Multiple sequence alignment - TraesCS2B01G312600

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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 TraesCS2B01G312600 chr2B 100.000 2722 0 0 1 2722 448079147 448081868 0.000000e+00 5027.0
1 TraesCS2B01G312600 chr2B 88.355 687 71 7 1 681 625914448 625915131 0.000000e+00 817.0
2 TraesCS2B01G312600 chr2B 85.211 142 10 4 2592 2722 500943540 500943681 4.730000e-28 135.0
3 TraesCS2B01G312600 chr2B 84.397 141 11 4 2593 2722 448105468 448105608 7.910000e-26 128.0
4 TraesCS2B01G312600 chr2B 71.569 408 90 20 1979 2380 598552363 598551976 1.340000e-13 87.9
5 TraesCS2B01G312600 chr2D 93.552 1706 76 11 697 2397 376620495 376622171 0.000000e+00 2510.0
6 TraesCS2B01G312600 chr2D 88.053 678 73 8 12 683 322501158 322501833 0.000000e+00 797.0
7 TraesCS2B01G312600 chr2D 74.658 438 90 17 1956 2379 289157102 289156672 1.000000e-39 174.0
8 TraesCS2B01G312600 chr2D 92.793 111 6 2 2481 2589 376622404 376622514 2.810000e-35 159.0
9 TraesCS2B01G312600 chr2D 72.414 435 107 13 1966 2395 640978174 640978600 2.850000e-25 126.0
10 TraesCS2B01G312600 chr2D 79.195 149 31 0 2252 2400 583526224 583526372 1.330000e-18 104.0
11 TraesCS2B01G312600 chr2A 90.464 1552 103 25 697 2234 510301376 510302896 0.000000e+00 2004.0
12 TraesCS2B01G312600 chr2A 80.000 150 10 7 2592 2721 775175306 775175455 2.890000e-15 93.5
13 TraesCS2B01G312600 chr4B 90.552 688 60 4 1 683 221185551 221184864 0.000000e+00 905.0
14 TraesCS2B01G312600 chr4A 89.481 694 62 8 1 686 712561309 712560619 0.000000e+00 867.0
15 TraesCS2B01G312600 chr4A 75.478 314 72 5 2029 2339 616621673 616621984 6.070000e-32 148.0
16 TraesCS2B01G312600 chr7D 88.071 679 73 6 12 683 397377431 397378108 0.000000e+00 798.0
17 TraesCS2B01G312600 chr7D 81.250 144 14 12 2590 2721 111351435 111351577 1.330000e-18 104.0
18 TraesCS2B01G312600 chr5B 87.699 691 76 7 1 684 584276031 584276719 0.000000e+00 797.0
19 TraesCS2B01G312600 chr5B 84.507 142 11 4 2592 2722 34775877 34775736 2.200000e-26 130.0
20 TraesCS2B01G312600 chr7B 87.572 692 75 7 1 683 522799465 522798776 0.000000e+00 791.0
21 TraesCS2B01G312600 chr3D 87.645 688 74 10 12 692 547931999 547932682 0.000000e+00 789.0
22 TraesCS2B01G312600 chr3D 75.064 393 79 16 1958 2341 497898088 497898470 6.030000e-37 165.0
23 TraesCS2B01G312600 chr3D 74.171 422 92 9 1996 2403 475640498 475640080 2.810000e-35 159.0
24 TraesCS2B01G312600 chr3D 83.099 142 12 6 2592 2721 108380332 108380473 4.760000e-23 119.0
25 TraesCS2B01G312600 chr1B 87.609 686 76 8 1 681 308914471 308915152 0.000000e+00 787.0
26 TraesCS2B01G312600 chr1B 76.127 377 86 4 1959 2333 366876214 366876588 7.690000e-46 195.0
27 TraesCS2B01G312600 chr1B 90.164 61 6 0 2592 2652 9177520 9177580 2.250000e-11 80.5
28 TraesCS2B01G312600 chr1A 77.444 399 80 9 2001 2395 239907027 239907419 2.110000e-56 230.0
29 TraesCS2B01G312600 chr5D 74.873 394 93 3 1957 2346 329437978 329438369 1.000000e-39 174.0
30 TraesCS2B01G312600 chr5D 85.821 134 11 8 2595 2721 343944142 343944010 4.730000e-28 135.0
31 TraesCS2B01G312600 chr5A 76.817 289 57 7 1958 2241 669121190 669120907 1.310000e-33 154.0
32 TraesCS2B01G312600 chr7A 85.106 141 10 10 2592 2721 112332465 112332325 1.700000e-27 134.0
33 TraesCS2B01G312600 chr7A 93.056 72 4 1 2650 2721 674002535 674002605 1.330000e-18 104.0
34 TraesCS2B01G312600 chr4D 84.397 141 11 5 2592 2721 72383920 72384060 7.910000e-26 128.0
35 TraesCS2B01G312600 chr4D 83.688 141 12 5 2592 2721 72270669 72270809 3.680000e-24 122.0
36 TraesCS2B01G312600 chr3B 73.438 384 85 15 2029 2402 22647488 22647864 7.910000e-26 128.0
37 TraesCS2B01G312600 chr3B 82.979 141 14 4 2592 2722 433528806 433528666 4.760000e-23 119.0
38 TraesCS2B01G312600 chr3B 83.333 132 6 8 2591 2722 684080277 684080162 1.030000e-19 108.0
39 TraesCS2B01G312600 chr6B 82.979 141 13 5 2592 2721 532157226 532157366 1.710000e-22 117.0
40 TraesCS2B01G312600 chr6B 90.278 72 6 1 2650 2721 281506308 281506238 2.890000e-15 93.5
41 TraesCS2B01G312600 chr6D 90.278 72 6 1 2650 2721 249007106 249007176 2.890000e-15 93.5


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 TraesCS2B01G312600 chr2B 448079147 448081868 2721 False 5027.0 5027 100.0000 1 2722 1 chr2B.!!$F1 2721
1 TraesCS2B01G312600 chr2B 625914448 625915131 683 False 817.0 817 88.3550 1 681 1 chr2B.!!$F4 680
2 TraesCS2B01G312600 chr2D 376620495 376622514 2019 False 1334.5 2510 93.1725 697 2589 2 chr2D.!!$F4 1892
3 TraesCS2B01G312600 chr2D 322501158 322501833 675 False 797.0 797 88.0530 12 683 1 chr2D.!!$F1 671
4 TraesCS2B01G312600 chr2A 510301376 510302896 1520 False 2004.0 2004 90.4640 697 2234 1 chr2A.!!$F1 1537
