2.441532 CAGCCAAGGCATGAGGGG 60.442 66.667 14.40 0.00 44.88 4.79
2855 2966 3.145551 GCAGCCAAGGCATGAGGG 61.146 66.667 14.40 0.00 44.88 4.30
2856 2967 3.515286 CGCAGCCAAGGCATGAGG 61.515 66.667 14.40 0.00 44.88 3.86
2857 2968 3.515286 CCGCAGCCAAGGCATGAG 61.515 66.667 14.40 9.97 44.88 2.90
2883 2994 3.929948 GCAAGCTCGCGGATTCGG 61.930 66.667 6.13 0.00 36.79 4.30


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

AutoCloner maintained by Alex Coulton.