Multiple sequence alignment - TraesCS1D01G371900

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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 TraesCS1D01G371900 chr1D 100.000 3018 0 0 1 3018 449984433 449981416 0.000000e+00 5574.0
1 TraesCS1D01G371900 chr1D 90.419 501 40 5 137 629 343276615 343277115 0.000000e+00 652.0
2 TraesCS1D01G371900 chr1D 88.031 518 56 4 1434 1945 449923213 449922696 2.570000e-170 608.0
3 TraesCS1D01G371900 chr1D 84.049 652 65 16 1435 2048 449847250 449847900 2.590000e-165 592.0
4 TraesCS1D01G371900 chr1D 87.475 495 51 7 1431 1915 449660770 449661263 7.310000e-156 560.0
5 TraesCS1D01G371900 chr1D 83.628 623 73 18 677 1277 449923927 449923312 2.630000e-155 558.0
6 TraesCS1D01G371900 chr1D 82.467 673 71 24 665 1312 449846507 449847157 2.050000e-151 545.0
7 TraesCS1D01G371900 chr1D 81.903 641 81 19 687 1306 449660074 449660700 2.680000e-140 508.0
8 TraesCS1D01G371900 chr1D 83.425 543 61 20 775 1302 449674419 449674947 7.570000e-131 477.0
9 TraesCS1D01G371900 chr1D 93.750 272 17 0 1000 1271 449752638 449752909 2.800000e-110 409.0
10 TraesCS1D01G371900 chr1D 77.951 449 57 26 781 1195 450046055 450046495 3.010000e-60 243.0
11 TraesCS1D01G371900 chr1D 85.075 67 10 0 2018 2084 449661449 449661515 5.400000e-08 69.4
12 TraesCS1D01G371900 chr1D 100.000 30 0 0 1399 1428 462295886 462295857 4.200000e-04 56.5
13 TraesCS1D01G371900 chr1A 90.339 766 42 11 1431 2168 545024901 545024140 0.000000e+00 976.0
14 TraesCS1D01G371900 chr1A 90.994 644 42 3 630 1272 545025608 545024980 0.000000e+00 854.0
15 TraesCS1D01G371900 chr1A 85.626 647 52 14 1439 2048 545000601 545001243 2.540000e-180 641.0
16 TraesCS1D01G371900 chr1A 84.448 643 61 7 1431 2034 545009115 545008473 5.570000e-167 597.0
17 TraesCS1D01G371900 chr1A 88.485 495 46 6 1431 1915 544928186 544928679 3.350000e-164 588.0
18 TraesCS1D01G371900 chr1A 81.098 656 77 30 671 1312 544999872 545000494 5.850000e-132 481.0
19 TraesCS1D01G371900 chr1A 95.221 272 13 0 1000 1271 544748298 544748569 5.980000e-117 431.0
20 TraesCS1D01G371900 chr1A 83.230 483 56 19 808 1277 545009685 545009215 1.290000e-113 420.0
21 TraesCS1D01G371900 chr1A 85.424 295 28 8 2731 3018 545024101 545023815 2.940000e-75 292.0
22 TraesCS1D01G371900 chr1A 79.928 279 36 14 809 1076 544927696 544927965 1.430000e-43 187.0
23 TraesCS1D01G371900 chr1A 89.855 138 12 2 7 143 585908309 585908445 3.090000e-40 176.0
24 TraesCS1D01G371900 chr1A 94.444 36 2 0 2018 2053 544749344 544749379 4.200000e-04 56.5
25 TraesCS1D01G371900 chr1B 88.622 791 47 8 648 1424 616136993 616136232 0.000000e+00 922.0
26 TraesCS1D01G371900 chr1B 88.889 765 36 14 1431 2168 616132240 616131498 0.000000e+00 896.0
27 TraesCS1D01G371900 chr1B 84.514 833 101 17 2192 3018 616131432 616130622 0.000000e+00 798.0
28 TraesCS1D01G371900 chr1B 86.872 617 66 4 1431 2032 615744806 615744190 0.000000e+00 676.0
29 TraesCS1D01G371900 chr1B 87.273 550 66 2 2183 2731 25227655 25227109 2.550000e-175 625.0
30 TraesCS1D01G371900 chr1B 86.823 554 67 4 2180 2731 644278294 644278843 5.530000e-172 614.0
31 TraesCS1D01G371900 chr1B 86.885 549 68 3 2184 2731 687076553 687077098 1.990000e-171 612.0
32 TraesCS1D01G371900 chr1B 88.462 494 48 4 1431 1915 615582122 615582615 3.350000e-164 588.0
33 TraesCS1D01G371900 chr1B 85.745 463 49 12 857 1306 615732010 615732468 9.790000e-130 473.0
34 TraesCS1D01G371900 chr1B 91.667 144 11 1 1 144 171217709 171217851 6.600000e-47 198.0
35 TraesCS1D01G371900 chr1B 96.000 50 2 0 1368 1417 52296378 52296427 6.930000e-12 82.4
36 TraesCS1D01G371900 chr1B 86.207 58 7 1 1369 1426 642964297 642964241 9.030000e-06 62.1
37 TraesCS1D01G371900 chr1B 100.000 28 0 0 1399 1426 637358568 637358541 5.000000e-03 52.8
38 TraesCS1D01G371900 chr6D 92.623 488 28 5 137 617 137121937 137121451 0.000000e+00 695.0
39 TraesCS1D01G371900 chr6D 90.369 488 33 11 137 617 408146428 408146908 1.970000e-176 628.0
40 TraesCS1D01G371900 chr6D 83.824 136 20 2 1135 1269 298207152 298207018 8.780000e-26 128.0
41 TraesCS1D01G371900 chr6D 82.609 138 18 5 1135 1269 297407246 297407112 1.900000e-22 117.0
42 TraesCS1D01G371900 chr6D 83.898 118 17 2 1127 1243 298399201 298399085 8.840000e-21 111.0
43 TraesCS1D01G371900 chr7D 90.138 507 39 7 137 634 244792468 244791964 0.000000e+00 649.0
44 TraesCS1D01G371900 chr4D 90.779 488 37 6 137 617 504406497 504406011 0.000000e+00 645.0
45 TraesCS1D01G371900 chr4D 90.574 488 39 5 137 617 504351023 504350536 9.120000e-180 640.0
46 TraesCS1D01G371900 chr4D 90.164 488 41 5 137 617 504377123 504376636 1.970000e-176 628.0
47 TraesCS1D01G371900 chr4D 80.882 136 24 2 1109 1243 506607002 506606868 4.110000e-19 106.0
48 TraesCS1D01G371900 chr4D 86.885 61 7 1 1367 1426 368863426 368863486 1.940000e-07 67.6
49 TraesCS1D01G371900 chr2D 90.574 488 39 4 137 617 386840137 386840624 9.120000e-180 640.0
50 TraesCS1D01G371900 chr2D 90.456 482 39 4 137 611 187619591 187620072 1.970000e-176 628.0
51 TraesCS1D01G371900 chr2D 95.238 42 2 0 1387 1428 11223970 11223929 1.940000e-07 67.6
52 TraesCS1D01G371900 chr7B 87.732 538 63 1 2183 2720 74093219 74092685 2.550000e-175 625.0
