Multiple sequence alignment - TraesCS2B01G420500

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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 TraesCS2B01G420500 chr2B 100.000 6705 0 0 1 6705 602999650 602992946 0.000000e+00 12382.0
1 TraesCS2B01G420500 chr2B 94.456 469 25 1 5667 6134 539375468 539375936 0.000000e+00 721.0
2 TraesCS2B01G420500 chr2B 94.215 242 10 3 1894 2133 795859393 795859632 3.820000e-97 366.0
3 TraesCS2B01G420500 chr2B 92.903 155 10 1 3198 3352 153858223 153858376 2.430000e-54 224.0
4 TraesCS2B01G420500 chr2B 100.000 72 0 0 5565 5636 539375400 539375471 4.220000e-27 134.0
5 TraesCS2B01G420500 chr2D 95.813 2221 76 10 2337 4548 512770202 512767990 0.000000e+00 3570.0
6 TraesCS2B01G420500 chr2D 91.684 2405 107 34 1 2352 512772750 512770386 0.000000e+00 3247.0
7 TraesCS2B01G420500 chr2D 95.067 1500 62 8 4722 6219 512767173 512765684 0.000000e+00 2350.0
8 TraesCS2B01G420500 chr2D 91.467 375 19 4 1730 2101 650786838 650786474 2.790000e-138 503.0
9 TraesCS2B01G420500 chr2D 91.525 354 17 5 913 1261 650787182 650786837 6.080000e-130 475.0
10 TraesCS2B01G420500 chr2D 87.112 419 28 14 6220 6620 512765641 512765231 1.030000e-122 451.0
11 TraesCS2B01G420500 chr2D 92.131 305 16 3 913 1217 291609108 291608812 2.240000e-114 424.0
12 TraesCS2B01G420500 chr2D 93.421 228 15 0 4547 4774 512767377 512767150 8.330000e-89 339.0
13 TraesCS2B01G420500 chr2D 95.882 170 7 0 4235 4404 268894294 268894463 6.620000e-70 276.0
14 TraesCS2B01G420500 chr2D 93.590 156 10 0 1293 1448 614385151 614384996 4.040000e-57 233.0
15 TraesCS2B01G420500 chr2A 88.908 1154 71 23 9 1127 656376777 656375646 0.000000e+00 1369.0
16 TraesCS2B01G420500 chr2A 92.155 854 43 6 5368 6220 656370916 656370086 0.000000e+00 1184.0
17 TraesCS2B01G420500 chr2A 86.258 946 75 29 2276 3198 656374012 656373099 0.000000e+00 976.0
18 TraesCS2B01G420500 chr2A 91.186 590 35 12 1677 2264 656375145 656374571 0.000000e+00 785.0
19 TraesCS2B01G420500 chr2A 88.206 407 34 6 6220 6620 656370046 656369648 2.190000e-129 473.0
20 TraesCS2B01G420500 chr2A 84.369 499 61 10 3724 4212 656372596 656372105 2.190000e-129 473.0
21 TraesCS2B01G420500 chr2A 91.860 344 19 4 1243 1585 656375470 656375135 7.870000e-129 472.0
22 TraesCS2B01G420500 chr2A 86.337 344 23 14 3353 3682 656373074 656372741 2.970000e-93 353.0
23 TraesCS2B01G420500 chr2A 95.906 171 6 1 4235 4404 317953337 317953167 6.620000e-70 276.0
24 TraesCS2B01G420500 chr2A 94.083 169 10 0 4236 4404 277139427 277139595 2.400000e-64 257.0
25 TraesCS2B01G420500 chr2A 89.362 47 3 2 2284 2329 656374094 656374049 2.610000e-04 58.4
26 TraesCS2B01G420500 chr5D 94.218 588 27 5 4964 5548 24886093 24885510 0.000000e+00 891.0
27 TraesCS2B01G420500 chr5D 93.423 593 26 2 5543 6134 24884210 24883630 0.000000e+00 867.0
28 TraesCS2B01G420500 chr5D 97.059 170 5 0 4235 4404 299073582 299073413 3.060000e-73 287.0
29 TraesCS2B01G420500 chr5D 94.194 155 8 1 3198 3352 256749799 256749952 1.120000e-57 235.0
30 TraesCS2B01G420500 chr5D 92.857 126 9 0 4722 4847 24886212 24886087 4.130000e-42 183.0
31 TraesCS2B01G420500 chr5B 94.396 571 31 1 5565 6134 588654073 588654643 0.000000e+00 876.0
32 TraesCS2B01G420500 chr5B 94.231 156 7 2 3198 3352 288327809 288327655 3.130000e-58 237.0
33 TraesCS2B01G420500 chr5B 93.407 91 4 1 1586 1676 282083170 282083082 4.220000e-27 134.0
34 TraesCS2B01G420500 chr5B 93.407 91 4 1 1586 1676 527147203 527147115 4.220000e-27 134.0
35 TraesCS2B01G420500 chr5A 95.100 551 26 1 5565 6114 37985524 37984974 0.000000e+00 867.0
36 TraesCS2B01G420500 chr5A 91.875 160 12 1 3198 3357 335291589 335291431 8.750000e-54 222.0
37 TraesCS2B01G420500 chr5A 92.857 154 10 1 3198 3351 337822837 337822989 8.750000e-54 222.0
38 TraesCS2B01G420500 chr6B 94.737 551 28 1 5565 6114 581855492 581854942 0.000000e+00 856.0
39 TraesCS2B01G420500 chr6B 92.469 571 42 1 5565 6134 279575713 279576283 0.000000e+00 815.0
40 TraesCS2B01G420500 chr1B 92.294 571 29 2 5565 6134 60967619 60967063 0.000000e+00 797.0
41 TraesCS2B01G420500 chr1B 87.346 648 61 12 2303 2946 659103934 659103304 0.000000e+00 723.0
42 TraesCS2B01G420500 chr6D 87.711 651 59 12 2300 2946 322698330 322698963 0.000000e+00 739.0
43 TraesCS2B01G420500 chr6D 87.346 648 60 13 2303 2946 384195906 384195277 0.000000e+00 723.0
44 TraesCS2B01G420500 chr6D 95.333 300 5 3 918 1217 67658532 67658822 1.020000e-127 468.0
45 TraesCS2B01G420500 chr6D 92.949 156 11 0 1293 1448 384196060 384195905 1.880000e-55 228.0
46 TraesCS2B01G420500 chr6D 91.026 156 14 0 1293 1448 322698179 322698334 1.890000e-50 211.0