5 TraesCS2B01G312600 chr4B 221184864 221185551 687 True 905.0 905 90.5520 1 683 1 chr4B.!!$R1 682
6 TraesCS2B01G312600 chr4A 712560619 712561309 690 True 867.0 867 89.4810 1 686 1 chr4A.!!$R1 685
7 TraesCS2B01G312600 chr7D 397377431 397378108 677 False 798.0 798 88.0710 12 683 1 chr7D.!!$F2 671
8 TraesCS2B01G312600 chr5B 584276031 584276719 688 False 797.0 797 87.6990 1 684 1 chr5B.!!$F1 683
9 TraesCS2B01G312600 chr7B 522798776 522799465 689 True 791.0 791 87.5720 1 683 1 chr7B.!!$R1 682
10 TraesCS2B01G312600 chr3D 547931999 547932682 683 False 789.0 789 87.6450 12 692 1 chr3D.!!$F3 680
11 TraesCS2B01G312600 chr1B 308914471 308915152 681 False 787.0 787 87.6090 1 681 1 chr1B.!!$F2 680

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
201 204 0.179006 GGGGTGGAGATCATGAAGGC 60.179 60.0 0.0 0.0 0.0 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2099 2157 0.327867 ATTCTGATGAGGGAGGGGCA 60.328 55.0 0.0 0.0 0.0 5.36 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
99 100 2.899339 GCTTGAGATGGAGGCGGC 60.899 66.667 0.00 0.00 0.00 6.53
124 125 3.212685 GCAAGCCAAGATGCTAGAGATT 58.787 45.455 0.00 0.00 41.80 2.40
138 139 2.435938 GATTGAGGCCGCCAACGA 60.436 61.111 13.15 5.61 43.93 3.85
201 204 0.179006 GGGGTGGAGATCATGAAGGC 60.179 60.000 0.00 0.00 0.00 4.35
204 207 0.533755 GTGGAGATCATGAAGGCGGG 60.534 60.000 0.00 0.00 0.00 6.13
210 213 0.467384 ATCATGAAGGCGGGTCTCAG 59.533 55.000 0.00 0.00 0.00 3.35
242 245 1.075601 AAGGAAGAGGCCATGGTTCA 58.924 50.000 14.67 0.00 0.00 3.18
274 277 1.645034 CCGACATGCTCAAGTTCGAT 58.355 50.000 0.00 0.00 0.00 3.59
296 301 1.373497 GAGTGATCTATGGCGGCGG 60.373 63.158 9.78 0.00 0.00 6.13
298 303 2.842462 TGATCTATGGCGGCGGGT 60.842 61.111 9.78 0.00 0.00 5.28
373 379 1.606350 GCGTGGTCGAACTCAAGTCG 61.606 60.000 0.33 0.00 39.71 4.18
386 395 1.673920 TCAAGTCGCACCCTTTTTGTC 59.326 47.619 0.00 0.00 0.00 3.18
436 448 5.122239 ACGAATACATCAACATGAACTGTGG 59.878 40.000 0.00 0.00 38.39 4.17
438 450 5.885230 ATACATCAACATGAACTGTGGTG 57.115 39.130 0.00 0.00 38.39 4.17
551 570 4.517952 TGTTGATTGCGGACATGAAATT 57.482 36.364 0.00 0.00 0.00 1.82
556 575 1.902938 TGCGGACATGAAATTGGTCA 58.097 45.000 0.00 0.00 33.26 4.02
661 682 1.176527 ATTCGCCATCTGTTTGGGTG 58.823 50.000 0.00 0.00 37.24 4.61
684 705 1.536284 CCCGTCGGAGTTGCTCTAATC 60.536 57.143 14.39 0.00 0.00 1.75
685 706 1.134367 CCGTCGGAGTTGCTCTAATCA 59.866 52.381 4.91 0.00 0.00 2.57
686 707 2.186076 CGTCGGAGTTGCTCTAATCAC 58.814 52.381 0.00 0.00 0.00 3.06
687 708 2.159366 CGTCGGAGTTGCTCTAATCACT 60.159 50.000 0.00 0.00 0.00 3.41
688 709 3.182967 GTCGGAGTTGCTCTAATCACTG 58.817 50.000 0.00 0.00 0.00 3.66
689 710 1.929836 CGGAGTTGCTCTAATCACTGC 59.070 52.381 0.00 0.00 0.00 4.40
690 711 2.675032 CGGAGTTGCTCTAATCACTGCA 60.675 50.000 0.00 0.00 0.00 4.41
691 712 2.935201 GGAGTTGCTCTAATCACTGCAG 59.065 50.000 13.48 13.48 36.75 4.41
692 713 3.594134 GAGTTGCTCTAATCACTGCAGT 58.406 45.455 15.25 15.25 36.75 4.40
693 714 4.382040 GGAGTTGCTCTAATCACTGCAGTA 60.382 45.833 21.20 8.74 36.75 2.74
694 715 4.499183 AGTTGCTCTAATCACTGCAGTAC 58.501 43.478 21.20 10.01 36.75 2.73
695 716 4.221703 AGTTGCTCTAATCACTGCAGTACT 59.778 41.667 21.20 12.29 36.75 2.73
696 717 5.419155 AGTTGCTCTAATCACTGCAGTACTA 59.581 40.000 21.20 8.67 36.75 1.82
697 718 5.914898 TGCTCTAATCACTGCAGTACTAA 57.085 39.130 21.20 5.94 0.00 2.24
698 719 6.280855 TGCTCTAATCACTGCAGTACTAAA 57.719 37.500 21.20 3.26 0.00 1.85
699 720 6.100004 TGCTCTAATCACTGCAGTACTAAAC 58.900 40.000 21.20 6.04 0.00 2.01
700 721 6.100004 GCTCTAATCACTGCAGTACTAAACA 58.900 40.000 21.20 0.12 0.00 2.83
701 722 6.254589 GCTCTAATCACTGCAGTACTAAACAG 59.745 42.308 21.20 11.19 36.22 3.16
702 723 6.631016 TCTAATCACTGCAGTACTAAACAGG 58.369 40.000 21.20 3.67 34.40 4.00
703 724 3.040147 TCACTGCAGTACTAAACAGGC 57.960 47.619 21.20 8.65 34.40 4.85
704 725 2.076863 CACTGCAGTACTAAACAGGCC 58.923 52.381 21.20 0.00 34.40 5.19
715 736 2.456287 AAACAGGCCAGCTCCGAGTC 62.456 60.000 5.01 0.00 0.00 3.36
731 752 3.191791 CCGAGTCTAGCTAGGATAAAGGC 59.808 52.174 20.58 0.00 41.83 4.35
748 769 2.551270 AGGCCACCATCGATATACCAT 58.449 47.619 5.01 0.00 0.00 3.55
845 866 2.179427 AGTGATCCACATCAGGAACGA 58.821 47.619 0.00 0.00 39.86 3.85
945 966 1.140816 GAAATAAGAGCTAGCCGGCG 58.859 55.000 23.20 9.22 37.29 6.46
1146 1177 3.666883 TTGACGTTGATGTTGTGTGTC 57.333 42.857 0.00 0.00 0.00 3.67
1173 1225 1.585006 CGTAGGCTTCACGAGTGGT 59.415 57.895 3.78 0.00 41.91 4.16
1175 1227 1.014564 GTAGGCTTCACGAGTGGTGC 61.015 60.000 0.00 7.87 46.56 5.01
1316 1368 4.156922 TGTCACTGACGGATTGTTTGTTTT 59.843 37.500 4.71 0.00 34.95 2.43
1320 1372 1.189227 GACGGATTGTTTGTTTTGCGC 59.811 47.619 0.00 0.00 0.00 6.09
1389 1441 1.146263 GATCGGGTTCGGGCTGATT 59.854 57.895 0.00 0.00 36.95 2.57