53 TraesCS1D01G371900 chr3D 86.949 544 70 1 2178 2721 505410252 505410794 7.150000e-171 610.0
54 TraesCS1D01G371900 chr3D 89.130 138 14 1 1 137 588978918 588979055 1.440000e-38 171.0
55 TraesCS1D01G371900 chr5B 86.618 553 68 5 2180 2731 67024714 67025261 9.250000e-170 606.0
56 TraesCS1D01G371900 chr5B 86.594 552 69 3 2180 2731 613614946 613615492 3.330000e-169 604.0
57 TraesCS1D01G371900 chr5B 89.855 138 13 1 2 138 662640235 662640372 3.090000e-40 176.0
58 TraesCS1D01G371900 chr6B 86.876 541 68 1 2180 2720 21063499 21064036 1.200000e-168 603.0
59 TraesCS1D01G371900 chr6B 90.476 63 4 2 1367 1428 643997899 643997960 6.930000e-12 82.4
60 TraesCS1D01G371900 chr6B 84.211 57 9 0 1367 1423 701829736 701829680 4.200000e-04 56.5
61 TraesCS1D01G371900 chr4A 86.462 554 69 5 2180 2732 727252516 727253064 1.200000e-168 603.0
62 TraesCS1D01G371900 chr4A 89.706 136 12 2 2 136 740957279 740957145 4.000000e-39 172.0
63 TraesCS1D01G371900 chr7A 94.074 135 8 0 3 137 89037982 89037848 3.940000e-49 206.0
64 TraesCS1D01G371900 chr7A 90.441 136 11 1 2 137 719039744 719039611 8.600000e-41 178.0
65 TraesCS1D01G371900 chr7A 87.162 148 18 1 2 149 98737384 98737238 1.860000e-37 167.0
66 TraesCS1D01G371900 chr5A 91.304 138 10 1 2 139 647160577 647160712 1.430000e-43 187.0
67 TraesCS1D01G371900 chrUn 95.000 60 3 0 1212 1271 364179870 364179929 8.910000e-16 95.3
68 TraesCS1D01G371900 chr2A 88.333 60 7 0 1367 1426 118489521 118489462 4.170000e-09 73.1
69 TraesCS1D01G371900 chr2B 87.097 62 6 2 1363 1423 10347669 10347729 5.400000e-08 69.4


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 TraesCS1D01G371900 chr1D 449981416 449984433 3017 True 5574.000000 5574 100.000000 1 3018 1 chr1D.!!$R1 3017
1 TraesCS1D01G371900 chr1D 343276615 343277115 500 False 652.000000 652 90.419000 137 629 1 chr1D.!!$F1 492
2 TraesCS1D01G371900 chr1D 449922696 449923927 1231 True 583.000000 608 85.829500 677 1945 2 chr1D.!!$R3 1268
3 TraesCS1D01G371900 chr1D 449846507 449847900 1393 False 568.500000 592 83.258000 665 2048 2 chr1D.!!$F6 1383
4 TraesCS1D01G371900 chr1D 449674419 449674947 528 False 477.000000 477 83.425000 775 1302 1 chr1D.!!$F2 527
5 TraesCS1D01G371900 chr1D 449660074 449661515 1441 False 379.133333 560 84.817667 687 2084 3 chr1D.!!$F5 1397
6 TraesCS1D01G371900 chr1A 545023815 545025608 1793 True 707.333333 976 88.919000 630 3018 3 chr1A.!!$R2 2388
7 TraesCS1D01G371900 chr1A 544999872 545001243 1371 False 561.000000 641 83.362000 671 2048 2 chr1A.!!$F4 1377
8 TraesCS1D01G371900 chr1A 545008473 545009685 1212 True 508.500000 597 83.839000 808 2034 2 chr1A.!!$R1 1226
9 TraesCS1D01G371900 chr1A 544927696 544928679 983 False 387.500000 588 84.206500 809 1915 2 chr1A.!!$F3 1106
10 TraesCS1D01G371900 chr1A 544748298 544749379 1081 False 243.750000 431 94.832500 1000 2053 2 chr1A.!!$F2 1053
11 TraesCS1D01G371900 chr1B 616130622 616136993 6371 True 872.000000 922 87.341667 648 3018 3 chr1B.!!$R5 2370
12 TraesCS1D01G371900 chr1B 615744190 615744806 616 True 676.000000 676 86.872000 1431 2032 1 chr1B.!!$R2 601
13 TraesCS1D01G371900 chr1B 25227109 25227655 546 True 625.000000 625 87.273000 2183 2731 1 chr1B.!!$R1 548
14 TraesCS1D01G371900 chr1B 644278294 644278843 549 False 614.000000 614 86.823000 2180 2731 1 chr1B.!!$F5 551
15 TraesCS1D01G371900 chr1B 687076553 687077098 545 False 612.000000 612 86.885000 2184 2731 1 chr1B.!!$F6 547
16 TraesCS1D01G371900 chr7D 244791964 244792468 504 True 649.000000 649 90.138000 137 634 1 chr7D.!!$R1 497
17 TraesCS1D01G371900 chr7B 74092685 74093219 534 True 625.000000 625 87.732000 2183 2720 1 chr7B.!!$R1 537
18 TraesCS1D01G371900 chr3D 505410252 505410794 542 False 610.000000 610 86.949000 2178 2721 1 chr3D.!!$F1 543
19 TraesCS1D01G371900 chr5B 67024714 67025261 547 False 606.000000 606 86.618000 2180 2731 1 chr5B.!!$F1 551
20 TraesCS1D01G371900 chr5B 613614946 613615492 546 False 604.000000 604 86.594000 2180 2731 1 chr5B.!!$F2 551
21 TraesCS1D01G371900 chr6B 21063499 21064036 537 False 603.000000 603 86.876000 2180 2720 1 chr6B.!!$F1 540
22 TraesCS1D01G371900 chr4A 727252516 727253064 548 False 603.000000 603 86.462000 2180 2732 1 chr4A.!!$F1 552

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
63 64 0.034059 CCTAACTATGCAGAGGCCGG 59.966 60.0 13.85 0.0 40.13 6.13 F
77 78 0.104304 GGCCGGGTGTGTACTCATAG 59.896 60.0 2.18 0.0 0.00 2.23 F
560 563 0.602638 AGATTCGTGCAAACTCGGCA 60.603 50.0 0.00 0.0 39.32 5.69 F
1369 5527 0.687920 TTTGGGACGGCATACACTCA 59.312 50.0 0.00 0.0 0.00 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1418 5576 0.110688 CACGCACATGTCGACAAAGG 60.111 55.0 24.13 17.01 0.00 3.11 R
1419 5577 0.722469 GCACGCACATGTCGACAAAG 60.722 55.0 24.13 19.87 0.00 2.77 R
1693 5872 0.955428 CCTCTGCAAAGCCGCTGTAA 60.955 55.0 0.00 0.00 33.05 2.41 R
2580 6962 0.028110 GCAAGCCTTCTTTATCGCCG 59.972 55.0 0.00 0.00 0.00 6.46 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
18 19 3.615099 CTTGTCGGCGTGTTTTTGT 57.385 47.368 6.85 0.00 0.00 2.83
19 20 2.741122 CTTGTCGGCGTGTTTTTGTA 57.259 45.000 6.85 0.00 0.00 2.41
20 21 3.262135 CTTGTCGGCGTGTTTTTGTAT 57.738 42.857 6.85 0.00 0.00 2.29
21 22 2.672188 TGTCGGCGTGTTTTTGTATG 57.328 45.000 6.85 0.00 0.00 2.39