47 TraesCS2B01G420500 chr7A 87.500 648 60 7 2303 2946 175945256 175944626 0.000000e+00 728.0
48 TraesCS2B01G420500 chr7A 92.459 305 15 3 913 1217 675749856 675749560 4.800000e-116 429.0
49 TraesCS2B01G420500 chr7A 94.675 169 7 1 4236 4404 503442319 503442485 1.850000e-65 261.0
50 TraesCS2B01G420500 chr7A 91.667 156 11 2 3198 3353 701301359 701301512 1.460000e-51 215.0
51 TraesCS2B01G420500 chr7D 87.365 649 60 13 2303 2946 548186140 548185509 0.000000e+00 725.0
52 TraesCS2B01G420500 chr7D 94.215 242 10 3 1894 2133 37622666 37622905 3.820000e-97 366.0
53 TraesCS2B01G420500 chr7D 95.455 132 6 0 1317 1448 548186270 548186139 1.890000e-50 211.0
54 TraesCS2B01G420500 chrUn 87.250 651 62 12 2300 2946 162682759 162683392 0.000000e+00 723.0
55 TraesCS2B01G420500 chrUn 87.191 648 62 12 2303 2946 102599522 102598892 0.000000e+00 717.0
56 TraesCS2B01G420500 chrUn 91.026 156 14 0 1293 1448 162682608 162682763 1.890000e-50 211.0
57 TraesCS2B01G420500 chr4D 87.167 639 61 11 2312 2946 410095630 410096251 0.000000e+00 706.0
58 TraesCS2B01G420500 chr4D 91.304 161 12 2 3194 3353 74079508 74079349 1.130000e-52 219.0
59 TraesCS2B01G420500 chr4D 93.407 91 4 1 1586 1676 123100634 123100546 4.220000e-27 134.0
60 TraesCS2B01G420500 chr3B 91.733 375 27 3 1730 2101 88151503 88151130 9.970000e-143 518.0
61 TraesCS2B01G420500 chr3B 94.505 91 2 3 1586 1676 481394014 481393927 3.260000e-28 137.0
62 TraesCS2B01G420500 chr1D 91.200 375 25 3 1730 2101 408916843 408916474 2.790000e-138 503.0
63 TraesCS2B01G420500 chr1D 92.655 354 13 5 913 1261 408917187 408916842 1.300000e-136 497.0
64 TraesCS2B01G420500 chr1D 91.026 156 14 0 1293 1448 353181266 353181421 1.890000e-50 211.0
65 TraesCS2B01G420500 chr1D 92.857 98 5 1 1583 1680 124917472 124917567 2.520000e-29 141.0
66 TraesCS2B01G420500 chr3D 92.787 305 11 4 913 1217 21769916 21769623 1.340000e-116 431.0
67 TraesCS2B01G420500 chr3D 83.281 317 32 11 3361 3669 21768367 21768064 8.570000e-69 272.0
68 TraesCS2B01G420500 chr3D 93.478 92 2 4 1586 1677 196945482 196945395 4.220000e-27 134.0
69 TraesCS2B01G420500 chr3D 92.553 94 4 3 1583 1676 390568252 390568342 1.520000e-26 132.0
70 TraesCS2B01G420500 chr4A 92.667 300 14 3 918 1217 504676917 504676626 6.210000e-115 425.0
71 TraesCS2B01G420500 chr4A 92.045 176 14 0 4229 4404 584667609 584667434 1.440000e-61 248.0
72 TraesCS2B01G420500 chr4A 92.308 156 12 0 1293 1448 658574039 658574194 8.750000e-54 222.0
73 TraesCS2B01G420500 chr4A 94.382 89 3 1 1586 1674 648889524 648889438 1.170000e-27 135.0
74 TraesCS2B01G420500 chr6A 94.492 236 10 2 1894 2128 138421774 138422007 1.780000e-95 361.0
75 TraesCS2B01G420500 chr6A 92.975 242 15 2 1894 2133 291915189 291915430 1.070000e-92 351.0
76 TraesCS2B01G420500 chr6A 92.653 245 16 2 1894 2136 584150850 584150606 1.070000e-92 351.0
77 TraesCS2B01G420500 chr4B 94.083 169 10 0 4233 4401 206802588 206802756 2.400000e-64 257.0
78 TraesCS2B01G420500 chr4B 93.478 92 3 3 1585 1676 79415924 79415836 4.220000e-27 134.0
79 TraesCS2B01G420500 chr3A 93.491 169 11 0 4236 4404 609950958 609951126 1.120000e-62 252.0
80 TraesCS2B01G420500 chr7B 95.172 145 5 2 3209 3353 700413789 700413931 1.880000e-55 228.0
81 TraesCS2B01G420500 chr7B 93.478 92 4 1 1583 1674 231724282 231724371 1.170000e-27 135.0
82 TraesCS2B01G420500 chr7B 94.382 89 3 1 1586 1674 517318301 517318215 1.170000e-27 135.0
83 TraesCS2B01G420500 chr1A 84.500 200 20 10 3159 3356 555641073 555641263 3.190000e-43 187.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2B01G420500 chr2B 602992946 602999650 6704 True 12382.0 12382 100.000000 1 6705 1 chr2B.!!$R1 6704
1 TraesCS2B01G420500 chr2B 539375400 539375936 536 False 427.5 721 97.228000 5565 6134 2 chr2B.!!$F3 569
2 TraesCS2B01G420500 chr2D 512765231 512772750 7519 True 1991.4 3570 92.619400 1 6620 5 chr2D.!!$R3 6619
3 TraesCS2B01G420500 chr2D 650786474 650787182 708 True 489.0 503 91.496000 913 2101 2 chr2D.!!$R4 1188
4 TraesCS2B01G420500 chr2A 656369648 656376777 7129 True 682.6 1369 88.737889 9 6620 9 chr2A.!!$R2 6611
5 TraesCS2B01G420500 chr5D 24883630 24886212 2582 True 647.0 891 93.499333 4722 6134 3 chr5D.!!$R2 1412
6 TraesCS2B01G420500 chr5B 588654073 588654643 570 False 876.0 876 94.396000 5565 6134 1 chr5B.!!$F1 569
7 TraesCS2B01G420500 chr5A 37984974 37985524 550 True 867.0 867 95.100000 5565 6114 1 chr5A.!!$R1 549
8 TraesCS2B01G420500 chr6B 581854942 581855492 550 True 856.0 856 94.737000 5565 6114 1 chr6B.!!$R1 549
9 TraesCS2B01G420500 chr6B 279575713 279576283 570 False 815.0 815 92.469000 5565 6134 1 chr6B.!!$F1 569
10 TraesCS2B01G420500 chr1B 60967063 60967619 556 True 797.0 797 92.294000 5565 6134 1 chr1B.!!$R1 569