1401 1453 2.036098 CTGATTGGGTGGCTGGCA 59.964 61.111 0.00 0.00 0.00 4.92
1485 1537 4.821589 GAGCTCGCCCACTTCCCG 62.822 72.222 0.00 0.00 0.00 5.14
1611 1667 7.124147 ACTTGGGGTTTGATTCTGGTTAATATG 59.876 37.037 0.00 0.00 0.00 1.78
1743 1799 4.092968 AGCGAATTAACTAGCTTTGGTTCG 59.907 41.667 0.00 3.65 39.87 3.95
1762 1818 2.316867 TGCATGTGCGTCGTCCTTG 61.317 57.895 0.01 0.00 45.83 3.61
1811 1867 4.225984 TGCGTGTTCAATGTAAAATCTGC 58.774 39.130 0.00 0.00 0.00 4.26
1887 1943 7.461182 TGTTTGTTAATTACCTCTTCCATGG 57.539 36.000 4.97 4.97 0.00 3.66
1911 1969 3.758300 AGCACAAAAGAGTTCAACAACG 58.242 40.909 0.00 0.00 37.61 4.10
1926 1984 6.375945 TCAACAACGACAACTACTACTACA 57.624 37.500 0.00 0.00 0.00 2.74
1927 1985 6.794374 TCAACAACGACAACTACTACTACAA 58.206 36.000 0.00 0.00 0.00 2.41
1946 2004 3.923461 ACAACAACAACAATTTGTCACCG 59.077 39.130 1.83 0.00 45.69 4.94
1970 2028 4.171005 GGCCTATACTTTTTGCGGAAAAC 58.829 43.478 14.81 0.67 33.78 2.43
1975 2033 6.926826 CCTATACTTTTTGCGGAAAACCTTTT 59.073 34.615 14.81 2.23 33.78 2.27
1976 2034 4.937696 ACTTTTTGCGGAAAACCTTTTG 57.062 36.364 14.81 4.11 33.78 2.44
2027 2085 9.953697 GTACAAAGGACACAAATAATACAAACA 57.046 29.630 0.00 0.00 0.00 2.83
2096 2154 1.285641 CCAAAAGTGCGCCGTCATT 59.714 52.632 4.18 0.00 0.00 2.57
2099 2157 2.415357 CCAAAAGTGCGCCGTCATTATT 60.415 45.455 4.18 0.00 0.00 1.40
2122 2180 1.709578 CCTCCCTCATCAGAATCGGA 58.290 55.000 0.00 0.00 0.00 4.55
2131 2189 3.686241 TCATCAGAATCGGACAAGCTTTG 59.314 43.478 0.00 0.00 0.00 2.77
2152 2210 6.869315 TTGTTGTCATAAACGATCAGGAAA 57.131 33.333 0.00 0.00 32.47 3.13
2200 2258 0.586319 CGCATCAGAACAACAACCGT 59.414 50.000 0.00 0.00 0.00 4.83
2276 2334 4.332819 CGTAGACTGGATCCAAACAAATCC 59.667 45.833 17.00 0.00 41.60 3.01
2278 2336 4.082125 AGACTGGATCCAAACAAATCCAC 58.918 43.478 17.00 0.00 45.05 4.02
2328 2386 4.003788 CCGCCGGAGACACACCTT 62.004 66.667 5.05 0.00 0.00 3.50
2335 2393 1.270305 CGGAGACACACCTTCACATGT 60.270 52.381 0.00 0.00 0.00 3.21
2339 2397 2.439507 AGACACACCTTCACATGTCCTT 59.560 45.455 0.00 0.00 41.99 3.36
2367 2425 1.404181 GCTAGACGCACCATCAAGACA 60.404 52.381 0.00 0.00 38.92 3.41
2377 2435 3.055530 CACCATCAAGACAGAGGCTAAGT 60.056 47.826 0.00 0.00 0.00 2.24
2381 2439 1.902508 CAAGACAGAGGCTAAGTGGGA 59.097 52.381 0.00 0.00 0.00 4.37
2383 2441 2.621070 AGACAGAGGCTAAGTGGGAAA 58.379 47.619 0.00 0.00 0.00 3.13
2391 2449 4.404640 AGGCTAAGTGGGAAAAACCTTAC 58.595 43.478 0.00 0.00 38.98 2.34
2397 2455 4.726583 AGTGGGAAAAACCTTACTCCTTC 58.273 43.478 0.00 0.00 38.98 3.46
2400 2458 6.102174 AGTGGGAAAAACCTTACTCCTTCTTA 59.898 38.462 0.00 0.00 38.98 2.10
2402 2460 7.286087 GTGGGAAAAACCTTACTCCTTCTTAAA 59.714 37.037 0.00 0.00 38.98 1.52
2403 2461 7.286087 TGGGAAAAACCTTACTCCTTCTTAAAC 59.714 37.037 0.00 0.00 38.98 2.01
2405 2463 8.133627 GGAAAAACCTTACTCCTTCTTAAACAC 58.866 37.037 0.00 0.00 35.41 3.32
2406 2464 8.818622 AAAAACCTTACTCCTTCTTAAACACT 57.181 30.769 0.00 0.00 0.00 3.55
2407 2465 9.910267 AAAAACCTTACTCCTTCTTAAACACTA 57.090 29.630 0.00 0.00 0.00 2.74
2408 2466 9.557061 AAAACCTTACTCCTTCTTAAACACTAG 57.443 33.333 0.00 0.00 0.00 2.57
2409 2467 6.699366 ACCTTACTCCTTCTTAAACACTAGC 58.301 40.000 0.00 0.00 0.00 3.42
2410 2468 6.269307 ACCTTACTCCTTCTTAAACACTAGCA 59.731 38.462 0.00 0.00 0.00 3.49
2411 2469 6.590677 CCTTACTCCTTCTTAAACACTAGCAC 59.409 42.308 0.00 0.00 0.00 4.40
2412 2470 5.546621 ACTCCTTCTTAAACACTAGCACA 57.453 39.130 0.00 0.00 0.00 4.57
2416 2474 4.455533 CCTTCTTAAACACTAGCACATGCA 59.544 41.667 6.64 0.00 45.16 3.96
2419 2477 4.819088 TCTTAAACACTAGCACATGCAACA 59.181 37.500 6.64 0.00 45.16 3.33
2429 2487 1.887854 CACATGCAACATCACCTTCCA 59.112 47.619 0.00 0.00 0.00 3.53
2430 2488 2.494471 CACATGCAACATCACCTTCCAT 59.506 45.455 0.00 0.00 0.00 3.41
2432 2490 3.696051 ACATGCAACATCACCTTCCATAC 59.304 43.478 0.00 0.00 0.00 2.39
2433 2491 3.431673 TGCAACATCACCTTCCATACA 57.568 42.857 0.00 0.00 0.00 2.29
2434 2492 3.081061 TGCAACATCACCTTCCATACAC 58.919 45.455 0.00 0.00 0.00 2.90
2435 2493 2.423538 GCAACATCACCTTCCATACACC 59.576 50.000 0.00 0.00 0.00 4.16
2436 2494 3.873801 GCAACATCACCTTCCATACACCT 60.874 47.826 0.00 0.00 0.00 4.00
2437 2495 3.914426 ACATCACCTTCCATACACCTC 57.086 47.619 0.00 0.00 0.00 3.85
2441 2499 0.902531 ACCTTCCATACACCTCCACG 59.097 55.000 0.00 0.00 0.00 4.94
2442 2500 0.902531 CCTTCCATACACCTCCACGT 59.097 55.000 0.00 0.00 0.00 4.49
2443 2501 1.405526 CCTTCCATACACCTCCACGTG 60.406 57.143 9.08 9.08 39.75 4.49
2445 2503 0.902984 TCCATACACCTCCACGTGCT 60.903 55.000 10.91 0.00 37.25 4.40
2446 2504 0.036388 CCATACACCTCCACGTGCTT 60.036 55.000 10.91 0.00 37.25 3.91
2447 2505 1.359848 CATACACCTCCACGTGCTTC 58.640 55.000 10.91 0.00 37.25 3.86
2448 2506 1.066858 CATACACCTCCACGTGCTTCT 60.067 52.381 10.91 0.00 37.25 2.85