22 23 1.941294 TGTCGGCGTGTTTTTGTATGT 59.059 42.857 6.85 0.00 0.00 2.29
23 24 2.286477 TGTCGGCGTGTTTTTGTATGTG 60.286 45.455 6.85 0.00 0.00 3.21
24 25 1.941294 TCGGCGTGTTTTTGTATGTGT 59.059 42.857 6.85 0.00 0.00 3.72
25 26 2.032722 TCGGCGTGTTTTTGTATGTGTC 60.033 45.455 6.85 0.00 0.00 3.67
26 27 2.303537 GGCGTGTTTTTGTATGTGTCG 58.696 47.619 0.00 0.00 0.00 4.35
27 28 2.303537 GCGTGTTTTTGTATGTGTCGG 58.696 47.619 0.00 0.00 0.00 4.79
28 29 2.286536 GCGTGTTTTTGTATGTGTCGGT 60.287 45.455 0.00 0.00 0.00 4.69
29 30 3.284914 CGTGTTTTTGTATGTGTCGGTG 58.715 45.455 0.00 0.00 0.00 4.94
30 31 3.242478 CGTGTTTTTGTATGTGTCGGTGT 60.242 43.478 0.00 0.00 0.00 4.16
31 32 4.664188 GTGTTTTTGTATGTGTCGGTGTT 58.336 39.130 0.00 0.00 0.00 3.32
32 33 4.497608 GTGTTTTTGTATGTGTCGGTGTTG 59.502 41.667 0.00 0.00 0.00 3.33
33 34 3.972950 TTTTGTATGTGTCGGTGTTGG 57.027 42.857 0.00 0.00 0.00 3.77
34 35 1.231221 TTGTATGTGTCGGTGTTGGC 58.769 50.000 0.00 0.00 0.00 4.52
35 36 0.394938 TGTATGTGTCGGTGTTGGCT 59.605 50.000 0.00 0.00 0.00 4.75
36 37 0.796312 GTATGTGTCGGTGTTGGCTG 59.204 55.000 0.00 0.00 0.00 4.85
37 38 0.394938 TATGTGTCGGTGTTGGCTGT 59.605 50.000 0.00 0.00 0.00 4.40
38 39 1.165907 ATGTGTCGGTGTTGGCTGTG 61.166 55.000 0.00 0.00 0.00 3.66
39 40 1.817941 GTGTCGGTGTTGGCTGTGT 60.818 57.895 0.00 0.00 0.00 3.72
40 41 1.817520 TGTCGGTGTTGGCTGTGTG 60.818 57.895 0.00 0.00 0.00 3.82
41 42 2.899838 TCGGTGTTGGCTGTGTGC 60.900 61.111 0.00 0.00 41.94 4.57
42 43 3.208383 CGGTGTTGGCTGTGTGCA 61.208 61.111 0.00 0.00 45.15 4.57
43 44 2.554636 CGGTGTTGGCTGTGTGCAT 61.555 57.895 0.00 0.00 45.15 3.96
44 45 1.286880 GGTGTTGGCTGTGTGCATC 59.713 57.895 0.00 0.00 45.15 3.91
45 46 1.286880 GTGTTGGCTGTGTGCATCC 59.713 57.895 0.00 0.00 45.15 3.51
46 47 1.151221 TGTTGGCTGTGTGCATCCT 59.849 52.632 0.00 0.00 45.15 3.24
47 48 0.399833 TGTTGGCTGTGTGCATCCTA 59.600 50.000 0.00 0.00 45.15 2.94
48 49 1.202867 TGTTGGCTGTGTGCATCCTAA 60.203 47.619 0.00 0.00 45.15 2.69
49 50 1.200020 GTTGGCTGTGTGCATCCTAAC 59.800 52.381 0.00 0.00 45.15 2.34
50 51 0.692476 TGGCTGTGTGCATCCTAACT 59.308 50.000 0.00 0.00 45.15 2.24
51 52 1.905894 TGGCTGTGTGCATCCTAACTA 59.094 47.619 0.00 0.00 45.15 2.24
52 53 2.505407 TGGCTGTGTGCATCCTAACTAT 59.495 45.455 0.00 0.00 45.15 2.12
53 54 2.874701 GGCTGTGTGCATCCTAACTATG 59.125 50.000 0.00 0.00 45.15 2.23
61 62 3.051081 CATCCTAACTATGCAGAGGCC 57.949 52.381 13.85 0.00 40.13 5.19
62 63 1.040646 TCCTAACTATGCAGAGGCCG 58.959 55.000 13.85 0.00 40.13 6.13
63 64 0.034059 CCTAACTATGCAGAGGCCGG 59.966 60.000 13.85 0.00 40.13 6.13
64 65 0.034059 CTAACTATGCAGAGGCCGGG 59.966 60.000 13.85 0.00 40.13 5.73
65 66 0.689745 TAACTATGCAGAGGCCGGGT 60.690 55.000 13.85 0.00 40.13 5.28
66 67 2.109799 CTATGCAGAGGCCGGGTG 59.890 66.667 2.18 0.00 40.13 4.61
67 68 2.687200 TATGCAGAGGCCGGGTGT 60.687 61.111 2.18 0.00 40.13 4.16
68 69 2.930385 CTATGCAGAGGCCGGGTGTG 62.930 65.000 2.18 0.00 40.13 3.82
70 71 3.702048 GCAGAGGCCGGGTGTGTA 61.702 66.667 2.18 0.00 0.00 2.90
71 72 2.264794 CAGAGGCCGGGTGTGTAC 59.735 66.667 2.18 0.00 0.00 2.90
72 73 2.119832 AGAGGCCGGGTGTGTACT 59.880 61.111 2.18 0.00 0.00 2.73
73 74 1.982938 AGAGGCCGGGTGTGTACTC 60.983 63.158 2.18 0.00 0.00 2.59
74 75 2.203728 AGGCCGGGTGTGTACTCA 60.204 61.111 2.18 0.00 0.00 3.41
75 76 1.612442 AGGCCGGGTGTGTACTCAT 60.612 57.895 2.18 0.00 0.00 2.90
76 77 0.324923 AGGCCGGGTGTGTACTCATA 60.325 55.000 2.18 0.00 0.00 2.15
77 78 0.104304 GGCCGGGTGTGTACTCATAG 59.896 60.000 2.18 0.00 0.00 2.23
78 79 0.822164 GCCGGGTGTGTACTCATAGT 59.178 55.000 2.18 0.00 0.00 2.12
79 80 1.470979 GCCGGGTGTGTACTCATAGTG 60.471 57.143 2.18 0.00 0.00 2.74
80 81 1.822990 CCGGGTGTGTACTCATAGTGT 59.177 52.381 0.24 0.00 0.00 3.55
81 82 2.232941 CCGGGTGTGTACTCATAGTGTT 59.767 50.000 0.24 0.00 0.00 3.32
82 83 3.306502 CCGGGTGTGTACTCATAGTGTTT 60.307 47.826 0.24 0.00 0.00 2.83
83 84 3.678072 CGGGTGTGTACTCATAGTGTTTG 59.322 47.826 0.24 0.00 0.00 2.93
84 85 4.638304 GGGTGTGTACTCATAGTGTTTGT 58.362 43.478 0.24 0.00 0.00 2.83
85 86 5.565242 CGGGTGTGTACTCATAGTGTTTGTA 60.565 44.000 0.24 0.00 0.00 2.41
86 87 6.403878 GGGTGTGTACTCATAGTGTTTGTAT 58.596 40.000 0.24 0.00 0.00 2.29
87 88 6.534079 GGGTGTGTACTCATAGTGTTTGTATC 59.466 42.308 0.24 0.00 0.00 2.24
88 89 6.534079 GGTGTGTACTCATAGTGTTTGTATCC 59.466 42.308 0.24 0.00 0.00 2.59
89 90 7.321153 GTGTGTACTCATAGTGTTTGTATCCT 58.679 38.462 0.24 0.00 0.00 3.24
90 91 7.488471 GTGTGTACTCATAGTGTTTGTATCCTC 59.512 40.741 0.24 0.00 0.00 3.71
91 92 7.396339 TGTGTACTCATAGTGTTTGTATCCTCT 59.604 37.037 0.00 0.00 0.00 3.69
92 93 8.251721 GTGTACTCATAGTGTTTGTATCCTCTT 58.748 37.037 0.00 0.00 0.00 2.85
93 94 8.251026 TGTACTCATAGTGTTTGTATCCTCTTG 58.749 37.037 0.00 0.00 0.00 3.02
94 95 7.482169 ACTCATAGTGTTTGTATCCTCTTGA 57.518 36.000 0.00 0.00 0.00 3.02
95 96 8.083828 ACTCATAGTGTTTGTATCCTCTTGAT 57.916 34.615 0.00 0.00 37.49 2.57
96 97 7.984050 ACTCATAGTGTTTGTATCCTCTTGATG 59.016 37.037 0.00 0.00 34.76 3.07
97 98 6.763135 TCATAGTGTTTGTATCCTCTTGATGC 59.237 38.462 0.00 0.00 36.68 3.91
98 99 5.171339 AGTGTTTGTATCCTCTTGATGCT 57.829 39.130 0.00 0.00 37.04 3.79
99 100 5.181748 AGTGTTTGTATCCTCTTGATGCTC 58.818 41.667 0.00 0.00 37.04 4.26