11 TraesCS2B01G420500 chr1B 659103304 659103934 630 True 723.0 723 87.346000 2303 2946 1 chr1B.!!$R2 643
12 TraesCS2B01G420500 chr6D 384195277 384196060 783 True 475.5 723 90.147500 1293 2946 2 chr6D.!!$R1 1653
13 TraesCS2B01G420500 chr6D 322698179 322698963 784 False 475.0 739 89.368500 1293 2946 2 chr6D.!!$F2 1653
14 TraesCS2B01G420500 chr7A 175944626 175945256 630 True 728.0 728 87.500000 2303 2946 1 chr7A.!!$R1 643
15 TraesCS2B01G420500 chr7D 548185509 548186270 761 True 468.0 725 91.410000 1317 2946 2 chr7D.!!$R1 1629
16 TraesCS2B01G420500 chrUn 102598892 102599522 630 True 717.0 717 87.191000 2303 2946 1 chrUn.!!$R1 643
17 TraesCS2B01G420500 chrUn 162682608 162683392 784 False 467.0 723 89.138000 1293 2946 2 chrUn.!!$F1 1653
18 TraesCS2B01G420500 chr4D 410095630 410096251 621 False 706.0 706 87.167000 2312 2946 1 chr4D.!!$F1 634
19 TraesCS2B01G420500 chr1D 408916474 408917187 713 True 500.0 503 91.927500 913 2101 2 chr1D.!!$R1 1188
20 TraesCS2B01G420500 chr3D 21768064 21769916 1852 True 351.5 431 88.034000 913 3669 2 chr3D.!!$R2 2756

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
341 348 0.830648 TATTCTTCGAGGGGGCACAG 59.169 55.0 0.00 0.0 0.00 3.66 F
1429 1996 0.319986 TTGCTACGACGCATTCACCA 60.320 50.0 0.00 0.0 40.04 4.17 F
1431 1998 1.006832 GCTACGACGCATTCACCAAT 58.993 50.0 0.00 0.0 0.00 3.16 F
3402 4747 0.179145 GCTGTGATCATGCTTGTGGC 60.179 55.0 14.02 1.5 42.22 5.01 F
4307 5894 0.249398 CGGGTTCGAGTCCTGGAAAT 59.751 55.0 0.00 0.0 39.00 2.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1646 2216 0.111639 AAGGCTTTCACCCCGCTTTA 59.888 50.000 0.00 0.00 0.00 1.85 R
3402 4747 0.029834 GTTGCTTGCTCACACACCAG 59.970 55.000 0.00 0.00 0.00 4.00 R
3455 4805 2.218953 TTCTAGCGAATTACAGGCCG 57.781 50.000 0.00 0.00 0.00 6.13 R
4904 7159 1.000731 GCAACATTAAGCCCAACAGCA 59.999 47.619 0.00 0.00 34.23 4.41 R
5713 9372 0.043334 AGTGCTGTCTACCCTGGGAT 59.957 55.000 22.23 6.39 0.00 3.85 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
59 60 1.616865 CACGAAAGAGACCACTACCCA 59.383 52.381 0.00 0.00 0.00 4.51
72 73 8.339720 AGACCACTACCCATACCATAAATTTA 57.660 34.615 0.00 0.00 0.00 1.40
163 167 1.730501 TCGTCCGTCGAACATACTCT 58.269 50.000 0.00 0.00 45.98 3.24
168 172 1.003759 CCGTCGAACATACTCTCTCGG 60.004 57.143 0.00 0.00 32.25 4.63
183 187 5.181622 ACTCTCTCGGCGTCTTATATTTAGG 59.818 44.000 6.85 0.00 0.00 2.69
186 190 6.263842 TCTCTCGGCGTCTTATATTTAGGAAA 59.736 38.462 6.85 0.00 0.00 3.13
190 194 5.987347 CGGCGTCTTATATTTAGGAAAGGAA 59.013 40.000 0.00 0.00 0.00 3.36
194 198 9.106070 GCGTCTTATATTTAGGAAAGGAAGAAA 57.894 33.333 0.00 0.00 0.00 2.52
223 227 1.160137 GCAGCTCGATTTGTGGAGTT 58.840 50.000 0.00 0.00 32.83 3.01
228 232 2.287547 GCTCGATTTGTGGAGTTGCAAA 60.288 45.455 0.00 0.00 38.68 3.68
241 245 1.731720 TTGCAAACAAAACACAGGCC 58.268 45.000 0.00 0.00 31.21 5.19
291 295 4.353191 AGAATCATTCCAGCCACCATAGAT 59.647 41.667 0.00 0.00 0.00 1.98
293 297 6.217074 AGAATCATTCCAGCCACCATAGATAT 59.783 38.462 0.00 0.00 0.00 1.63
339 346 1.694696 AGATATTCTTCGAGGGGGCAC 59.305 52.381 0.00 0.00 0.00 5.01
340 347 1.416401 GATATTCTTCGAGGGGGCACA 59.584 52.381 0.00 0.00 0.00 4.57
341 348 0.830648 TATTCTTCGAGGGGGCACAG 59.169 55.000 0.00 0.00 0.00 3.66
342 349 0.909610 ATTCTTCGAGGGGGCACAGA 60.910 55.000 0.00 0.00 0.00 3.41
374 384 1.332028 CGAGCACTGAAAACGACACAC 60.332 52.381 0.00 0.00 0.00 3.82
405 418 5.745227 TCCAATAAACAGGAGTGAGAATCC 58.255 41.667 0.00 0.00 37.07 3.01
409 422 3.971245 AACAGGAGTGAGAATCCAGAC 57.029 47.619 0.00 0.00 39.47 3.51
418 431 5.026121 AGTGAGAATCCAGACCATCTTACA 58.974 41.667 0.00 0.00 32.58 2.41
419 432 5.485353 AGTGAGAATCCAGACCATCTTACAA 59.515 40.000 0.00 0.00 32.58 2.41
420 433 5.814705 GTGAGAATCCAGACCATCTTACAAG 59.185 44.000 0.00 0.00 31.07 3.16
421 434 5.485353 TGAGAATCCAGACCATCTTACAAGT 59.515 40.000 0.00 0.00 0.00 3.16
475 488 3.132111 ACAAGAACATCCCAACCAACAAC 59.868 43.478 0.00 0.00 0.00 3.32
482 495 1.036707 CCCAACCAACAACCGAACAT 58.963 50.000 0.00 0.00 0.00 2.71
501 514 6.530019 AACATAATCCAACCAGAACATTCC 57.470 37.500 0.00 0.00 0.00 3.01
526 540 5.119694 TCCCCCAAAAAGAAAACAAATTCG 58.880 37.500 0.00 0.00 34.46 3.34
568 583 2.097680 TACGGCCGGGTAAAGAAAAG 57.902 50.000 31.76 0.00 0.00 2.27
574 589 4.053295 GGCCGGGTAAAGAAAAGAAAAAC 58.947 43.478 2.18 0.00 0.00 2.43
592 607 2.980246 ACCCAAAGAAAGGAGGAAGG 57.020 50.000 0.00 0.00 0.00 3.46
595 610 2.376855 CCCAAAGAAAGGAGGAAGGAGT 59.623 50.000 0.00 0.00 0.00 3.85
597 612 4.565861 CCCAAAGAAAGGAGGAAGGAGTAC 60.566 50.000 0.00 0.00 0.00 2.73
598 613 4.287326 CCAAAGAAAGGAGGAAGGAGTACT 59.713 45.833 0.00 0.00 0.00 2.73