2449 2507 1.045407 TACACCTCCACGTGCTTCTT 58.955 50.000 10.91 0.00 37.25 2.52
2452 2510 2.069273 CACCTCCACGTGCTTCTTAAG 58.931 52.381 10.91 0.00 0.00 1.85
2453 2511 1.002087 ACCTCCACGTGCTTCTTAAGG 59.998 52.381 10.91 9.53 0.00 2.69
2454 2512 1.002087 CCTCCACGTGCTTCTTAAGGT 59.998 52.381 10.91 0.00 0.00 3.50
2457 2515 2.367567 TCCACGTGCTTCTTAAGGTCTT 59.632 45.455 10.91 0.00 0.00 3.01
2459 2517 4.222145 TCCACGTGCTTCTTAAGGTCTTAT 59.778 41.667 10.91 0.00 0.00 1.73
2460 2518 4.935808 CCACGTGCTTCTTAAGGTCTTATT 59.064 41.667 10.91 0.00 0.00 1.40
2461 2519 5.063564 CCACGTGCTTCTTAAGGTCTTATTC 59.936 44.000 10.91 0.00 0.00 1.75
2462 2520 5.063564 CACGTGCTTCTTAAGGTCTTATTCC 59.936 44.000 0.82 0.00 0.00 3.01
2463 2521 5.046520 ACGTGCTTCTTAAGGTCTTATTCCT 60.047 40.000 1.85 0.00 36.81 3.36
2464 2522 5.875359 CGTGCTTCTTAAGGTCTTATTCCTT 59.125 40.000 1.85 2.81 45.72 3.36
2465 2523 6.036191 CGTGCTTCTTAAGGTCTTATTCCTTC 59.964 42.308 1.85 0.00 43.26 3.46
2466 2524 6.036191 GTGCTTCTTAAGGTCTTATTCCTTCG 59.964 42.308 1.85 0.00 43.26 3.79
2467 2525 6.107343 GCTTCTTAAGGTCTTATTCCTTCGT 58.893 40.000 1.85 0.00 43.26 3.85
2468 2526 6.256104 GCTTCTTAAGGTCTTATTCCTTCGTC 59.744 42.308 1.85 0.00 43.26 4.20
2469 2527 7.477945 TTCTTAAGGTCTTATTCCTTCGTCT 57.522 36.000 1.85 0.00 43.26 4.18
2470 2528 7.477945 TCTTAAGGTCTTATTCCTTCGTCTT 57.522 36.000 1.85 0.00 43.26 3.01
2472 2530 9.198475 TCTTAAGGTCTTATTCCTTCGTCTTAT 57.802 33.333 1.85 0.00 43.26 1.73
2473 2531 9.819267 CTTAAGGTCTTATTCCTTCGTCTTATT 57.181 33.333 0.29 0.00 43.26 1.40
2474 2532 9.813446 TTAAGGTCTTATTCCTTCGTCTTATTC 57.187 33.333 0.29 0.00 43.26 1.75
2475 2533 6.818233 AGGTCTTATTCCTTCGTCTTATTCC 58.182 40.000 0.00 0.00 30.18 3.01
2476 2534 6.612049 AGGTCTTATTCCTTCGTCTTATTCCT 59.388 38.462 0.00 0.00 30.18 3.36
2477 2535 7.125963 AGGTCTTATTCCTTCGTCTTATTCCTT 59.874 37.037 0.00 0.00 30.18 3.36
2479 2537 7.980099 GTCTTATTCCTTCGTCTTATTCCTTGA 59.020 37.037 0.00 0.00 0.00 3.02
2487 2696 6.817765 TCGTCTTATTCCTTGAAAATGCTT 57.182 33.333 0.00 0.00 0.00 3.91
2595 2806 7.951530 AAAGATATGGCTTTTGAAGTTGTTG 57.048 32.000 0.00 0.00 34.60 3.33
2596 2807 6.899393 AGATATGGCTTTTGAAGTTGTTGA 57.101 33.333 0.00 0.00 0.00 3.18
2597 2808 6.917533 AGATATGGCTTTTGAAGTTGTTGAG 58.082 36.000 0.00 0.00 0.00 3.02
2598 2809 6.491403 AGATATGGCTTTTGAAGTTGTTGAGT 59.509 34.615 0.00 0.00 0.00 3.41
2599 2810 4.799564 TGGCTTTTGAAGTTGTTGAGTT 57.200 36.364 0.00 0.00 0.00 3.01
2600 2811 4.493547 TGGCTTTTGAAGTTGTTGAGTTG 58.506 39.130 0.00 0.00 0.00 3.16
2601 2812 4.021544 TGGCTTTTGAAGTTGTTGAGTTGT 60.022 37.500 0.00 0.00 0.00 3.32
2602 2813 5.184096 TGGCTTTTGAAGTTGTTGAGTTGTA 59.816 36.000 0.00 0.00 0.00 2.41
2603 2814 6.127479 TGGCTTTTGAAGTTGTTGAGTTGTAT 60.127 34.615 0.00 0.00 0.00 2.29
2604 2815 6.756542 GGCTTTTGAAGTTGTTGAGTTGTATT 59.243 34.615 0.00 0.00 0.00 1.89
2605 2816 7.277760 GGCTTTTGAAGTTGTTGAGTTGTATTT 59.722 33.333 0.00 0.00 0.00 1.40
2606 2817 8.655970 GCTTTTGAAGTTGTTGAGTTGTATTTT 58.344 29.630 0.00 0.00 0.00 1.82
2607 2818 9.956797 CTTTTGAAGTTGTTGAGTTGTATTTTG 57.043 29.630 0.00 0.00 0.00 2.44
2608 2819 9.482627 TTTTGAAGTTGTTGAGTTGTATTTTGT 57.517 25.926 0.00 0.00 0.00 2.83
2609 2820 8.459521 TTGAAGTTGTTGAGTTGTATTTTGTG 57.540 30.769 0.00 0.00 0.00 3.33
2610 2821 7.598278 TGAAGTTGTTGAGTTGTATTTTGTGT 58.402 30.769 0.00 0.00 0.00 3.72
2611 2822 8.085296 TGAAGTTGTTGAGTTGTATTTTGTGTT 58.915 29.630 0.00 0.00 0.00 3.32
2612 2823 7.810766 AGTTGTTGAGTTGTATTTTGTGTTG 57.189 32.000 0.00 0.00 0.00 3.33
2613 2824 6.310224 AGTTGTTGAGTTGTATTTTGTGTTGC 59.690 34.615 0.00 0.00 0.00 4.17
2614 2825 5.714047 TGTTGAGTTGTATTTTGTGTTGCA 58.286 33.333 0.00 0.00 0.00 4.08
2615 2826 6.336566 TGTTGAGTTGTATTTTGTGTTGCAT 58.663 32.000 0.00 0.00 0.00 3.96
2616 2827 6.255237 TGTTGAGTTGTATTTTGTGTTGCATG 59.745 34.615 0.00 0.00 0.00 4.06
2617 2828 5.900425 TGAGTTGTATTTTGTGTTGCATGT 58.100 33.333 0.00 0.00 0.00 3.21
2618 2829 7.032377 TGAGTTGTATTTTGTGTTGCATGTA 57.968 32.000 0.00 0.00 0.00 2.29
2619 2830 7.656412 TGAGTTGTATTTTGTGTTGCATGTAT 58.344 30.769 0.00 0.00 0.00 2.29
2620 2831 8.787852 TGAGTTGTATTTTGTGTTGCATGTATA 58.212 29.630 0.00 0.00 0.00 1.47
2621 2832 9.787532 GAGTTGTATTTTGTGTTGCATGTATAT 57.212 29.630 0.00 0.00 0.00 0.86
2630 2841 9.973450 TTTGTGTTGCATGTATATTAAAGTTGT 57.027 25.926 0.00 0.00 0.00 3.32
2631 2842 8.962857 TGTGTTGCATGTATATTAAAGTTGTG 57.037 30.769 0.00 0.00 0.00 3.33
2632 2843 8.787852 TGTGTTGCATGTATATTAAAGTTGTGA 58.212 29.630 0.00 0.00 0.00 3.58
2633 2844 9.061610 GTGTTGCATGTATATTAAAGTTGTGAC 57.938 33.333 0.00 0.00 0.00 3.67
2634 2845 8.240682 TGTTGCATGTATATTAAAGTTGTGACC 58.759 33.333 0.00 0.00 0.00 4.02
2635 2846 7.328277 TGCATGTATATTAAAGTTGTGACCC 57.672 36.000 0.00 0.00 0.00 4.46