100 101 4.333926 GTGTTTGTATCCTCTTGATGCTCC 59.666 45.833 0.00 0.00 37.04 4.70
101 102 4.019411 TGTTTGTATCCTCTTGATGCTCCA 60.019 41.667 0.00 0.00 37.04 3.86
102 103 5.128919 GTTTGTATCCTCTTGATGCTCCAT 58.871 41.667 0.00 0.00 37.04 3.41
103 104 5.378230 TTGTATCCTCTTGATGCTCCATT 57.622 39.130 0.00 0.00 37.04 3.16
104 105 5.378230 TGTATCCTCTTGATGCTCCATTT 57.622 39.130 0.00 0.00 37.04 2.32
105 106 5.759059 TGTATCCTCTTGATGCTCCATTTT 58.241 37.500 0.00 0.00 37.04 1.82
106 107 6.899089 TGTATCCTCTTGATGCTCCATTTTA 58.101 36.000 0.00 0.00 37.04 1.52
107 108 7.345691 TGTATCCTCTTGATGCTCCATTTTAA 58.654 34.615 0.00 0.00 37.04 1.52
108 109 6.956202 ATCCTCTTGATGCTCCATTTTAAG 57.044 37.500 0.00 0.00 30.54 1.85
109 110 4.641989 TCCTCTTGATGCTCCATTTTAAGC 59.358 41.667 0.00 0.00 39.02 3.09
110 111 4.643784 CCTCTTGATGCTCCATTTTAAGCT 59.356 41.667 0.00 0.00 39.31 3.74
111 112 5.824624 CCTCTTGATGCTCCATTTTAAGCTA 59.175 40.000 0.00 0.00 39.31 3.32
112 113 6.319658 CCTCTTGATGCTCCATTTTAAGCTAA 59.680 38.462 0.00 0.00 39.31 3.09
113 114 7.014038 CCTCTTGATGCTCCATTTTAAGCTAAT 59.986 37.037 0.00 0.00 39.31 1.73
114 115 8.978874 TCTTGATGCTCCATTTTAAGCTAATA 57.021 30.769 0.00 0.00 39.31 0.98
115 116 9.407380 TCTTGATGCTCCATTTTAAGCTAATAA 57.593 29.630 0.00 0.00 39.31 1.40
120 121 9.987272 ATGCTCCATTTTAAGCTAATAAAATCC 57.013 29.630 11.52 4.36 41.30 3.01
121 122 8.976353 TGCTCCATTTTAAGCTAATAAAATCCA 58.024 29.630 11.52 6.17 41.30 3.41
122 123 9.987272 GCTCCATTTTAAGCTAATAAAATCCAT 57.013 29.630 11.52 0.00 41.30 3.41
131 132 7.264373 AGCTAATAAAATCCATCCTTTGTCG 57.736 36.000 0.00 0.00 0.00 4.35
132 133 7.054124 AGCTAATAAAATCCATCCTTTGTCGA 58.946 34.615 0.00 0.00 0.00 4.20
133 134 7.556275 AGCTAATAAAATCCATCCTTTGTCGAA 59.444 33.333 0.00 0.00 0.00 3.71
134 135 8.188139 GCTAATAAAATCCATCCTTTGTCGAAA 58.812 33.333 0.00 0.00 0.00 3.46
185 186 5.300539 TGTGTTTACCTAGTTACCACGTGTA 59.699 40.000 15.65 4.31 0.00 2.90
262 264 3.033764 CCACGTACGCGCAACTGT 61.034 61.111 16.72 5.00 42.83 3.55
299 302 7.039270 AGCAACGAATCATAGTTACATGTGTA 58.961 34.615 9.11 0.00 0.00 2.90
404 407 2.703798 GCGCGTGGACTAGGTGGTA 61.704 63.158 8.43 0.00 0.00 3.25
427 430 3.214328 CTGTGTGGGCAGAAACTAGTTT 58.786 45.455 20.67 20.67 38.70 2.66
451 454 1.226916 CACAACGCAGCTGGCAAAA 60.227 52.632 17.12 0.00 45.17 2.44
497 500 2.111043 CTCCAACGCCCACACACT 59.889 61.111 0.00 0.00 0.00 3.55
503 506 3.706373 CGCCCACACACTAGCCCT 61.706 66.667 0.00 0.00 0.00 5.19
558 561 1.798223 TCAAGATTCGTGCAAACTCGG 59.202 47.619 0.00 0.00 33.71 4.63
560 563 0.602638 AGATTCGTGCAAACTCGGCA 60.603 50.000 0.00 0.00 39.32 5.69
573 581 4.794439 CGGCAGTGATCCACGCGA 62.794 66.667 15.93 0.00 39.64 5.87
574 582 2.434185 GGCAGTGATCCACGCGAA 60.434 61.111 15.93 0.00 39.64 4.70
617 626 3.252400 CACGTGTGGGCGTTAGTATTTA 58.748 45.455 7.58 0.00 43.83 1.40
618 627 3.679025 CACGTGTGGGCGTTAGTATTTAA 59.321 43.478 7.58 0.00 43.83 1.52
752 773 2.827322 TCCAATCCATTGTCTTTGCCTG 59.173 45.455 0.00 0.00 36.06 4.85
798 819 4.379243 CGCGGCCTCACCTCACTT 62.379 66.667 0.00 0.00 35.61 3.16
936 985 7.009265 CGACCATATATACAACCATCGATGTTC 59.991 40.741 23.27 0.00 0.00 3.18
949 1001 2.623889 TCGATGTTCCCTAGCTTAGCTC 59.376 50.000 11.09 0.00 40.44 4.09
956 1008 1.609555 CCCTAGCTTAGCTCGATCGTT 59.390 52.381 11.09 4.96 40.44 3.85
1195 1272 1.987855 CTCAACTACCTCCGCCCCA 60.988 63.158 0.00 0.00 0.00 4.96
1240 5354 1.267574 GCAGGAGGAGGACCACATCA 61.268 60.000 5.94 0.00 38.94 3.07
1248 5362 2.528743 GGACCACATCATCGCGCTG 61.529 63.158 5.56 2.97 0.00 5.18
1281 5395 2.156098 GGCAACAGGTTCGTCCAATTA 58.844 47.619 2.77 0.00 39.02 1.40
1292 5406 4.603231 TCGTCCAATTACGCAATTTACC 57.397 40.909 0.00 0.00 42.56 2.85
1302 5416 1.732077 CGCAATTTACCGTGCAATGCT 60.732 47.619 6.82 0.00 40.94 3.79
1344 5502 1.306654 ACGGGAGTGATTGGGGCTA 60.307 57.895 0.00 0.00 44.82 3.93
1365 5523 2.799126 AAGATTTGGGACGGCATACA 57.201 45.000 0.00 0.00 0.00 2.29
1366 5524 2.038387 AGATTTGGGACGGCATACAC 57.962 50.000 0.00 0.00 0.00 2.90
1367 5525 1.559682 AGATTTGGGACGGCATACACT 59.440 47.619 0.00 0.00 0.00 3.55
1368 5526 1.940613 GATTTGGGACGGCATACACTC 59.059 52.381 0.00 0.00 0.00 3.51
1369 5527 0.687920 TTTGGGACGGCATACACTCA 59.312 50.000 0.00 0.00 0.00 3.41
1371 5529 0.908910 TGGGACGGCATACACTCATT 59.091 50.000 0.00 0.00 0.00 2.57
1372 5530 1.299541 GGGACGGCATACACTCATTG 58.700 55.000 0.00 0.00 0.00 2.82
1388 5546 7.613247 CACTCATTGTGTTTGTATTCAGTTG 57.387 36.000 0.00 0.00 41.53 3.16
1389 5547 7.416817 CACTCATTGTGTTTGTATTCAGTTGA 58.583 34.615 0.00 0.00 41.53 3.18
1390 5548 8.077991 CACTCATTGTGTTTGTATTCAGTTGAT 58.922 33.333 0.00 0.00 41.53 2.57
1391 5549 8.077991 ACTCATTGTGTTTGTATTCAGTTGATG 58.922 33.333 0.00 0.00 0.00 3.07
1392 5550 6.862608 TCATTGTGTTTGTATTCAGTTGATGC 59.137 34.615 0.00 0.00 0.00 3.91
1393 5551 5.119931 TGTGTTTGTATTCAGTTGATGCC 57.880 39.130 0.00 0.00 0.00 4.40
1394 5552 4.826733 TGTGTTTGTATTCAGTTGATGCCT 59.173 37.500 0.00 0.00 0.00 4.75
1395 5553 5.301551 TGTGTTTGTATTCAGTTGATGCCTT 59.698 36.000 0.00 0.00 0.00 4.35
1396 5554 6.488344 TGTGTTTGTATTCAGTTGATGCCTTA 59.512 34.615 0.00 0.00 0.00 2.69
1397 5555 7.176515 TGTGTTTGTATTCAGTTGATGCCTTAT 59.823 33.333 0.00 0.00 0.00 1.73
1398 5556 8.028938 GTGTTTGTATTCAGTTGATGCCTTATT 58.971 33.333 0.00 0.00 0.00 1.40