818 865 1.306226 GCTGACCTACCCTCACCCT 60.306 63.158 0.00 0.00 0.00 4.34
819 866 1.331399 GCTGACCTACCCTCACCCTC 61.331 65.000 0.00 0.00 0.00 4.30
1218 1275 2.367512 CCTCCCCTCCCTCCCTTG 60.368 72.222 0.00 0.00 0.00 3.61
1282 1396 2.522436 TGCTTGCTTGGCTTGGCT 60.522 55.556 0.00 0.00 0.00 4.75
1284 1398 1.666872 GCTTGCTTGGCTTGGCTTG 60.667 57.895 0.00 0.00 0.00 4.01
1286 1400 3.167822 TTGCTTGGCTTGGCTTGGC 62.168 57.895 0.00 0.00 0.00 4.52
1332 1446 3.243839 TGCGGTTCGAGTTAGTTTACCTT 60.244 43.478 0.00 0.00 0.00 3.50
1426 1993 2.482336 ACAAATTGCTACGACGCATTCA 59.518 40.909 0.00 0.00 40.04 2.57
1429 1996 0.319986 TTGCTACGACGCATTCACCA 60.320 50.000 0.00 0.00 40.04 4.17
1431 1998 1.006832 GCTACGACGCATTCACCAAT 58.993 50.000 0.00 0.00 0.00 3.16
1445 2013 4.853468 TCACCAATCCTGCCAACTAATA 57.147 40.909 0.00 0.00 0.00 0.98
1446 2014 5.186256 TCACCAATCCTGCCAACTAATAA 57.814 39.130 0.00 0.00 0.00 1.40
1447 2015 5.575157 TCACCAATCCTGCCAACTAATAAA 58.425 37.500 0.00 0.00 0.00 1.40
1448 2016 6.194235 TCACCAATCCTGCCAACTAATAAAT 58.806 36.000 0.00 0.00 0.00 1.40
1449 2017 6.667414 TCACCAATCCTGCCAACTAATAAATT 59.333 34.615 0.00 0.00 0.00 1.82
1680 2250 2.148768 AGCCTTTTTCGGTAAACCTCG 58.851 47.619 0.00 0.00 0.00 4.63
1795 2365 5.048782 TGTTGTTATGTCTTGCATGTTCCTC 60.049 40.000 0.00 0.00 38.47 3.71
1814 2384 7.069578 TGTTCCTCCCTTATGAGTATACAGAAC 59.930 40.741 5.50 0.00 31.94 3.01
1863 2435 9.559732 TTGATGTCTCATTTCTACTCTCAAAAA 57.440 29.630 0.00 0.00 0.00 1.94
1879 2451 9.598517 ACTCTCAAAAATGTTGAAATAGCAAAA 57.401 25.926 0.00 0.00 0.00 2.44
2224 2799 4.104102 TGGAGCAGGAGGAAAGACTAAAAA 59.896 41.667 0.00 0.00 0.00 1.94
2286 3408 3.493334 CAGGGTATGCATTGTCATGGAT 58.507 45.455 3.54 0.00 43.47 3.41
2377 3698 6.959311 GCTTGCATTTAATCATTCTTTTGCTG 59.041 34.615 0.00 0.00 0.00 4.41
2425 3746 4.741321 AATGTAGTGGCAAAATCCATGG 57.259 40.909 4.97 4.97 38.57 3.66
2428 3749 3.763360 TGTAGTGGCAAAATCCATGGAAG 59.237 43.478 20.67 10.34 38.57 3.46
2471 3792 3.444034 GCAGTTCTATTTTCCCCAACCTC 59.556 47.826 0.00 0.00 0.00 3.85
2540 3866 6.964807 ATTGTGAAGCATGCCATCTATTTA 57.035 33.333 15.66 0.00 0.00 1.40
2541 3867 6.964807 TTGTGAAGCATGCCATCTATTTAT 57.035 33.333 15.66 0.00 0.00 1.40
2542 3868 6.564709 TGTGAAGCATGCCATCTATTTATC 57.435 37.500 15.66 0.00 0.00 1.75
2957 4302 7.118680 GGATTGGGCATTGCTTTGAATATAATG 59.881 37.037 8.82 0.00 33.18 1.90
3143 4488 1.825090 TCTTCGTGGCTTCATGCATT 58.175 45.000 0.00 0.00 45.15 3.56
3254 4599 9.869757 TGGATATTTCAATATGGACTACATACG 57.130 33.333 0.00 0.00 44.41 3.06
3260 4605 6.066032 TCAATATGGACTACATACGGACTGA 58.934 40.000 0.00 0.00 44.41 3.41
3269 4614 3.861840 ACATACGGACTGAAATGAGTGG 58.138 45.455 7.93 0.00 0.00 4.00
3310 4655 6.552629 GCGTCTATATACATCCGATTCAGAA 58.447 40.000 0.00 0.00 0.00 3.02
3402 4747 0.179145 GCTGTGATCATGCTTGTGGC 60.179 55.000 14.02 1.50 42.22 5.01
3811 5280 8.959548 TCATGACTTTAATGATTTGTGTATGCT 58.040 29.630 0.00 0.00 0.00 3.79
3821 5290 6.497437 TGATTTGTGTATGCTGCATGTTATC 58.503 36.000 24.59 16.45 0.00 1.75
3825 5294 7.565323 TTGTGTATGCTGCATGTTATCATTA 57.435 32.000 24.59 0.00 31.15 1.90
3836 5305 8.846943 TGCATGTTATCATTATAGGACGAATT 57.153 30.769 0.00 0.00 31.15 2.17
4033 5509 2.628178 TGCGCTCATATAGGCTAACAGT 59.372 45.455 9.73 0.00 0.00 3.55
4121 5598 6.481976 TGATAAATATTAACGGTCTGCACCAG 59.518 38.462 0.00 0.00 44.02 4.00
4182 5662 7.228308 GCCTGCTAATTTGTATCTCTTGAAGAT 59.772 37.037 0.00 0.00 46.70 2.40
4307 5894 0.249398 CGGGTTCGAGTCCTGGAAAT 59.751 55.000 0.00 0.00 39.00 2.17
4349 5936 3.552478 GGGAAAGGCTGCGTACTATAGAC 60.552 52.174 6.78 0.00 0.00 2.59
4375 5962 4.681978 GTCGGACCCTGCGCAAGT 62.682 66.667 13.05 12.57 41.68 3.16
4384 5971 2.047274 TGCGCAAGTGGGAGCTAC 60.047 61.111 8.16 0.00 41.68 3.58
4408 5995 2.750237 CGGGCTGCCCTTTGGTAC 60.750 66.667 33.39 6.69 42.67 3.34
4477 6064 2.907910 TCTCCTAAACGTCGCTACAC 57.092 50.000 0.00 0.00 0.00 2.90
4528 6115 2.859165 TCGTTGCCCAGAATTTCTCT 57.141 45.000 0.00 0.00 33.23 3.10
4540 6127 6.808008 CAGAATTTCTCTGTTAGGCAAGAA 57.192 37.500 0.00 0.00 45.76 2.52
4562 6763 3.315191 ACCCAGAAGAATGTGTGAAAACG 59.685 43.478 0.00 0.00 0.00 3.60
4582 6783 2.050836 TTTTGGACCTGGAGCGAGCA 62.051 55.000 0.00 0.00 0.00 4.26
4591 6792 1.293498 GGAGCGAGCAAGAGTCCAA 59.707 57.895 0.00 0.00 0.00 3.53
4601 6802 2.499289 GCAAGAGTCCAATGGAGAGAGA 59.501 50.000 0.27 0.00 29.39 3.10
4679 6880 3.194308 GCTTGAGCTCGCTGAGGC 61.194 66.667 9.64 0.00 38.21 4.70
4717 6918 3.851128 GGGAGCGGAGGTAGGTGC 61.851 72.222 0.00 0.00 39.88 5.01
4718 6919 3.075005 GGAGCGGAGGTAGGTGCA 61.075 66.667 0.00 0.00 39.88 4.57
4720 6921 2.037367 AGCGGAGGTAGGTGCAGA 59.963 61.111 0.00 0.00 35.08 4.26