2636 2847 6.887002 TGCATGTATATTAAAGTTGTGACCCA 59.113 34.615 0.00 0.00 0.00 4.51
2637 2848 7.559533 TGCATGTATATTAAAGTTGTGACCCAT 59.440 33.333 0.00 0.00 0.00 4.00
2638 2849 8.076178 GCATGTATATTAAAGTTGTGACCCATC 58.924 37.037 0.00 0.00 0.00 3.51
2639 2850 9.342308 CATGTATATTAAAGTTGTGACCCATCT 57.658 33.333 0.00 0.00 0.00 2.90
2640 2851 8.958119 TGTATATTAAAGTTGTGACCCATCTC 57.042 34.615 0.00 0.00 0.00 2.75
2641 2852 8.544622 TGTATATTAAAGTTGTGACCCATCTCA 58.455 33.333 0.00 0.00 0.00 3.27
2642 2853 9.561069 GTATATTAAAGTTGTGACCCATCTCAT 57.439 33.333 0.00 0.00 0.00 2.90
2646 2857 8.506168 TTAAAGTTGTGACCCATCTCATATTC 57.494 34.615 0.00 0.00 0.00 1.75
2647 2858 5.965033 AGTTGTGACCCATCTCATATTCT 57.035 39.130 0.00 0.00 0.00 2.40
2648 2859 6.319048 AGTTGTGACCCATCTCATATTCTT 57.681 37.500 0.00 0.00 0.00 2.52
2649 2860 6.118170 AGTTGTGACCCATCTCATATTCTTG 58.882 40.000 0.00 0.00 0.00 3.02
2650 2861 5.698741 TGTGACCCATCTCATATTCTTGT 57.301 39.130 0.00 0.00 0.00 3.16
2651 2862 6.806668 TGTGACCCATCTCATATTCTTGTA 57.193 37.500 0.00 0.00 0.00 2.41
2652 2863 6.820335 TGTGACCCATCTCATATTCTTGTAG 58.180 40.000 0.00 0.00 0.00 2.74
2653 2864 6.611236 TGTGACCCATCTCATATTCTTGTAGA 59.389 38.462 0.00 0.00 0.00 2.59
2654 2865 7.125659 TGTGACCCATCTCATATTCTTGTAGAA 59.874 37.037 0.00 0.00 38.78 2.10
2655 2866 7.987458 GTGACCCATCTCATATTCTTGTAGAAA 59.013 37.037 0.00 0.00 37.82 2.52
2656 2867 7.987458 TGACCCATCTCATATTCTTGTAGAAAC 59.013 37.037 0.00 0.00 37.82 2.78
2657 2868 7.283329 ACCCATCTCATATTCTTGTAGAAACC 58.717 38.462 0.00 0.00 37.82 3.27
2658 2869 7.127955 ACCCATCTCATATTCTTGTAGAAACCT 59.872 37.037 0.00 0.00 37.82 3.50
2659 2870 7.995488 CCCATCTCATATTCTTGTAGAAACCTT 59.005 37.037 0.00 0.00 37.82 3.50
2660 2871 9.401058 CCATCTCATATTCTTGTAGAAACCTTT 57.599 33.333 0.00 0.00 37.82 3.11
2662 2873 9.620259 ATCTCATATTCTTGTAGAAACCTTTCC 57.380 33.333 0.00 0.00 37.82 3.13
2663 2874 8.826765 TCTCATATTCTTGTAGAAACCTTTCCT 58.173 33.333 0.00 0.00 37.82 3.36
2664 2875 9.454859 CTCATATTCTTGTAGAAACCTTTCCTT 57.545 33.333 0.00 0.00 37.82 3.36
2692 2903 8.752005 AATTATATATATGTGCACCATCACCC 57.248 34.615 15.69 0.00 36.17 4.61
2693 2904 2.949177 TATATGTGCACCATCACCCC 57.051 50.000 15.69 0.00 36.17 4.95
2694 2905 0.925558 ATATGTGCACCATCACCCCA 59.074 50.000 15.69 0.00 36.17 4.96
2695 2906 0.925558 TATGTGCACCATCACCCCAT 59.074 50.000 15.69 0.00 36.17 4.00
2696 2907 0.396139 ATGTGCACCATCACCCCATC 60.396 55.000 15.69 0.00 36.17 3.51
2697 2908 1.001020 GTGCACCATCACCCCATCA 60.001 57.895 5.22 0.00 0.00 3.07
2698 2909 0.611618 GTGCACCATCACCCCATCAA 60.612 55.000 5.22 0.00 0.00 2.57
2699 2910 0.335705 TGCACCATCACCCCATCAAT 59.664 50.000 0.00 0.00 0.00 2.57
2700 2911 1.568123 TGCACCATCACCCCATCAATA 59.432 47.619 0.00 0.00 0.00 1.90
2701 2912 1.956477 GCACCATCACCCCATCAATAC 59.044 52.381 0.00 0.00 0.00 1.89
2702 2913 2.686416 GCACCATCACCCCATCAATACA 60.686 50.000 0.00 0.00 0.00 2.29
2703 2914 3.630168 CACCATCACCCCATCAATACAA 58.370 45.455 0.00 0.00 0.00 2.41
2704 2915 3.381272 CACCATCACCCCATCAATACAAC 59.619 47.826 0.00 0.00 0.00 3.32
2705 2916 2.618241 CCATCACCCCATCAATACAACG 59.382 50.000 0.00 0.00 0.00 4.10
2706 2917 3.278574 CATCACCCCATCAATACAACGT 58.721 45.455 0.00 0.00 0.00 3.99
2707 2918 2.980568 TCACCCCATCAATACAACGTC 58.019 47.619 0.00 0.00 0.00 4.34
2708 2919 2.569853 TCACCCCATCAATACAACGTCT 59.430 45.455 0.00 0.00 0.00 4.18
2709 2920 3.770388 TCACCCCATCAATACAACGTCTA 59.230 43.478 0.00 0.00 0.00 2.59
2710 2921 4.407621 TCACCCCATCAATACAACGTCTAT 59.592 41.667 0.00 0.00 0.00 1.98
2711 2922 5.104693 TCACCCCATCAATACAACGTCTATT 60.105 40.000 0.00 0.00 0.00 1.73
2712 2923 5.007626 CACCCCATCAATACAACGTCTATTG 59.992 44.000 15.24 15.24 34.24 1.90
2713 2924 5.123227 CCCCATCAATACAACGTCTATTGT 58.877 41.667 18.51 9.88 44.87 2.71
2714 2925 6.126997 ACCCCATCAATACAACGTCTATTGTA 60.127 38.462 18.51 11.44 46.33 2.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
42 43 0.907486 CTCCATGTCAAGCCTCCTCA 59.093 55.000 0.00 0.00 0.00 3.86
99 100 1.329906 CTAGCATCTTGGCTTGCTTCG 59.670 52.381 2.43 0.00 46.71 3.79
124 125 4.243008 TTGTCGTTGGCGGCCTCA 62.243 61.111 21.46 3.74 42.91 3.86
138 139 2.310538 CTTCTTTGGCCTTGGTCTTGT 58.689 47.619 3.32 0.00 0.00 3.16
178 181 0.620410 TCATGATCTCCACCCCGGTT 60.620 55.000 0.00 0.00 35.57 4.44
201 204 3.916392 GACACGGTGCTGAGACCCG 62.916 68.421 8.30 8.41 46.93 5.28
204 207 3.106407 GCGACACGGTGCTGAGAC 61.106 66.667 8.30 0.00 0.00 3.36
242 245 0.254178 ATGTCGGCCTGCATCTTCTT 59.746 50.000 0.00 0.00 0.00 2.52
274 277 0.668535 CCGCCATAGATCACTCGTCA 59.331 55.000 0.00 0.00 0.00 4.35
373 379 0.032540 CCAGCAGACAAAAAGGGTGC 59.967 55.000 0.00 0.00 0.00 5.01
416 425 5.316167 ACACCACAGTTCATGTTGATGTAT 58.684 37.500 0.00 0.00 41.41 2.29