1399 5557 8.584157 TGTTTGTATTCAGTTGATGCCTTATTT 58.416 29.630 0.00 0.00 0.00 1.40
1400 5558 9.423061 GTTTGTATTCAGTTGATGCCTTATTTT 57.577 29.630 0.00 0.00 0.00 1.82
1401 5559 8.984891 TTGTATTCAGTTGATGCCTTATTTTG 57.015 30.769 0.00 0.00 0.00 2.44
1402 5560 8.347004 TGTATTCAGTTGATGCCTTATTTTGA 57.653 30.769 0.00 0.00 0.00 2.69
1403 5561 8.461222 TGTATTCAGTTGATGCCTTATTTTGAG 58.539 33.333 0.00 0.00 0.00 3.02
1404 5562 6.899393 TTCAGTTGATGCCTTATTTTGAGT 57.101 33.333 0.00 0.00 0.00 3.41
1405 5563 6.899393 TCAGTTGATGCCTTATTTTGAGTT 57.101 33.333 0.00 0.00 0.00 3.01
1406 5564 7.994425 TCAGTTGATGCCTTATTTTGAGTTA 57.006 32.000 0.00 0.00 0.00 2.24
1407 5565 8.402798 TCAGTTGATGCCTTATTTTGAGTTAA 57.597 30.769 0.00 0.00 0.00 2.01
1408 5566 9.023962 TCAGTTGATGCCTTATTTTGAGTTAAT 57.976 29.630 0.00 0.00 0.00 1.40
1426 5584 8.673711 TGAGTTAATAAAATCCATCCTTTGTCG 58.326 33.333 0.00 0.00 0.00 4.35
1427 5585 8.801882 AGTTAATAAAATCCATCCTTTGTCGA 57.198 30.769 0.00 0.00 0.00 4.20
1428 5586 8.674607 AGTTAATAAAATCCATCCTTTGTCGAC 58.325 33.333 9.11 9.11 0.00 4.20
1429 5587 8.455682 GTTAATAAAATCCATCCTTTGTCGACA 58.544 33.333 15.76 15.76 0.00 4.35
1672 5851 2.629656 GCAGCAGGCGGTGTTTGAT 61.630 57.895 9.51 0.00 42.79 2.57
1708 5890 1.643868 CCGATTACAGCGGCTTTGCA 61.644 55.000 0.00 0.00 42.55 4.08
2129 6469 3.625764 AGCACGCTGAAAAGTTTACAAGA 59.374 39.130 0.00 0.00 0.00 3.02
2217 6599 4.658786 AAGGGCCGGTGAGAGGGT 62.659 66.667 1.90 0.00 0.00 4.34
2301 6683 2.130426 GGCGGCTCTCTGGAGATGA 61.130 63.158 0.00 0.00 41.86 2.92
2302 6684 1.067250 GCGGCTCTCTGGAGATGAC 59.933 63.158 0.48 0.00 41.86 3.06
2330 6712 4.528039 CCCCGTCTAGCCCCCGTA 62.528 72.222 0.00 0.00 0.00 4.02
2331 6713 2.442643 CCCGTCTAGCCCCCGTAA 60.443 66.667 0.00 0.00 0.00 3.18
2363 6745 1.605971 TAGCATCGTTGGTGGGCGTA 61.606 55.000 8.40 0.00 34.79 4.42
2373 6755 1.332144 GGTGGGCGTATGGAGGTGTA 61.332 60.000 0.00 0.00 0.00 2.90
2377 6759 1.692519 GGGCGTATGGAGGTGTATCTT 59.307 52.381 0.00 0.00 0.00 2.40
2383 6765 2.225382 TGGAGGTGTATCTTCGGTGA 57.775 50.000 0.00 0.00 0.00 4.02
2395 6777 7.640240 GTGTATCTTCGGTGAATTTATCTTTGC 59.360 37.037 0.00 0.00 0.00 3.68
2430 6812 5.575957 GGATCTCGTCGTTGTTTGTCTATA 58.424 41.667 0.00 0.00 0.00 1.31
2433 6815 7.859377 GGATCTCGTCGTTGTTTGTCTATATTA 59.141 37.037 0.00 0.00 0.00 0.98
2555 6937 2.484065 CCCGACTGTCCACTACAACAAA 60.484 50.000 1.55 0.00 37.74 2.83
2587 6969 2.734591 GGTGATGGAGCGGCGATA 59.265 61.111 12.98 0.00 0.00 2.92
2592 6974 1.138069 TGATGGAGCGGCGATAAAGAA 59.862 47.619 12.98 0.00 0.00 2.52
2596 6978 0.530870 GAGCGGCGATAAAGAAGGCT 60.531 55.000 12.98 0.00 0.00 4.58
2635 7017 1.135746 GTGCTTGTAGTCGTCGCTAGT 60.136 52.381 0.00 0.00 0.00 2.57
2638 7020 2.413765 GCTTGTAGTCGTCGCTAGTTGA 60.414 50.000 0.00 0.00 0.00 3.18
2709 7091 7.945134 ACTACCATGATTGAAAATGAATAGGC 58.055 34.615 0.00 0.00 0.00 3.93
2745 7130 6.292811 CCAAGTAAAAAGTTGCGCATCAAATT 60.293 34.615 19.92 12.82 43.87 1.82
2746 7131 7.095857 CCAAGTAAAAAGTTGCGCATCAAATTA 60.096 33.333 19.92 11.95 41.51 1.40
2754 7139 2.983136 TGCGCATCAAATTAAACAACCG 59.017 40.909 5.66 0.00 0.00 4.44
2779 7164 7.312899 GGGGTGAATTAGTTTAGTTCAACATG 58.687 38.462 10.29 0.00 42.02 3.21
2795 7180 5.197451 TCAACATGTTGACCCTTGTTTACT 58.803 37.500 32.36 0.00 43.90 2.24
2796 7181 5.654650 TCAACATGTTGACCCTTGTTTACTT 59.345 36.000 32.36 0.00 43.90 2.24
2798 7183 6.144078 ACATGTTGACCCTTGTTTACTTTC 57.856 37.500 0.00 0.00 0.00 2.62
2799 7184 5.068591 ACATGTTGACCCTTGTTTACTTTCC 59.931 40.000 0.00 0.00 0.00 3.13
2800 7185 4.601084 TGTTGACCCTTGTTTACTTTCCA 58.399 39.130 0.00 0.00 0.00 3.53
2817 7204 1.303888 CAGCATGTGCCTGGGTTCT 60.304 57.895 0.57 0.00 43.38 3.01
2845 7232 3.669251 TTTACATTTCCCCCGCAAAAG 57.331 42.857 0.00 0.00 0.00 2.27
2985 7377 9.160496 ACAATGCAAAAGTTTGATCAAGTTTAA 57.840 25.926 8.41 4.05 37.07 1.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 2.355132 ACATACAAAAACACGCCGACAA 59.645 40.909 0.00 0.00 0.00 3.18
2 3 1.941294 ACATACAAAAACACGCCGACA 59.059 42.857 0.00 0.00 0.00 4.35
4 5 1.941294 ACACATACAAAAACACGCCGA 59.059 42.857 0.00 0.00 0.00 5.54
5 6 2.303537 GACACATACAAAAACACGCCG 58.696 47.619 0.00 0.00 0.00 6.46
7 8 2.286536 ACCGACACATACAAAAACACGC 60.287 45.455 0.00 0.00 0.00 5.34
8 9 3.242478 ACACCGACACATACAAAAACACG 60.242 43.478 0.00 0.00 0.00 4.49
9 10 4.281525 ACACCGACACATACAAAAACAC 57.718 40.909 0.00 0.00 0.00 3.32
10 11 4.438880 CCAACACCGACACATACAAAAACA 60.439 41.667 0.00 0.00 0.00 2.83
11 12 4.039032 CCAACACCGACACATACAAAAAC 58.961 43.478 0.00 0.00 0.00 2.43
12 13 3.489398 GCCAACACCGACACATACAAAAA 60.489 43.478 0.00 0.00 0.00 1.94
13 14 2.033550 GCCAACACCGACACATACAAAA 59.966 45.455 0.00 0.00 0.00 2.44
14 15 1.604755 GCCAACACCGACACATACAAA 59.395 47.619 0.00 0.00 0.00 2.83
15 16 1.202710 AGCCAACACCGACACATACAA 60.203 47.619 0.00 0.00 0.00 2.41
16 17 0.394938 AGCCAACACCGACACATACA 59.605 50.000 0.00 0.00 0.00 2.29
17 18 0.796312 CAGCCAACACCGACACATAC 59.204 55.000 0.00 0.00 0.00 2.39
18 19 0.394938 ACAGCCAACACCGACACATA 59.605 50.000 0.00 0.00 0.00 2.29
19 20 1.148273 ACAGCCAACACCGACACAT 59.852 52.632 0.00 0.00 0.00 3.21
20 21 1.817520 CACAGCCAACACCGACACA 60.818 57.895 0.00 0.00 0.00 3.72