4749 6979 1.724545 TGGGAAAGAGAAGGTTCGGA 58.275 50.000 0.00 0.00 0.00 4.55
4790 7020 2.925706 TGGTAAGGGCGGTGCAGA 60.926 61.111 0.00 0.00 0.00 4.26
4825 7055 2.279784 GATTGAGCTAGGCGCGCT 60.280 61.111 32.29 19.12 45.59 5.92
4852 7082 1.408969 GGAGCTGGGTTAGAGAGAGG 58.591 60.000 0.00 0.00 0.00 3.69
4860 7090 3.532232 TGGGTTAGAGAGAGGTAGGATGT 59.468 47.826 0.00 0.00 0.00 3.06
4904 7159 6.183361 GGTTAGTGTTGGGTCATATAGTCCAT 60.183 42.308 0.00 0.00 0.00 3.41
4989 7244 4.065088 GGAATTTGCTGCCGTATGAGATA 58.935 43.478 0.00 0.00 0.00 1.98
5046 7309 2.394930 ATTAATTTTGCCCAACGCCC 57.605 45.000 0.00 0.00 36.24 6.13
5081 7344 2.202932 CCCTGGGCTCGACGAATG 60.203 66.667 0.00 0.00 0.00 2.67
5213 7495 1.737838 TGTTCGGCAGGCTTCTAATG 58.262 50.000 0.00 0.00 0.00 1.90
5218 7500 1.812571 CGGCAGGCTTCTAATGTTTGT 59.187 47.619 0.00 0.00 0.00 2.83
5366 7719 6.430000 AGAAGCTAAACCGTGAATTGTATGTT 59.570 34.615 0.00 0.00 0.00 2.71
5460 7814 9.146984 CTTGTCTGAACGTAAATACATCCTTTA 57.853 33.333 0.00 0.00 0.00 1.85
5647 9306 2.135933 GCAGTCACAGTACTGGTTGTC 58.864 52.381 26.12 13.81 45.75 3.18
5872 9531 2.038557 AGAGAAACGCTAAAAGGCCTGA 59.961 45.455 5.69 0.00 0.00 3.86
5891 9550 4.376615 CCTGAAAAATGATGCTGTTTTGCG 60.377 41.667 0.00 0.00 35.36 4.85
5989 9650 0.034059 ACAGTTTCTCCGTGCCTGAG 59.966 55.000 0.00 0.00 0.00 3.35
5999 9661 1.164041 CGTGCCTGAGGTTTTCCGTT 61.164 55.000 0.00 0.00 46.35 4.44
6010 9672 2.616256 GGTTTTCCGTTCTATTCCCCGT 60.616 50.000 0.00 0.00 0.00 5.28
6088 9750 4.683334 GTCGTGCGCAAACCTGCC 62.683 66.667 14.00 0.00 46.56 4.85
6135 9797 0.106708 TGTGCAGTGAGACCCAGAAC 59.893 55.000 0.00 0.00 0.00 3.01
6179 9841 3.256631 TGCCCTTCTCTTCTGAAATTTGC 59.743 43.478 0.00 0.00 0.00 3.68
6199 9861 4.604156 TGCATGGGAAATGGTTGTGTATA 58.396 39.130 0.00 0.00 0.00 1.47
6377 10084 6.252036 GTGTCGTCACTTATTTACCATACG 57.748 41.667 5.50 0.00 40.98 3.06
6383 10090 6.237996 CGTCACTTATTTACCATACGCACATT 60.238 38.462 0.00 0.00 0.00 2.71
6385 10092 6.819146 TCACTTATTTACCATACGCACATTCA 59.181 34.615 0.00 0.00 0.00 2.57
6481 10188 5.466127 TTTATTAGAGGCCATGGAAGGTT 57.534 39.130 18.40 0.00 0.00 3.50
6490 10197 2.630580 GCCATGGAAGGTTAAACAACCA 59.369 45.455 18.40 10.31 45.23 3.67
6509 10222 3.674997 CCAGTTTGGTACTATGCACACT 58.325 45.455 0.00 0.00 34.56 3.55
6513 10226 4.997395 AGTTTGGTACTATGCACACTCTTG 59.003 41.667 0.00 0.00 34.56 3.02
6521 10234 5.853936 ACTATGCACACTCTTGACTTGTTA 58.146 37.500 0.00 0.00 0.00 2.41
6528 10241 5.119279 CACACTCTTGACTTGTTATCCTTCG 59.881 44.000 0.00 0.00 0.00 3.79
6529 10242 5.221461 ACACTCTTGACTTGTTATCCTTCGT 60.221 40.000 0.00 0.00 0.00 3.85
6530 10243 5.696724 CACTCTTGACTTGTTATCCTTCGTT 59.303 40.000 0.00 0.00 0.00 3.85
6535 10248 6.780706 TGACTTGTTATCCTTCGTTTCTTC 57.219 37.500 0.00 0.00 0.00 2.87
6536 10249 5.699458 TGACTTGTTATCCTTCGTTTCTTCC 59.301 40.000 0.00 0.00 0.00 3.46
6551 10273 1.148310 CTTCCGTTGAGTGCGAATGT 58.852 50.000 0.00 0.00 0.00 2.71
6564 10286 2.425989 CGAATGTTCGTCACAGATGC 57.574 50.000 6.97 0.00 45.09 3.91
6565 10287 1.726248 CGAATGTTCGTCACAGATGCA 59.274 47.619 6.97 0.00 45.09 3.96
6566 10288 2.222663 CGAATGTTCGTCACAGATGCAG 60.223 50.000 6.97 0.00 45.09 4.41
6567 10289 2.749280 ATGTTCGTCACAGATGCAGA 57.251 45.000 0.00 0.00 39.40 4.26
6568 10290 2.749280 TGTTCGTCACAGATGCAGAT 57.251 45.000 0.00 0.00 0.00 2.90
6608 10331 1.021390 CAACCTCAGCATGGTCCGTC 61.021 60.000 0.00 0.00 36.69 4.79
6611 10334 2.994995 TCAGCATGGTCCGTCCGT 60.995 61.111 0.00 0.00 39.52 4.69
6612 10335 2.509336 CAGCATGGTCCGTCCGTC 60.509 66.667 0.00 0.00 39.52 4.79
6641 10364 3.001870 GCGAGCTAGCTTGCTTCG 58.998 61.111 38.79 28.00 46.92 3.79
6642 10365 1.807573 GCGAGCTAGCTTGCTTCGT 60.808 57.895 38.79 9.11 46.92 3.85
6643 10366 1.994467 CGAGCTAGCTTGCTTCGTG 59.006 57.895 23.44 10.50 44.17 4.35
6644 10367 0.456824 CGAGCTAGCTTGCTTCGTGA 60.457 55.000 23.44 0.00 44.17 4.35
6645 10368 0.995728 GAGCTAGCTTGCTTCGTGAC 59.004 55.000 23.44 6.33 44.17 3.67
6646 10369 0.734253 AGCTAGCTTGCTTCGTGACG 60.734 55.000 17.30 0.00 40.93 4.35
6647 10370 0.732880 GCTAGCTTGCTTCGTGACGA 60.733 55.000 13.17 2.39 0.00 4.20
6648 10371 1.698165 CTAGCTTGCTTCGTGACGAA 58.302 50.000 19.97 19.97 43.75 3.85
6657 10380 1.860676 TTCGTGACGAAGGAAAGTGG 58.139 50.000 17.28 0.00 41.05 4.00
6658 10381 0.599204 TCGTGACGAAGGAAAGTGGC 60.599 55.000 4.69 0.00 31.06 5.01
6659 10382 1.860078 GTGACGAAGGAAAGTGGCG 59.140 57.895 0.00 0.00 0.00 5.69
6660 10383 0.599204 GTGACGAAGGAAAGTGGCGA 60.599 55.000 0.00 0.00 0.00 5.54
6661 10384 0.320374 TGACGAAGGAAAGTGGCGAT 59.680 50.000 0.00 0.00 0.00 4.58
6662 10385 0.721718 GACGAAGGAAAGTGGCGATG 59.278 55.000 0.00 0.00 0.00 3.84
6663 10386 1.298859 ACGAAGGAAAGTGGCGATGC 61.299 55.000 0.00 0.00 0.00 3.91