418 427 3.554934 ACACCACAGTTCATGTTGATGT 58.445 40.909 0.00 0.00 41.41 3.06
421 430 5.398603 AAAAACACCACAGTTCATGTTGA 57.601 34.783 0.00 0.00 41.41 3.18
474 488 4.758251 TGTCTCATGCCGGCACCG 62.758 66.667 35.50 26.22 39.44 4.94
612 632 1.440938 TTTGTCTGTTTGGGTCGGCG 61.441 55.000 0.00 0.00 0.00 6.46
669 690 1.929836 GCAGTGATTAGAGCAACTCCG 59.070 52.381 0.00 0.00 0.00 4.63
684 705 2.076863 GGCCTGTTTAGTACTGCAGTG 58.923 52.381 29.57 10.08 0.00 3.66
685 706 1.697432 TGGCCTGTTTAGTACTGCAGT 59.303 47.619 25.12 25.12 0.00 4.40
686 707 2.350522 CTGGCCTGTTTAGTACTGCAG 58.649 52.381 13.48 13.48 0.00 4.41
687 708 1.610624 GCTGGCCTGTTTAGTACTGCA 60.611 52.381 11.69 1.14 0.00 4.41
688 709 1.087501 GCTGGCCTGTTTAGTACTGC 58.912 55.000 11.69 0.00 0.00 4.40
689 710 2.622436 GAGCTGGCCTGTTTAGTACTG 58.378 52.381 11.69 0.00 0.00 2.74
690 711 1.555533 GGAGCTGGCCTGTTTAGTACT 59.444 52.381 11.69 0.00 0.00 2.73
691 712 1.739371 CGGAGCTGGCCTGTTTAGTAC 60.739 57.143 11.69 0.00 0.00 2.73
692 713 0.535335 CGGAGCTGGCCTGTTTAGTA 59.465 55.000 11.69 0.00 0.00 1.82
693 714 1.192146 TCGGAGCTGGCCTGTTTAGT 61.192 55.000 11.69 0.00 0.00 2.24
694 715 0.460987 CTCGGAGCTGGCCTGTTTAG 60.461 60.000 11.69 3.92 0.00 1.85
695 716 1.192146 ACTCGGAGCTGGCCTGTTTA 61.192 55.000 11.69 0.00 0.00 2.01
696 717 2.348998 CTCGGAGCTGGCCTGTTT 59.651 61.111 11.69 0.00 0.00 2.83
697 718 2.925170 ACTCGGAGCTGGCCTGTT 60.925 61.111 11.69 4.88 0.00 3.16
698 719 2.500815 TAGACTCGGAGCTGGCCTGT 62.501 60.000 11.69 0.00 0.00 4.00
699 720 1.733402 CTAGACTCGGAGCTGGCCTG 61.733 65.000 3.32 4.26 0.00 4.85
700 721 1.454847 CTAGACTCGGAGCTGGCCT 60.455 63.158 3.32 0.00 0.00 5.19
701 722 3.124686 CTAGACTCGGAGCTGGCC 58.875 66.667 4.58 0.00 0.00 5.36
702 723 2.415426 GCTAGACTCGGAGCTGGC 59.585 66.667 16.95 16.95 35.73 4.85
715 736 2.972713 TGGTGGCCTTTATCCTAGCTAG 59.027 50.000 14.20 14.20 0.00 3.42
731 752 2.237143 AGGCATGGTATATCGATGGTGG 59.763 50.000 8.54 0.00 33.76 4.61
748 769 4.165950 ACTTGGATATGTGTGGATAAGGCA 59.834 41.667 0.00 0.00 0.00 4.75
845 866 1.774300 GGGGAGATTGTTGTGGGGT 59.226 57.895 0.00 0.00 0.00 4.95
1119 1143 3.383185 ACAACATCAACGTCAAATGGGTT 59.617 39.130 8.91 1.58 0.00 4.11
1146 1177 2.474526 CGTGAAGCCTACGCATTTCAAG 60.475 50.000 0.00 0.00 32.72 3.02
1320 1372 1.026718 GGAACCTGATCGCCCAACAG 61.027 60.000 0.00 0.00 0.00 3.16
1611 1667 0.520404 CACAGCCTGCAGTGTCAATC 59.480 55.000 13.81 0.00 0.00 2.67
1722 1778 5.313623 CACGAACCAAAGCTAGTTAATTCG 58.686 41.667 13.11 13.11 42.44 3.34
1743 1799 2.317609 AAGGACGACGCACATGCAC 61.318 57.895 4.49 0.00 42.21 4.57
1811 1867 1.603326 GCACAAAACCAAAAGGCATGG 59.397 47.619 0.00 2.85 43.84 3.66
1887 1943 5.227184 CGTTGTTGAACTCTTTTGTGCTTAC 59.773 40.000 0.00 0.00 0.00 2.34
1911 1969 7.760131 TGTTGTTGTTGTAGTAGTAGTTGTC 57.240 36.000 0.00 0.00 0.00 3.18
1946 2004 2.361789 TCCGCAAAAAGTATAGGCCAC 58.638 47.619 5.01 0.00 0.00 5.01
1970 2028 8.681486 TGATGTATGATGAATAGACCAAAAGG 57.319 34.615 0.00 0.00 0.00 3.11
1975 2033 7.965718 TGTCATGATGTATGATGAATAGACCA 58.034 34.615 0.00 0.00 46.85 4.02
1976 2034 8.093307 ACTGTCATGATGTATGATGAATAGACC 58.907 37.037 0.00 0.00 46.85 3.85
1998 2056 8.911918 TGTATTATTTGTGTCCTTTGTACTGT 57.088 30.769 0.00 0.00 0.00 3.55
2089 2147 0.537371 GGGAGGGGCAATAATGACGG 60.537 60.000 0.00 0.00 34.32 4.79
2096 2154 1.061424 TCTGATGAGGGAGGGGCAATA 60.061 52.381 0.00 0.00 0.00 1.90
2099 2157 0.327867 ATTCTGATGAGGGAGGGGCA 60.328 55.000 0.00 0.00 0.00 5.36
2131 2189 7.305474 ACAATTTCCTGATCGTTTATGACAAC 58.695 34.615 0.00 0.00 0.00 3.32
2152 2210 5.242838 TCCTTTGGAATTTTAGCACGACAAT 59.757 36.000 0.00 0.00 0.00 2.71
2200 2258 5.134202 TCTACGCTTCTCTTCATTGTTGA 57.866 39.130 0.00 0.00 0.00 3.18
2240 2298 6.140303 TCCAGTCTACGTCCATATGTTAAC 57.860 41.667 1.24 0.00 0.00 2.01
2276 2334 2.680841 TGGTCGGTGTTTTTCTTCAGTG 59.319 45.455 0.00 0.00 0.00 3.66
2278 2336 4.364415 TTTGGTCGGTGTTTTTCTTCAG 57.636 40.909 0.00 0.00 0.00 3.02
2328 2386 1.601903 GCGTTGTTGAAGGACATGTGA 59.398 47.619 1.15 0.00 0.00 3.58
2335 2393 1.933500 GCGTCTAGCGTTGTTGAAGGA 60.934 52.381 8.08 0.00 43.66 3.36
2356 2414 3.055530 CACTTAGCCTCTGTCTTGATGGT 60.056 47.826 0.00 0.00 0.00 3.55
2367 2425 2.716969 AGGTTTTTCCCACTTAGCCTCT 59.283 45.455 0.00 0.00 36.75 3.69
2377 2435 5.397553 AAGAAGGAGTAAGGTTTTTCCCA 57.602 39.130 0.00 0.00 36.75 4.37
2381 2439 8.818622 AGTGTTTAAGAAGGAGTAAGGTTTTT 57.181 30.769 0.00 0.00 0.00 1.94
2383 2441 7.660617 GCTAGTGTTTAAGAAGGAGTAAGGTTT 59.339 37.037 0.00 0.00 0.00 3.27
2391 2449 5.163814 GCATGTGCTAGTGTTTAAGAAGGAG 60.164 44.000 0.00 0.00 38.21 3.69
2397 2455 5.107109 TGTTGCATGTGCTAGTGTTTAAG 57.893 39.130 6.55 0.00 42.66 1.85
2400 2458 3.569277 TGATGTTGCATGTGCTAGTGTTT 59.431 39.130 6.55 0.00 42.66 2.83