21 22 1.817941 ACACAGCCAACACCGACAC 60.818 57.895 0.00 0.00 0.00 3.67
22 23 1.817520 CACACAGCCAACACCGACA 60.818 57.895 0.00 0.00 0.00 4.35
23 24 3.022287 CACACAGCCAACACCGAC 58.978 61.111 0.00 0.00 0.00 4.79
24 25 2.899838 GCACACAGCCAACACCGA 60.900 61.111 0.00 0.00 37.23 4.69
25 26 2.462255 GATGCACACAGCCAACACCG 62.462 60.000 0.00 0.00 44.83 4.94
26 27 1.286880 GATGCACACAGCCAACACC 59.713 57.895 0.00 0.00 44.83 4.16
27 28 4.950744 GATGCACACAGCCAACAC 57.049 55.556 0.00 0.00 44.83 3.32
41 42 2.611473 CGGCCTCTGCATAGTTAGGATG 60.611 54.545 0.00 0.00 40.13 3.51
42 43 1.620819 CGGCCTCTGCATAGTTAGGAT 59.379 52.381 0.00 0.00 40.13 3.24
43 44 1.040646 CGGCCTCTGCATAGTTAGGA 58.959 55.000 0.00 0.00 40.13 2.94
44 45 0.034059 CCGGCCTCTGCATAGTTAGG 59.966 60.000 0.00 0.00 40.13 2.69
45 46 0.034059 CCCGGCCTCTGCATAGTTAG 59.966 60.000 0.00 0.00 40.13 2.34
46 47 0.689745 ACCCGGCCTCTGCATAGTTA 60.690 55.000 0.00 0.00 40.13 2.24
47 48 1.995626 ACCCGGCCTCTGCATAGTT 60.996 57.895 0.00 0.00 40.13 2.24
48 49 2.365635 ACCCGGCCTCTGCATAGT 60.366 61.111 0.00 0.00 40.13 2.12
49 50 2.109799 CACCCGGCCTCTGCATAG 59.890 66.667 0.00 0.00 40.13 2.23
50 51 2.687200 ACACCCGGCCTCTGCATA 60.687 61.111 0.00 0.00 40.13 3.14
51 52 4.415150 CACACCCGGCCTCTGCAT 62.415 66.667 0.00 0.00 40.13 3.96
53 54 3.702048 TACACACCCGGCCTCTGC 61.702 66.667 0.00 0.00 0.00 4.26
54 55 2.227089 GAGTACACACCCGGCCTCTG 62.227 65.000 0.00 0.00 0.00 3.35
55 56 1.982938 GAGTACACACCCGGCCTCT 60.983 63.158 0.00 0.00 0.00 3.69
56 57 1.614241 ATGAGTACACACCCGGCCTC 61.614 60.000 0.00 0.00 0.00 4.70
57 58 0.324923 TATGAGTACACACCCGGCCT 60.325 55.000 0.00 0.00 0.00 5.19
58 59 0.104304 CTATGAGTACACACCCGGCC 59.896 60.000 0.00 0.00 0.00 6.13
59 60 0.822164 ACTATGAGTACACACCCGGC 59.178 55.000 0.00 0.00 0.00 6.13
60 61 1.822990 ACACTATGAGTACACACCCGG 59.177 52.381 0.00 0.00 0.00 5.73
61 62 3.587797 AACACTATGAGTACACACCCG 57.412 47.619 0.00 0.00 0.00 5.28
62 63 4.638304 ACAAACACTATGAGTACACACCC 58.362 43.478 0.00 0.00 0.00 4.61
63 64 6.534079 GGATACAAACACTATGAGTACACACC 59.466 42.308 0.00 0.00 0.00 4.16
64 65 7.321153 AGGATACAAACACTATGAGTACACAC 58.679 38.462 0.00 0.00 41.41 3.82
65 66 7.396339 AGAGGATACAAACACTATGAGTACACA 59.604 37.037 0.00 0.00 41.41 3.72
66 67 7.773149 AGAGGATACAAACACTATGAGTACAC 58.227 38.462 0.00 0.00 41.41 2.90
67 68 7.956328 AGAGGATACAAACACTATGAGTACA 57.044 36.000 0.00 0.00 41.41 2.90
68 69 8.467598 TCAAGAGGATACAAACACTATGAGTAC 58.532 37.037 0.00 0.00 41.41 2.73
69 70 8.589701 TCAAGAGGATACAAACACTATGAGTA 57.410 34.615 0.00 0.00 41.41 2.59
70 71 7.482169 TCAAGAGGATACAAACACTATGAGT 57.518 36.000 0.00 0.00 41.41 3.41
71 72 7.042187 GCATCAAGAGGATACAAACACTATGAG 60.042 40.741 0.00 0.00 41.41 2.90
72 73 6.763135 GCATCAAGAGGATACAAACACTATGA 59.237 38.462 0.00 0.00 41.41 2.15
73 74 6.765036 AGCATCAAGAGGATACAAACACTATG 59.235 38.462 0.00 0.00 41.41 2.23
74 75 6.893583 AGCATCAAGAGGATACAAACACTAT 58.106 36.000 0.00 0.00 41.41 2.12
75 76 6.299805 AGCATCAAGAGGATACAAACACTA 57.700 37.500 0.00 0.00 41.41 2.74
76 77 5.171339 AGCATCAAGAGGATACAAACACT 57.829 39.130 0.00 0.00 41.41 3.55
77 78 4.333926 GGAGCATCAAGAGGATACAAACAC 59.666 45.833 0.00 0.00 36.25 3.32
78 79 4.019411 TGGAGCATCAAGAGGATACAAACA 60.019 41.667 0.00 0.00 36.25 2.83
79 80 4.517285 TGGAGCATCAAGAGGATACAAAC 58.483 43.478 0.00 0.00 36.25 2.93
80 81 4.842531 TGGAGCATCAAGAGGATACAAA 57.157 40.909 0.00 0.00 36.25 2.83
81 82 5.378230 AATGGAGCATCAAGAGGATACAA 57.622 39.130 0.00 0.00 36.25 2.41
82 83 5.378230 AAATGGAGCATCAAGAGGATACA 57.622 39.130 0.00 0.00 36.25 2.29
83 84 7.521261 GCTTAAAATGGAGCATCAAGAGGATAC 60.521 40.741 0.00 0.00 38.73 2.24
84 85 6.488006 GCTTAAAATGGAGCATCAAGAGGATA 59.512 38.462 0.00 0.00 38.73 2.59
85 86 5.301298 GCTTAAAATGGAGCATCAAGAGGAT 59.699 40.000 0.00 0.00 38.73 3.24
86 87 4.641989 GCTTAAAATGGAGCATCAAGAGGA 59.358 41.667 0.00 0.00 38.73 3.71
87 88 4.643784 AGCTTAAAATGGAGCATCAAGAGG 59.356 41.667 0.00 0.00 41.31 3.69
88 89 5.831702 AGCTTAAAATGGAGCATCAAGAG 57.168 39.130 0.00 0.00 41.31 2.85
89 90 7.886629 ATTAGCTTAAAATGGAGCATCAAGA 57.113 32.000 0.00 0.00 41.31 3.02
94 95 9.987272 GGATTTTATTAGCTTAAAATGGAGCAT 57.013 29.630 17.04 0.00 40.25 3.79
95 96 8.976353 TGGATTTTATTAGCTTAAAATGGAGCA 58.024 29.630 17.04 0.00 40.25 4.26
96 97 9.987272 ATGGATTTTATTAGCTTAAAATGGAGC 57.013 29.630 17.04 6.31 40.25 4.70
105 106 8.836413 CGACAAAGGATGGATTTTATTAGCTTA 58.164 33.333 0.00 0.00 0.00 3.09
106 107 7.556275 TCGACAAAGGATGGATTTTATTAGCTT 59.444 33.333 0.00 0.00 0.00 3.74
107 108 7.054124 TCGACAAAGGATGGATTTTATTAGCT 58.946 34.615 0.00 0.00 0.00 3.32
108 109 7.259290 TCGACAAAGGATGGATTTTATTAGC 57.741 36.000 0.00 0.00 0.00 3.09
111 112 9.942850 ATTTTTCGACAAAGGATGGATTTTATT 57.057 25.926 2.86 0.00 0.00 1.40
114 115 9.369904 CATATTTTTCGACAAAGGATGGATTTT 57.630 29.630 2.86 0.00 0.00 1.82
115 116 7.981225 CCATATTTTTCGACAAAGGATGGATTT 59.019 33.333 23.77 2.03 36.25 2.17
116 117 7.124147 ACCATATTTTTCGACAAAGGATGGATT 59.876 33.333 29.54 16.26 36.95 3.01
117 118 6.607198 ACCATATTTTTCGACAAAGGATGGAT 59.393 34.615 29.54 18.79 36.95 3.41
118 119 5.949354 ACCATATTTTTCGACAAAGGATGGA 59.051 36.000 29.54 1.19 36.95 3.41