6674 10397 3.474570 GCGATGCCAGGACTCCCT 61.475 66.667 0.00 0.00 45.74 4.20
6675 10398 2.818132 CGATGCCAGGACTCCCTC 59.182 66.667 0.00 0.00 42.02 4.30
6676 10399 1.760086 CGATGCCAGGACTCCCTCT 60.760 63.158 0.00 0.00 42.02 3.69
6677 10400 1.333636 CGATGCCAGGACTCCCTCTT 61.334 60.000 0.00 0.00 42.02 2.85
6678 10401 0.467804 GATGCCAGGACTCCCTCTTC 59.532 60.000 0.00 0.00 42.02 2.87
6679 10402 0.252881 ATGCCAGGACTCCCTCTTCA 60.253 55.000 0.00 0.00 42.02 3.02
6680 10403 0.906756 TGCCAGGACTCCCTCTTCAG 60.907 60.000 0.00 0.00 42.02 3.02
6681 10404 0.907230 GCCAGGACTCCCTCTTCAGT 60.907 60.000 0.00 0.00 42.02 3.41
6682 10405 1.190643 CCAGGACTCCCTCTTCAGTC 58.809 60.000 0.00 0.00 42.02 3.51
6683 10406 1.551099 CCAGGACTCCCTCTTCAGTCA 60.551 57.143 1.76 0.00 42.02 3.41
6684 10407 2.251818 CAGGACTCCCTCTTCAGTCAA 58.748 52.381 1.76 0.00 42.02 3.18
6685 10408 2.233431 CAGGACTCCCTCTTCAGTCAAG 59.767 54.545 1.76 0.00 42.02 3.02
6686 10409 1.066502 GGACTCCCTCTTCAGTCAAGC 60.067 57.143 1.76 0.00 40.85 4.01
6687 10410 0.980423 ACTCCCTCTTCAGTCAAGCC 59.020 55.000 0.00 0.00 31.26 4.35
6688 10411 0.979665 CTCCCTCTTCAGTCAAGCCA 59.020 55.000 0.00 0.00 31.26 4.75
6689 10412 0.687354 TCCCTCTTCAGTCAAGCCAC 59.313 55.000 0.00 0.00 31.26 5.01
6690 10413 0.397941 CCCTCTTCAGTCAAGCCACA 59.602 55.000 0.00 0.00 31.26 4.17
6691 10414 1.610102 CCCTCTTCAGTCAAGCCACAG 60.610 57.143 0.00 0.00 31.26 3.66
6692 10415 1.071385 CCTCTTCAGTCAAGCCACAGT 59.929 52.381 0.00 0.00 31.26 3.55
6693 10416 2.486191 CCTCTTCAGTCAAGCCACAGTT 60.486 50.000 0.00 0.00 31.26 3.16
6694 10417 2.805099 CTCTTCAGTCAAGCCACAGTTC 59.195 50.000 0.00 0.00 31.26 3.01
6695 10418 1.876156 CTTCAGTCAAGCCACAGTTCC 59.124 52.381 0.00 0.00 0.00 3.62
6696 10419 0.836606 TCAGTCAAGCCACAGTTCCA 59.163 50.000 0.00 0.00 0.00 3.53
6697 10420 1.202687 TCAGTCAAGCCACAGTTCCAG 60.203 52.381 0.00 0.00 0.00 3.86
6698 10421 0.536006 AGTCAAGCCACAGTTCCAGC 60.536 55.000 0.00 0.00 0.00 4.85
6699 10422 1.597854 TCAAGCCACAGTTCCAGCG 60.598 57.895 0.00 0.00 0.00 5.18
6700 10423 1.893808 CAAGCCACAGTTCCAGCGT 60.894 57.895 0.00 0.00 0.00 5.07
6701 10424 0.602638 CAAGCCACAGTTCCAGCGTA 60.603 55.000 0.00 0.00 0.00 4.42
6702 10425 0.602905 AAGCCACAGTTCCAGCGTAC 60.603 55.000 0.00 0.00 0.00 3.67
6703 10426 2.033194 GCCACAGTTCCAGCGTACC 61.033 63.158 0.00 0.00 0.00 3.34
6704 10427 1.369692 CCACAGTTCCAGCGTACCA 59.630 57.895 0.00 0.00 0.00 3.25
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
99 100 4.342378 GGAAAATTTCCCCTTCTCCATAGC 59.658 45.833 13.61 0.00 44.30 2.97
163 167 6.395426 TTTCCTAAATATAAGACGCCGAGA 57.605 37.500 0.00 0.00 0.00 4.04
168 172 8.658499 TTCTTCCTTTCCTAAATATAAGACGC 57.342 34.615 0.00 0.00 0.00 5.19
186 190 8.150945 TCGAGCTGCTAAATAATATTTCTTCCT 58.849 33.333 0.15 0.00 0.00 3.36
194 198 7.661437 TCCACAAATCGAGCTGCTAAATAATAT 59.339 33.333 0.15 0.00 0.00 1.28
223 227 0.107945 GGGCCTGTGTTTTGTTTGCA 60.108 50.000 0.84 0.00 0.00 4.08
228 232 1.756561 AAGCGGGCCTGTGTTTTGT 60.757 52.632 14.55 0.00 0.00 2.83
241 245 7.201530 GCTTAATATAATACTAGTGCCAAGCGG 60.202 40.741 5.39 0.00 0.00 5.52
303 307 2.138535 ATCTATGATTCCTGCCCCCA 57.861 50.000 0.00 0.00 0.00 4.96
304 308 4.476479 AGAATATCTATGATTCCTGCCCCC 59.524 45.833 0.00 0.00 34.42 5.40
305 309 5.707066 AGAATATCTATGATTCCTGCCCC 57.293 43.478 0.00 0.00 34.42 5.80
306 310 5.814705 CGAAGAATATCTATGATTCCTGCCC 59.185 44.000 0.00 0.00 34.42 5.36
307 311 6.634805 TCGAAGAATATCTATGATTCCTGCC 58.365 40.000 0.00 0.00 34.42 4.85
310 317 6.382570 CCCCTCGAAGAATATCTATGATTCCT 59.617 42.308 0.00 0.00 34.42 3.36
315 322 3.769844 GCCCCCTCGAAGAATATCTATGA 59.230 47.826 0.00 0.00 34.09 2.15
339 346 2.094894 GTGCTCGGTGATGTTCATTCTG 59.905 50.000 0.00 0.00 0.00 3.02
340 347 2.027745 AGTGCTCGGTGATGTTCATTCT 60.028 45.455 0.00 0.00 0.00 2.40
341 348 2.094894 CAGTGCTCGGTGATGTTCATTC 59.905 50.000 0.00 0.00 0.00 2.67
342 349 2.079158 CAGTGCTCGGTGATGTTCATT 58.921 47.619 0.00 0.00 0.00 2.57
405 418 6.253727 CGCTAACTTACTTGTAAGATGGTCTG 59.746 42.308 22.59 7.67 0.00 3.51
409 422 4.868171 TGCGCTAACTTACTTGTAAGATGG 59.132 41.667 22.59 15.47 0.00 3.51
475 488 4.006989 TGTTCTGGTTGGATTATGTTCGG 58.993 43.478 0.00 0.00 0.00 4.30
482 495 4.325030 GGAGGGAATGTTCTGGTTGGATTA 60.325 45.833 0.00 0.00 0.00 1.75
501 514 4.495690 TTTGTTTTCTTTTTGGGGGAGG 57.504 40.909 0.00 0.00 0.00 4.30
568 583 5.453339 CCTTCCTCCTTTCTTTGGGTTTTTC 60.453 44.000 0.00 0.00 0.00 2.29
574 589 2.376855 ACTCCTTCCTCCTTTCTTTGGG 59.623 50.000 0.00 0.00 0.00 4.12
846 893 0.035343 GTAGGAGGGCCTGGTTTGTC 60.035 60.000 12.95 0.00 46.45 3.18
1332 1446 1.207339 CGCACGAAGCAAGCAATCA 59.793 52.632 0.00 0.00 46.13 2.57