2402 2460 2.485426 GTGATGTTGCATGTGCTAGTGT 59.515 45.455 6.55 0.00 42.66 3.55
2403 2461 2.159476 GGTGATGTTGCATGTGCTAGTG 60.159 50.000 6.55 0.00 42.66 2.74
2405 2463 2.362736 AGGTGATGTTGCATGTGCTAG 58.637 47.619 6.55 0.00 42.66 3.42
2406 2464 2.495155 AGGTGATGTTGCATGTGCTA 57.505 45.000 6.55 0.00 42.66 3.49
2407 2465 1.542915 GAAGGTGATGTTGCATGTGCT 59.457 47.619 6.55 0.00 42.66 4.40
2408 2466 1.403249 GGAAGGTGATGTTGCATGTGC 60.403 52.381 0.00 0.00 42.50 4.57
2409 2467 1.887854 TGGAAGGTGATGTTGCATGTG 59.112 47.619 0.00 0.00 0.00 3.21
2410 2468 2.291209 TGGAAGGTGATGTTGCATGT 57.709 45.000 0.00 0.00 0.00 3.21
2411 2469 3.695556 TGTATGGAAGGTGATGTTGCATG 59.304 43.478 0.00 0.00 36.70 4.06
2412 2470 3.696051 GTGTATGGAAGGTGATGTTGCAT 59.304 43.478 0.00 0.00 39.13 3.96
2416 2474 3.054361 GGAGGTGTATGGAAGGTGATGTT 60.054 47.826 0.00 0.00 0.00 2.71
2419 2477 2.505819 GTGGAGGTGTATGGAAGGTGAT 59.494 50.000 0.00 0.00 0.00 3.06
2429 2487 1.267121 AGAAGCACGTGGAGGTGTAT 58.733 50.000 18.88 0.00 40.08 2.29
2430 2488 1.045407 AAGAAGCACGTGGAGGTGTA 58.955 50.000 18.88 0.00 40.08 2.90
2432 2490 2.069273 CTTAAGAAGCACGTGGAGGTG 58.931 52.381 18.88 0.00 40.89 4.00
2433 2491 1.002087 CCTTAAGAAGCACGTGGAGGT 59.998 52.381 18.88 0.00 0.00 3.85
2434 2492 1.002087 ACCTTAAGAAGCACGTGGAGG 59.998 52.381 18.88 1.98 0.00 4.30
2435 2493 2.028930 AGACCTTAAGAAGCACGTGGAG 60.029 50.000 18.88 0.00 0.00 3.86
2436 2494 1.968493 AGACCTTAAGAAGCACGTGGA 59.032 47.619 18.88 0.00 0.00 4.02
2437 2495 2.457366 AGACCTTAAGAAGCACGTGG 57.543 50.000 18.88 0.00 0.00 4.94
2441 2499 6.036191 CGAAGGAATAAGACCTTAAGAAGCAC 59.964 42.308 3.36 0.00 46.14 4.40
2442 2500 6.106673 CGAAGGAATAAGACCTTAAGAAGCA 58.893 40.000 3.36 0.00 46.14 3.91
2443 2501 6.107343 ACGAAGGAATAAGACCTTAAGAAGC 58.893 40.000 3.36 0.00 46.14 3.86
2445 2503 7.477945 AGACGAAGGAATAAGACCTTAAGAA 57.522 36.000 3.36 0.00 46.14 2.52
2446 2504 7.477945 AAGACGAAGGAATAAGACCTTAAGA 57.522 36.000 3.36 0.00 46.14 2.10
2447 2505 9.819267 AATAAGACGAAGGAATAAGACCTTAAG 57.181 33.333 0.00 0.00 46.14 1.85
2448 2506 9.813446 GAATAAGACGAAGGAATAAGACCTTAA 57.187 33.333 0.00 0.00 46.14 1.85
2449 2507 8.419442 GGAATAAGACGAAGGAATAAGACCTTA 58.581 37.037 0.00 0.00 46.14 2.69
2452 2510 6.818233 AGGAATAAGACGAAGGAATAAGACC 58.182 40.000 0.00 0.00 0.00 3.85
2453 2511 7.980099 TCAAGGAATAAGACGAAGGAATAAGAC 59.020 37.037 0.00 0.00 0.00 3.01
2454 2512 8.074613 TCAAGGAATAAGACGAAGGAATAAGA 57.925 34.615 0.00 0.00 0.00 2.10
2457 2515 9.681062 ATTTTCAAGGAATAAGACGAAGGAATA 57.319 29.630 0.00 0.00 0.00 1.75
2459 2517 7.574967 GCATTTTCAAGGAATAAGACGAAGGAA 60.575 37.037 0.00 0.00 0.00 3.36
2460 2518 6.128007 GCATTTTCAAGGAATAAGACGAAGGA 60.128 38.462 0.00 0.00 0.00 3.36
2461 2519 6.030228 GCATTTTCAAGGAATAAGACGAAGG 58.970 40.000 0.00 0.00 0.00 3.46
2462 2520 6.846350 AGCATTTTCAAGGAATAAGACGAAG 58.154 36.000 0.00 0.00 0.00 3.79
2463 2521 6.817765 AGCATTTTCAAGGAATAAGACGAA 57.182 33.333 0.00 0.00 0.00 3.85
2464 2522 6.429692 TGAAGCATTTTCAAGGAATAAGACGA 59.570 34.615 0.00 0.00 0.00 4.20
2465 2523 6.611381 TGAAGCATTTTCAAGGAATAAGACG 58.389 36.000 0.00 0.00 0.00 4.18
2466 2524 7.490402 CCATGAAGCATTTTCAAGGAATAAGAC 59.510 37.037 5.48 0.00 39.03 3.01
2467 2525 7.549839 CCATGAAGCATTTTCAAGGAATAAGA 58.450 34.615 5.48 0.00 39.03 2.10
2468 2526 6.257193 GCCATGAAGCATTTTCAAGGAATAAG 59.743 38.462 13.55 0.00 39.03 1.73
2469 2527 6.108015 GCCATGAAGCATTTTCAAGGAATAA 58.892 36.000 13.55 0.00 39.03 1.40
2470 2528 5.395546 GGCCATGAAGCATTTTCAAGGAATA 60.396 40.000 13.55 0.00 39.03 1.75
2472 2530 3.306919 GGCCATGAAGCATTTTCAAGGAA 60.307 43.478 13.55 0.00 39.03 3.36
2473 2531 2.234414 GGCCATGAAGCATTTTCAAGGA 59.766 45.455 13.55 0.00 39.03 3.36
2474 2532 2.235402 AGGCCATGAAGCATTTTCAAGG 59.765 45.455 5.01 6.76 39.53 3.61
2475 2533 3.259064 CAGGCCATGAAGCATTTTCAAG 58.741 45.455 5.01 0.00 31.55 3.02
2476 2534 2.633967 ACAGGCCATGAAGCATTTTCAA 59.366 40.909 5.01 0.00 31.55 2.69
2477 2535 2.250031 ACAGGCCATGAAGCATTTTCA 58.750 42.857 5.01 0.00 0.00 2.69
2479 2537 5.599656 ACATATACAGGCCATGAAGCATTTT 59.400 36.000 5.01 0.00 0.00 1.82
2487 2696 8.162746 TCATAATCAAACATATACAGGCCATGA 58.837 33.333 5.01 0.00 0.00 3.07
2579 2790 4.494484 ACAACTCAACAACTTCAAAAGCC 58.506 39.130 0.00 0.00 0.00 4.35
2589 2800 6.090088 TGCAACACAAAATACAACTCAACAAC 59.910 34.615 0.00 0.00 0.00 3.32
2590 2801 6.159293 TGCAACACAAAATACAACTCAACAA 58.841 32.000 0.00 0.00 0.00 2.83
2591 2802 5.714047 TGCAACACAAAATACAACTCAACA 58.286 33.333 0.00 0.00 0.00 3.33
2592 2803 6.255453 ACATGCAACACAAAATACAACTCAAC 59.745 34.615 0.00 0.00 0.00 3.18
2593 2804 6.336566 ACATGCAACACAAAATACAACTCAA 58.663 32.000 0.00 0.00 0.00 3.02
2594 2805 5.900425 ACATGCAACACAAAATACAACTCA 58.100 33.333 0.00 0.00 0.00 3.41