119 120 6.127758 TGACCATATTTTTCGACAAAGGATGG 60.128 38.462 25.12 25.12 38.21 3.51
120 121 6.851609 TGACCATATTTTTCGACAAAGGATG 58.148 36.000 7.57 9.94 0.00 3.51
121 122 7.461182 TTGACCATATTTTTCGACAAAGGAT 57.539 32.000 7.57 0.00 0.00 3.24
122 123 6.885952 TTGACCATATTTTTCGACAAAGGA 57.114 33.333 7.57 0.00 0.00 3.36
123 124 6.920758 TGTTTGACCATATTTTTCGACAAAGG 59.079 34.615 2.86 1.62 0.00 3.11
124 125 7.647715 ACTGTTTGACCATATTTTTCGACAAAG 59.352 33.333 2.86 0.00 0.00 2.77
125 126 7.484975 ACTGTTTGACCATATTTTTCGACAAA 58.515 30.769 0.00 0.00 0.00 2.83
126 127 7.033530 ACTGTTTGACCATATTTTTCGACAA 57.966 32.000 0.00 0.00 0.00 3.18
127 128 6.627395 ACTGTTTGACCATATTTTTCGACA 57.373 33.333 0.00 0.00 0.00 4.35
128 129 7.803724 ACTACTGTTTGACCATATTTTTCGAC 58.196 34.615 0.00 0.00 0.00 4.20
129 130 7.972832 ACTACTGTTTGACCATATTTTTCGA 57.027 32.000 0.00 0.00 0.00 3.71
130 131 7.060633 GCAACTACTGTTTGACCATATTTTTCG 59.939 37.037 0.00 0.00 33.52 3.46
131 132 7.328493 GGCAACTACTGTTTGACCATATTTTTC 59.672 37.037 0.00 0.00 33.52 2.29
132 133 7.151976 GGCAACTACTGTTTGACCATATTTTT 58.848 34.615 0.00 0.00 33.52 1.94
133 134 6.266558 TGGCAACTACTGTTTGACCATATTTT 59.733 34.615 0.00 0.00 33.52 1.82
134 135 5.772672 TGGCAACTACTGTTTGACCATATTT 59.227 36.000 0.00 0.00 33.52 1.40
135 136 5.321102 TGGCAACTACTGTTTGACCATATT 58.679 37.500 0.00 0.00 33.52 1.28
269 271 6.859017 TGTAACTATGATTCGTTGCTAGACA 58.141 36.000 0.00 0.00 0.00 3.41
299 302 3.514645 CGTACGTGGCAACTAGGTAAAT 58.485 45.455 7.22 0.00 37.61 1.40
360 363 1.652012 CGAACTGCTTTTCGCCCAA 59.348 52.632 7.23 0.00 41.73 4.12
404 407 0.764890 TAGTTTCTGCCCACACAGCT 59.235 50.000 0.00 0.00 37.59 4.24
427 430 4.873810 AGCTGCGTTGTGTGGGCA 62.874 61.111 0.00 0.00 35.07 5.36
497 500 2.056223 GCCACGTAGGACAGGGCTA 61.056 63.158 8.04 0.00 41.39 3.93
503 506 2.646117 TTTGCGTGCCACGTAGGACA 62.646 55.000 19.57 4.68 44.73 4.02
529 532 3.058983 TGCACGAATCTTGACACATTGAC 60.059 43.478 0.00 0.00 0.00 3.18
558 561 1.349627 CATTCGCGTGGATCACTGC 59.650 57.895 5.77 0.00 33.30 4.40
560 563 1.897423 TCCATTCGCGTGGATCACT 59.103 52.632 13.96 0.00 43.20 3.41
573 581 2.769893 GCATTTTGCAACCTGTCCATT 58.230 42.857 0.00 0.00 44.26 3.16
574 582 2.460757 GCATTTTGCAACCTGTCCAT 57.539 45.000 0.00 0.00 44.26 3.41
578 586 0.829333 TGTGGCATTTTGCAACCTGT 59.171 45.000 0.00 0.00 46.58 4.00
580 588 0.249405 CGTGTGGCATTTTGCAACCT 60.249 50.000 0.00 0.00 46.58 3.50
581 589 0.529555 ACGTGTGGCATTTTGCAACC 60.530 50.000 0.00 0.00 46.58 3.77
641 650 3.819877 AAACGGACCGTGTCAGGGC 62.820 63.158 22.53 4.69 39.99 5.19
708 717 1.751924 AGAAGACACCAGCGGTCTATC 59.248 52.381 0.00 0.00 44.50 2.08
710 719 0.888619 CAGAAGACACCAGCGGTCTA 59.111 55.000 0.00 0.00 44.50 2.59
768 789 1.022451 GGCCGCGATCAAGTGGTTTA 61.022 55.000 8.23 0.00 43.39 2.01
771 792 3.665675 GAGGCCGCGATCAAGTGGT 62.666 63.158 8.23 0.00 43.39 4.16
936 985 1.240256 ACGATCGAGCTAAGCTAGGG 58.760 55.000 24.34 0.00 39.88 3.53
949 1001 3.791887 CCTTGTAGCTACTTCAACGATCG 59.208 47.826 23.84 14.88 0.00 3.69
956 1008 0.535335 CCGGCCTTGTAGCTACTTCA 59.465 55.000 23.84 7.95 0.00 3.02
1240 5354 2.587194 GATCTGGTGCAGCGCGAT 60.587 61.111 12.10 17.10 0.00 4.58
1248 5362 2.109126 GTTGCCGAGGATCTGGTGC 61.109 63.158 0.00 0.00 32.58 5.01
1281 5395 1.975837 CATTGCACGGTAAATTGCGT 58.024 45.000 0.00 0.00 41.96 5.24
1292 5406 4.346734 ACTAATCTGAAAGCATTGCACG 57.653 40.909 11.91 0.00 0.00 5.34
1302 5416 6.768029 GCACATTGCAAAACTAATCTGAAA 57.232 33.333 1.71 0.00 44.26 2.69
1326 5464 0.912487 TTAGCCCCAATCACTCCCGT 60.912 55.000 0.00 0.00 0.00 5.28
1327 5465 0.254747 TTTAGCCCCAATCACTCCCG 59.745 55.000 0.00 0.00 0.00 5.14
1328 5466 2.025321 TCTTTTAGCCCCAATCACTCCC 60.025 50.000 0.00 0.00 0.00 4.30
1330 5468 5.394553 CCAAATCTTTTAGCCCCAATCACTC 60.395 44.000 0.00 0.00 0.00 3.51
1331 5469 4.467438 CCAAATCTTTTAGCCCCAATCACT 59.533 41.667 0.00 0.00 0.00 3.41
1332 5470 4.383010 CCCAAATCTTTTAGCCCCAATCAC 60.383 45.833 0.00 0.00 0.00 3.06
1333 5471 3.774216 CCCAAATCTTTTAGCCCCAATCA 59.226 43.478 0.00 0.00 0.00 2.57
1334 5472 4.030216 TCCCAAATCTTTTAGCCCCAATC 58.970 43.478 0.00 0.00 0.00 2.67
1335 5473 3.774766 GTCCCAAATCTTTTAGCCCCAAT 59.225 43.478 0.00 0.00 0.00 3.16
1336 5474 3.169908 GTCCCAAATCTTTTAGCCCCAA 58.830 45.455 0.00 0.00 0.00 4.12
1337 5475 2.815158 GTCCCAAATCTTTTAGCCCCA 58.185 47.619 0.00 0.00 0.00 4.96
1344 5502 3.192633 GTGTATGCCGTCCCAAATCTTTT 59.807 43.478 0.00 0.00 0.00 2.27
1365 5523 7.566760 TCAACTGAATACAAACACAATGAGT 57.433 32.000 0.00 0.00 0.00 3.41
1366 5524 7.061441 GCATCAACTGAATACAAACACAATGAG 59.939 37.037 0.00 0.00 0.00 2.90
1367 5525 6.862608 GCATCAACTGAATACAAACACAATGA 59.137 34.615 0.00 0.00 0.00 2.57
1368 5526 6.089820 GGCATCAACTGAATACAAACACAATG 59.910 38.462 0.00 0.00 0.00 2.82
1369 5527 6.015180 AGGCATCAACTGAATACAAACACAAT 60.015 34.615 0.00 0.00 0.00 2.71
1371 5529 4.826733 AGGCATCAACTGAATACAAACACA 59.173 37.500 0.00 0.00 0.00 3.72
1372 5530 5.376854 AGGCATCAACTGAATACAAACAC 57.623 39.130 0.00 0.00 0.00 3.32
1375 5533 9.421806 CAAAATAAGGCATCAACTGAATACAAA 57.578 29.630 0.00 0.00 0.00 2.83
1378 5536 8.462016 ACTCAAAATAAGGCATCAACTGAATAC 58.538 33.333 0.00 0.00 0.00 1.89
1379 5537 8.579850 ACTCAAAATAAGGCATCAACTGAATA 57.420 30.769 0.00 0.00 0.00 1.75