1426 1993 7.494922 AAATTTATTAGTTGGCAGGATTGGT 57.505 32.000 0.00 0.00 0.00 3.67
1429 1996 7.823799 CACCAAAATTTATTAGTTGGCAGGATT 59.176 33.333 4.56 0.00 43.62 3.01
1431 1998 6.696411 CACCAAAATTTATTAGTTGGCAGGA 58.304 36.000 4.56 0.00 43.62 3.86
1445 2013 6.165577 CAAGCCAATACTAGCACCAAAATTT 58.834 36.000 0.00 0.00 0.00 1.82
1446 2014 5.337491 CCAAGCCAATACTAGCACCAAAATT 60.337 40.000 0.00 0.00 0.00 1.82
1447 2015 4.160252 CCAAGCCAATACTAGCACCAAAAT 59.840 41.667 0.00 0.00 0.00 1.82
1448 2016 3.509575 CCAAGCCAATACTAGCACCAAAA 59.490 43.478 0.00 0.00 0.00 2.44
1449 2017 3.088532 CCAAGCCAATACTAGCACCAAA 58.911 45.455 0.00 0.00 0.00 3.28
1646 2216 0.111639 AAGGCTTTCACCCCGCTTTA 59.888 50.000 0.00 0.00 0.00 1.85
1647 2217 0.759060 AAAGGCTTTCACCCCGCTTT 60.759 50.000 6.68 0.00 0.00 3.51
1656 2226 3.955551 AGGTTTACCGAAAAAGGCTTTCA 59.044 39.130 13.76 0.00 42.08 2.69
1680 2250 1.009829 CTGAAATGCAGGCTACCGTC 58.990 55.000 0.00 0.00 41.07 4.79
1814 2384 8.363390 TCAATCCTTGCTAGTGATACTTATCTG 58.637 37.037 0.00 0.00 33.88 2.90
1854 2426 9.853921 GTTTTGCTATTTCAACATTTTTGAGAG 57.146 29.630 0.00 0.00 0.00 3.20
1855 2427 9.376075 TGTTTTGCTATTTCAACATTTTTGAGA 57.624 25.926 0.00 0.00 0.00 3.27
1879 2451 1.494721 CCAACAGGGGCATACCTATGT 59.505 52.381 0.00 0.00 39.34 2.29
2224 2799 2.485426 CACAACGCATCACCTCTGAATT 59.515 45.455 0.00 0.00 0.00 2.17
2399 3720 7.867403 CCATGGATTTTGCCACTACATTATTAC 59.133 37.037 5.56 0.00 41.56 1.89
2425 3746 6.620089 GCGGTATTTCACTACCAGAAAACTTC 60.620 42.308 1.59 0.00 41.12 3.01
2428 3749 4.453136 TGCGGTATTTCACTACCAGAAAAC 59.547 41.667 1.59 0.00 41.12 2.43
2508 3830 6.741109 TGGCATGCTTCACAATATAATCTTG 58.259 36.000 18.92 0.00 0.00 3.02
2529 3851 8.677300 TGACAACAGAAAAGATAAATAGATGGC 58.323 33.333 0.00 0.00 0.00 4.40
2540 3866 8.242729 AGGAAAGAAATGACAACAGAAAAGAT 57.757 30.769 0.00 0.00 0.00 2.40
2541 3867 7.645058 AGGAAAGAAATGACAACAGAAAAGA 57.355 32.000 0.00 0.00 0.00 2.52
2542 3868 9.971922 ATTAGGAAAGAAATGACAACAGAAAAG 57.028 29.630 0.00 0.00 0.00 2.27
2758 4084 2.094026 GCCCCCAAAAGCAGTATTGAAG 60.094 50.000 0.00 0.00 0.00 3.02
2862 4191 8.743099 GTTACTAACAAGTGATCTTTGCAAAAC 58.257 33.333 13.84 8.43 0.00 2.43
2957 4302 2.932498 TGATGTCGCTTGCACAAAATC 58.068 42.857 0.00 0.00 0.00 2.17
3254 4599 3.882888 TGTTTGTCCACTCATTTCAGTCC 59.117 43.478 0.00 0.00 0.00 3.85
3260 4605 7.221838 CGTTTTAATGTGTTTGTCCACTCATTT 59.778 33.333 6.47 0.00 40.01 2.32
3269 4614 4.276460 AGACGCGTTTTAATGTGTTTGTC 58.724 39.130 15.53 0.00 38.65 3.18
3402 4747 0.029834 GTTGCTTGCTCACACACCAG 59.970 55.000 0.00 0.00 0.00 4.00
3455 4805 2.218953 TTCTAGCGAATTACAGGCCG 57.781 50.000 0.00 0.00 0.00 6.13
3596 4959 7.596494 AGACACAACATACTGGATTTTGATTG 58.404 34.615 5.79 0.00 30.94 2.67
3799 5268 6.453926 TGATAACATGCAGCATACACAAAT 57.546 33.333 7.82 0.00 0.00 2.32
3807 5276 6.314648 CGTCCTATAATGATAACATGCAGCAT 59.685 38.462 0.52 0.52 36.79 3.79
3811 5280 8.846943 AATTCGTCCTATAATGATAACATGCA 57.153 30.769 0.00 0.00 36.79 3.96
3881 5350 5.941948 TCTGCAAGGAGCTAAGTAAAAAC 57.058 39.130 0.00 0.00 45.94 2.43
4033 5509 4.836175 TCCTTAACAGACCGATATGGCATA 59.164 41.667 10.07 10.07 43.94 3.14
4095 5572 6.481976 TGGTGCAGACCGTTAATATTTATCAG 59.518 38.462 0.00 0.00 46.62 2.90
4349 5936 2.033602 GGGTCCGACCACTTTGGG 59.966 66.667 19.43 0.00 43.37 4.12
4408 5995 6.849305 GGATAACTATGTACAAAATTTCCGCG 59.151 38.462 0.00 0.00 0.00 6.46
4528 6115 2.708861 TCTTCTGGGTTCTTGCCTAACA 59.291 45.455 0.00 0.00 0.00 2.41
4540 6127 3.315191 CGTTTTCACACATTCTTCTGGGT 59.685 43.478 0.00 0.00 31.32 4.51
4562 6763 1.578206 GCTCGCTCCAGGTCCAAAAC 61.578 60.000 0.00 0.00 0.00 2.43
4582 6783 3.373830 CCTCTCTCTCCATTGGACTCTT 58.626 50.000 0.00 0.00 0.00 2.85
4591 6792 2.841988 GGCGGCCTCTCTCTCCAT 60.842 66.667 12.87 0.00 0.00 3.41
4612 6813 1.530419 AAGCAAATCGGCCACACCA 60.530 52.632 2.24 0.00 39.03 4.17
4717 6918 3.287222 TCTTTCCCAACAACCAACTCTG 58.713 45.455 0.00 0.00 0.00 3.35
4718 6919 3.202151 TCTCTTTCCCAACAACCAACTCT 59.798 43.478 0.00 0.00 0.00 3.24
4720 6921 3.662759 TCTCTTTCCCAACAACCAACT 57.337 42.857 0.00 0.00 0.00 3.16
4749 6979 3.662759 TCTCTTTCCCAACAACCAACT 57.337 42.857 0.00 0.00 0.00 3.16
4790 7020 1.681229 TCTTTCCCTGTATGCCCCTT 58.319 50.000 0.00 0.00 0.00 3.95
4796 7026 5.303971 CCTAGCTCAATCTTTCCCTGTATG 58.696 45.833 0.00 0.00 0.00 2.39
4797 7027 4.202409 GCCTAGCTCAATCTTTCCCTGTAT 60.202 45.833 0.00 0.00 0.00 2.29
4825 7055 1.906574 CTAACCCAGCTCCCTTGTACA 59.093 52.381 0.00 0.00 0.00 2.90
4852 7082 1.001158 GCTCTACCGCTCACATCCTAC 60.001 57.143 0.00 0.00 0.00 3.18
4860 7090 1.103987 CCTAGCAGCTCTACCGCTCA 61.104 60.000 0.00 0.00 38.41 4.26
4904 7159 1.000731 GCAACATTAAGCCCAACAGCA 59.999 47.619 0.00 0.00 34.23 4.41