2595 2806 9.787532 ATATACATGCAACACAAAATACAACTC 57.212 29.630 0.00 0.00 0.00 3.01
2604 2815 9.973450 ACAACTTTAATATACATGCAACACAAA 57.027 25.926 0.00 0.00 0.00 2.83
2605 2816 9.404348 CACAACTTTAATATACATGCAACACAA 57.596 29.630 0.00 0.00 0.00 3.33
2606 2817 8.787852 TCACAACTTTAATATACATGCAACACA 58.212 29.630 0.00 0.00 0.00 3.72
2607 2818 9.061610 GTCACAACTTTAATATACATGCAACAC 57.938 33.333 0.00 0.00 0.00 3.32
2608 2819 8.240682 GGTCACAACTTTAATATACATGCAACA 58.759 33.333 0.00 0.00 0.00 3.33
2609 2820 7.700656 GGGTCACAACTTTAATATACATGCAAC 59.299 37.037 0.00 0.00 0.00 4.17
2610 2821 7.394641 TGGGTCACAACTTTAATATACATGCAA 59.605 33.333 0.00 0.00 0.00 4.08
2611 2822 6.887002 TGGGTCACAACTTTAATATACATGCA 59.113 34.615 0.00 0.00 0.00 3.96
2612 2823 7.328277 TGGGTCACAACTTTAATATACATGC 57.672 36.000 0.00 0.00 0.00 4.06
2613 2824 9.342308 AGATGGGTCACAACTTTAATATACATG 57.658 33.333 0.00 0.00 0.00 3.21
2614 2825 9.561069 GAGATGGGTCACAACTTTAATATACAT 57.439 33.333 0.00 0.00 31.65 2.29
2615 2826 8.544622 TGAGATGGGTCACAACTTTAATATACA 58.455 33.333 0.00 0.00 31.65 2.29
2616 2827 8.958119 TGAGATGGGTCACAACTTTAATATAC 57.042 34.615 0.00 0.00 31.65 1.47
2620 2831 9.125026 GAATATGAGATGGGTCACAACTTTAAT 57.875 33.333 0.00 0.00 31.65 1.40
2621 2832 8.328758 AGAATATGAGATGGGTCACAACTTTAA 58.671 33.333 0.00 0.00 31.65 1.52
2622 2833 7.861629 AGAATATGAGATGGGTCACAACTTTA 58.138 34.615 0.00 0.00 31.65 1.85
2623 2834 6.725364 AGAATATGAGATGGGTCACAACTTT 58.275 36.000 0.00 0.00 31.65 2.66
2624 2835 6.319048 AGAATATGAGATGGGTCACAACTT 57.681 37.500 0.00 0.00 31.65 2.66
2625 2836 5.965033 AGAATATGAGATGGGTCACAACT 57.035 39.130 0.00 0.00 34.56 3.16
2626 2837 5.882557 ACAAGAATATGAGATGGGTCACAAC 59.117 40.000 0.00 0.00 0.00 3.32
2627 2838 6.065976 ACAAGAATATGAGATGGGTCACAA 57.934 37.500 0.00 0.00 0.00 3.33
2628 2839 5.698741 ACAAGAATATGAGATGGGTCACA 57.301 39.130 0.00 0.00 0.00 3.58
2629 2840 7.055667 TCTACAAGAATATGAGATGGGTCAC 57.944 40.000 0.00 0.00 0.00 3.67
2630 2841 7.675161 TTCTACAAGAATATGAGATGGGTCA 57.325 36.000 0.00 0.00 0.00 4.02
2631 2842 7.442666 GGTTTCTACAAGAATATGAGATGGGTC 59.557 40.741 0.00 0.00 33.67 4.46
2632 2843 7.127955 AGGTTTCTACAAGAATATGAGATGGGT 59.872 37.037 0.00 0.00 33.67 4.51
2633 2844 7.512992 AGGTTTCTACAAGAATATGAGATGGG 58.487 38.462 0.00 0.00 33.67 4.00
2634 2845 8.970859 AAGGTTTCTACAAGAATATGAGATGG 57.029 34.615 0.00 0.00 33.67 3.51
2636 2847 9.620259 GGAAAGGTTTCTACAAGAATATGAGAT 57.380 33.333 2.60 0.00 33.67 2.75
2637 2848 8.826765 AGGAAAGGTTTCTACAAGAATATGAGA 58.173 33.333 2.60 0.00 33.67 3.27
2638 2849 9.454859 AAGGAAAGGTTTCTACAAGAATATGAG 57.545 33.333 2.60 0.00 33.67 2.90
2666 2877 9.845740 GGGTGATGGTGCACATATATATAATTA 57.154 33.333 20.43 0.00 40.72 1.40
2667 2878 7.779798 GGGGTGATGGTGCACATATATATAATT 59.220 37.037 20.43 0.00 40.72 1.40
2668 2879 7.092038 TGGGGTGATGGTGCACATATATATAAT 60.092 37.037 20.43 0.00 40.72 1.28
2669 2880 6.216456 TGGGGTGATGGTGCACATATATATAA 59.784 38.462 20.43 0.00 40.72 0.98
2670 2881 5.728741 TGGGGTGATGGTGCACATATATATA 59.271 40.000 20.43 0.00 40.72 0.86
2671 2882 4.539696 TGGGGTGATGGTGCACATATATAT 59.460 41.667 20.43 2.54 40.72 0.86
2672 2883 3.913163 TGGGGTGATGGTGCACATATATA 59.087 43.478 20.43 2.81 40.72 0.86
2673 2884 2.715880 TGGGGTGATGGTGCACATATAT 59.284 45.455 20.43 7.00 40.72 0.86
2674 2885 2.131023 TGGGGTGATGGTGCACATATA 58.869 47.619 20.43 1.75 40.72 0.86
2675 2886 0.925558 TGGGGTGATGGTGCACATAT 59.074 50.000 20.43 12.38 40.72 1.78
2676 2887 0.925558 ATGGGGTGATGGTGCACATA 59.074 50.000 20.43 7.39 40.72 2.29
2677 2888 0.396139 GATGGGGTGATGGTGCACAT 60.396 55.000 20.43 10.28 44.18 3.21
2678 2889 1.001020 GATGGGGTGATGGTGCACA 60.001 57.895 20.43 5.24 40.52 4.57
2679 2890 0.611618 TTGATGGGGTGATGGTGCAC 60.612 55.000 8.80 8.80 38.05 4.57
2680 2891 0.335705 ATTGATGGGGTGATGGTGCA 59.664 50.000 0.00 0.00 0.00 4.57
2681 2892 1.956477 GTATTGATGGGGTGATGGTGC 59.044 52.381 0.00 0.00 0.00 5.01
2682 2893 3.295585 TGTATTGATGGGGTGATGGTG 57.704 47.619 0.00 0.00 0.00 4.17
2683 2894 3.631250 GTTGTATTGATGGGGTGATGGT 58.369 45.455 0.00 0.00 0.00 3.55
2684 2895 2.618241 CGTTGTATTGATGGGGTGATGG 59.382 50.000 0.00 0.00 0.00 3.51
2685 2896 3.278574 ACGTTGTATTGATGGGGTGATG 58.721 45.455 0.00 0.00 0.00 3.07
2686 2897 3.199946 AGACGTTGTATTGATGGGGTGAT 59.800 43.478 0.00 0.00 0.00 3.06
2687 2898 2.569853 AGACGTTGTATTGATGGGGTGA 59.430 45.455 0.00 0.00 0.00 4.02
2688 2899 2.985896 AGACGTTGTATTGATGGGGTG 58.014 47.619 0.00 0.00 0.00 4.61
2689 2900 5.123227 CAATAGACGTTGTATTGATGGGGT 58.877 41.667 19.53 0.00 39.34 4.95
2690 2901 5.123227 ACAATAGACGTTGTATTGATGGGG 58.877 41.667 26.27 9.29 40.35 4.96


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

AutoCloner maintained by Alex Coulton.