1380 5538 7.472334 ACTCAAAATAAGGCATCAACTGAAT 57.528 32.000 0.00 0.00 0.00 2.57
1400 5558 8.673711 CGACAAAGGATGGATTTTATTAACTCA 58.326 33.333 0.00 0.00 0.00 3.41
1401 5559 8.889717 TCGACAAAGGATGGATTTTATTAACTC 58.110 33.333 0.00 0.00 0.00 3.01
1402 5560 8.674607 GTCGACAAAGGATGGATTTTATTAACT 58.325 33.333 11.55 0.00 0.00 2.24
1403 5561 8.455682 TGTCGACAAAGGATGGATTTTATTAAC 58.544 33.333 17.62 0.00 0.00 2.01
1404 5562 8.568676 TGTCGACAAAGGATGGATTTTATTAA 57.431 30.769 17.62 0.00 0.00 1.40
1405 5563 8.620416 CATGTCGACAAAGGATGGATTTTATTA 58.380 33.333 24.13 0.00 0.00 0.98
1406 5564 7.122650 ACATGTCGACAAAGGATGGATTTTATT 59.877 33.333 24.13 0.00 0.00 1.40
1407 5565 6.603201 ACATGTCGACAAAGGATGGATTTTAT 59.397 34.615 24.13 0.00 0.00 1.40
1408 5566 5.943416 ACATGTCGACAAAGGATGGATTTTA 59.057 36.000 24.13 0.00 0.00 1.52
1409 5567 4.766891 ACATGTCGACAAAGGATGGATTTT 59.233 37.500 24.13 0.00 0.00 1.82
1410 5568 4.156556 CACATGTCGACAAAGGATGGATTT 59.843 41.667 24.13 0.00 0.00 2.17
1411 5569 3.691118 CACATGTCGACAAAGGATGGATT 59.309 43.478 24.13 0.00 0.00 3.01
1412 5570 3.273434 CACATGTCGACAAAGGATGGAT 58.727 45.455 24.13 0.00 0.00 3.41
1413 5571 2.698803 CACATGTCGACAAAGGATGGA 58.301 47.619 24.13 0.00 0.00 3.41
1414 5572 1.131126 GCACATGTCGACAAAGGATGG 59.869 52.381 24.13 10.56 0.00 3.51
1415 5573 1.201954 CGCACATGTCGACAAAGGATG 60.202 52.381 24.13 17.87 0.00 3.51
1416 5574 1.078709 CGCACATGTCGACAAAGGAT 58.921 50.000 24.13 1.85 0.00 3.24
1417 5575 0.249699 ACGCACATGTCGACAAAGGA 60.250 50.000 24.13 0.00 0.00 3.36
1418 5576 0.110688 CACGCACATGTCGACAAAGG 60.111 55.000 24.13 17.01 0.00 3.11
1419 5577 0.722469 GCACGCACATGTCGACAAAG 60.722 55.000 24.13 19.87 0.00 2.77
1420 5578 1.278337 GCACGCACATGTCGACAAA 59.722 52.632 24.13 0.00 0.00 2.83
1421 5579 1.830368 CTGCACGCACATGTCGACAA 61.830 55.000 24.13 6.23 0.00 3.18
1422 5580 2.279784 TGCACGCACATGTCGACA 60.280 55.556 22.48 22.48 0.00 4.35
1423 5581 2.471607 CTGCACGCACATGTCGAC 59.528 61.111 19.74 9.11 0.00 4.20
1424 5582 2.738139 CCTGCACGCACATGTCGA 60.738 61.111 19.74 0.00 0.00 4.20
1425 5583 3.043713 ACCTGCACGCACATGTCG 61.044 61.111 13.71 13.71 0.00 4.35
1426 5584 2.557805 CACCTGCACGCACATGTC 59.442 61.111 0.00 0.00 0.00 3.06
1427 5585 2.979676 CCACCTGCACGCACATGT 60.980 61.111 0.00 0.00 0.00 3.21
1428 5586 2.969806 GACCACCTGCACGCACATG 61.970 63.158 0.00 0.00 0.00 3.21
1429 5587 2.669569 GACCACCTGCACGCACAT 60.670 61.111 0.00 0.00 0.00 3.21
1693 5872 0.955428 CCTCTGCAAAGCCGCTGTAA 60.955 55.000 0.00 0.00 33.05 2.41
1697 5876 2.359230 GTCCTCTGCAAAGCCGCT 60.359 61.111 0.00 0.00 0.00 5.52
1728 5910 2.352686 CATACAATGCCGCAGCGC 60.353 61.111 10.07 0.00 44.31 5.92
1820 6002 1.366366 CCAGGTTCTCCGACACGTT 59.634 57.895 0.00 0.00 39.05 3.99
2129 6469 2.620242 AGTTTGTACGTTGTGTCCGTT 58.380 42.857 0.00 0.00 39.60 4.44
2209 6591 3.553508 CGACTAAAAACGGAACCCTCTCA 60.554 47.826 0.00 0.00 0.00 3.27
2246 6628 5.876357 TCTAAGCAGGACACAAACCTTAAT 58.124 37.500 0.00 0.00 35.35 1.40
2250 6632 3.857157 TTCTAAGCAGGACACAAACCT 57.143 42.857 0.00 0.00 38.40 3.50
2330 6712 2.582498 GCTAGACGCATCGCCGTT 60.582 61.111 0.00 0.00 42.24 4.44
2331 6713 3.822192 TGCTAGACGCATCGCCGT 61.822 61.111 0.00 0.00 45.47 5.68
2363 6745 2.747177 TCACCGAAGATACACCTCCAT 58.253 47.619 0.00 0.00 0.00 3.41
2373 6755 6.183360 CCAGCAAAGATAAATTCACCGAAGAT 60.183 38.462 0.00 0.00 0.00 2.40
2377 6759 4.584874 TCCAGCAAAGATAAATTCACCGA 58.415 39.130 0.00 0.00 0.00 4.69
2383 6765 6.038356 CGAGCAAATCCAGCAAAGATAAATT 58.962 36.000 0.00 0.00 0.00 1.82
2395 6777 1.202463 ACGAGATCCGAGCAAATCCAG 60.202 52.381 10.05 0.00 41.76 3.86
2430 6812 4.819105 TCCATTCCGAAGACACACTAAT 57.181 40.909 0.00 0.00 0.00 1.73
2433 6815 2.093447 GGATCCATTCCGAAGACACACT 60.093 50.000 6.95 0.00 33.93 3.55
2580 6962 0.028110 GCAAGCCTTCTTTATCGCCG 59.972 55.000 0.00 0.00 0.00 6.46
2687 7069 6.183360 CCTGCCTATTCATTTTCAATCATGGT 60.183 38.462 0.00 0.00 0.00 3.55
2724 7106 8.058915 TGTTTAATTTGATGCGCAACTTTTTAC 58.941 29.630 17.11 6.32 35.91 2.01
2725 7107 8.131455 TGTTTAATTTGATGCGCAACTTTTTA 57.869 26.923 17.11 7.77 35.91 1.52
2729 7114 5.050431 GGTTGTTTAATTTGATGCGCAACTT 60.050 36.000 17.11 4.89 35.91 2.66
2734 7119 2.344142 CCGGTTGTTTAATTTGATGCGC 59.656 45.455 0.00 0.00 0.00 6.09
2745 7130 4.370094 ACTAATTCACCCCGGTTGTTTA 57.630 40.909 0.00 0.44 0.00 2.01
2746 7131 3.232720 ACTAATTCACCCCGGTTGTTT 57.767 42.857 0.00 0.00 0.00 2.83
2754 7139 6.887626 TGTTGAACTAAACTAATTCACCCC 57.112 37.500 0.00 0.00 32.21 4.95
2779 7164 4.499188 GCTGGAAAGTAAACAAGGGTCAAC 60.499 45.833 0.00 0.00 0.00 3.18
2795 7180 1.607178 CCCAGGCACATGCTGGAAA 60.607 57.895 16.86 0.00 39.83 3.13
2796 7181 2.036098 CCCAGGCACATGCTGGAA 59.964 61.111 16.86 0.00 39.83 3.53
2798 7183 2.283388 AACCCAGGCACATGCTGG 60.283 61.111 10.11 10.11 41.70 4.85
2799 7184 1.303888 AGAACCCAGGCACATGCTG 60.304 57.895 3.48 0.56 41.70 4.41
2800 7185 1.303888 CAGAACCCAGGCACATGCT 60.304 57.895 3.48 0.00 41.70 3.79
2817 7204 4.013728 CGGGGGAAATGTAAATCTTGACA 58.986 43.478 0.00 0.00 0.00 3.58
2897 7286 6.476378 ACAGAAGGAGTAGCATACAATGTTT 58.524 36.000 0.00 0.00 46.26 2.83


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

AutoCloner maintained by Alex Coulton.