5046 7309 2.202557 TGCTACGTCGACATGGCG 60.203 61.111 16.88 16.88 0.00 5.69
5058 7321 3.075005 TCGAGCCCAGGGTGCTAC 61.075 66.667 7.55 0.00 39.69 3.58
5081 7344 2.767505 AGGTTTCATGTCGTTGAGTCC 58.232 47.619 0.00 0.00 0.00 3.85
5344 7697 5.472137 ACAACATACAATTCACGGTTTAGCT 59.528 36.000 0.00 0.00 0.00 3.32
5366 7719 8.220755 AGTTCTTAAAATAGCACAGTTCAACA 57.779 30.769 0.00 0.00 0.00 3.33
5533 7887 3.711704 ACAGAGACATCCCCGTAAATCAT 59.288 43.478 0.00 0.00 0.00 2.45
5647 9306 0.247145 GCATGTTCGGTAGTTTCGCG 60.247 55.000 0.00 0.00 0.00 5.87
5713 9372 0.043334 AGTGCTGTCTACCCTGGGAT 59.957 55.000 22.23 6.39 0.00 3.85
5872 9531 4.370917 AGTCGCAAAACAGCATCATTTTT 58.629 34.783 0.00 0.00 0.00 1.94
5891 9550 1.433837 AACGTGTGTCGGGCAAAGTC 61.434 55.000 0.00 0.00 44.69 3.01
5954 9615 7.766278 GGAGAAACTGTACATGTATCAAGTGAT 59.234 37.037 9.18 6.69 38.51 3.06
5989 9650 2.011947 CGGGGAATAGAACGGAAAACC 58.988 52.381 0.00 0.00 0.00 3.27
5999 9661 6.612456 TCTTACCTCAAATTACGGGGAATAGA 59.388 38.462 0.72 0.00 0.00 1.98
6010 9672 9.807921 AGTTCCTTTTGATCTTACCTCAAATTA 57.192 29.630 0.00 0.00 41.03 1.40
6048 9710 2.203337 GGCCTGTGGACAAGCACA 60.203 61.111 0.00 0.00 35.10 4.57
6135 9797 5.925397 GCATCTCATCCAGATTACTGTACTG 59.075 44.000 0.00 0.00 40.20 2.74
6179 9841 4.952957 TGGTATACACAACCATTTCCCATG 59.047 41.667 5.01 0.00 42.10 3.66
6199 9861 1.053424 TCCTAAGGCGAAGTGTTGGT 58.947 50.000 0.00 0.00 0.00 3.67
6299 10006 4.138487 AGATGGTTAACTCCGTGATTCC 57.862 45.455 5.42 0.00 0.00 3.01
6359 10066 6.598753 ATGTGCGTATGGTAAATAAGTGAC 57.401 37.500 0.00 0.00 0.00 3.67
6377 10084 1.335324 GCAGTGACAACCTGAATGTGC 60.335 52.381 0.00 0.00 31.38 4.57
6383 10090 0.815213 GCAGTGCAGTGACAACCTGA 60.815 55.000 25.76 0.00 31.38 3.86
6385 10092 1.224315 TGCAGTGCAGTGACAACCT 59.776 52.632 25.76 0.00 33.32 3.50
6404 10111 4.284550 TGGCCAGCCAAGTCACCC 62.285 66.667 9.42 0.00 44.12 4.61
6490 10197 4.891992 AGAGTGTGCATAGTACCAAACT 57.108 40.909 0.00 0.00 42.62 2.66
6496 10203 5.230942 ACAAGTCAAGAGTGTGCATAGTAC 58.769 41.667 0.00 0.00 0.00 2.73
6506 10219 5.230942 ACGAAGGATAACAAGTCAAGAGTG 58.769 41.667 0.00 0.00 0.00 3.51
6509 10222 6.522054 AGAAACGAAGGATAACAAGTCAAGA 58.478 36.000 0.00 0.00 0.00 3.02
6513 10226 5.163982 CGGAAGAAACGAAGGATAACAAGTC 60.164 44.000 0.00 0.00 0.00 3.01
6521 10234 3.244112 ACTCAACGGAAGAAACGAAGGAT 60.244 43.478 0.00 0.00 34.93 3.24
6528 10241 1.214367 TCGCACTCAACGGAAGAAAC 58.786 50.000 0.00 0.00 0.00 2.78
6529 10242 1.942677 TTCGCACTCAACGGAAGAAA 58.057 45.000 0.00 0.00 0.00 2.52
6530 10243 1.798223 CATTCGCACTCAACGGAAGAA 59.202 47.619 0.00 0.00 0.00 2.52
6535 10248 0.179250 CGAACATTCGCACTCAACGG 60.179 55.000 0.37 0.00 44.26 4.44
6536 10249 3.258498 CGAACATTCGCACTCAACG 57.742 52.632 0.37 0.00 44.26 4.10
6551 10273 1.362768 GCATCTGCATCTGTGACGAA 58.637 50.000 0.00 0.00 41.59 3.85
6563 10285 0.950555 TTGACGTGGACTGCATCTGC 60.951 55.000 0.00 0.00 42.50 4.26
6564 10286 0.792640 GTTGACGTGGACTGCATCTG 59.207 55.000 0.00 0.00 0.00 2.90
6565 10287 0.681733 AGTTGACGTGGACTGCATCT 59.318 50.000 0.00 0.00 0.00 2.90
6566 10288 0.792640 CAGTTGACGTGGACTGCATC 59.207 55.000 13.15 0.00 37.11 3.91
6567 10289 2.918571 CAGTTGACGTGGACTGCAT 58.081 52.632 13.15 0.00 37.11 3.96
6568 10290 4.436515 CAGTTGACGTGGACTGCA 57.563 55.556 13.15 0.00 37.11 4.41
6621 10344 4.521062 AGCAAGCTAGCTCGCCCG 62.521 66.667 23.82 8.62 42.18 6.13
6622 10345 2.124942 AAGCAAGCTAGCTCGCCC 60.125 61.111 23.82 9.55 45.89 6.13
6623 10346 2.520904 CGAAGCAAGCTAGCTCGCC 61.521 63.158 23.82 8.87 45.89 5.54
6624 10347 1.807573 ACGAAGCAAGCTAGCTCGC 60.808 57.895 20.23 20.23 45.89 5.03
6625 10348 0.456824 TCACGAAGCAAGCTAGCTCG 60.457 55.000 19.65 18.94 45.89 5.03
6626 10349 0.995728 GTCACGAAGCAAGCTAGCTC 59.004 55.000 19.65 6.50 45.89 4.09
6628 10351 0.732880 TCGTCACGAAGCAAGCTAGC 60.733 55.000 6.62 6.62 31.06 3.42
6629 10352 1.698165 TTCGTCACGAAGCAAGCTAG 58.302 50.000 9.01 0.00 41.05 3.42
6630 10353 3.877874 TTCGTCACGAAGCAAGCTA 57.122 47.368 9.01 0.00 41.05 3.32
6631 10354 4.750460 TTCGTCACGAAGCAAGCT 57.250 50.000 9.01 0.00 41.05 3.74
6638 10361 1.860676 CCACTTTCCTTCGTCACGAA 58.139 50.000 13.02 13.02 43.75 3.85
6639 10362 0.599204 GCCACTTTCCTTCGTCACGA 60.599 55.000 0.00 0.00 0.00 4.35
6640 10363 1.860078 GCCACTTTCCTTCGTCACG 59.140 57.895 0.00 0.00 0.00 4.35
6641 10364 0.599204 TCGCCACTTTCCTTCGTCAC 60.599 55.000 0.00 0.00 0.00 3.67
6642 10365 0.320374 ATCGCCACTTTCCTTCGTCA 59.680 50.000 0.00 0.00 0.00 4.35
6643 10366 0.721718 CATCGCCACTTTCCTTCGTC 59.278 55.000 0.00 0.00 0.00 4.20
6644 10367 1.298859 GCATCGCCACTTTCCTTCGT 61.299 55.000 0.00 0.00 0.00 3.85
6645 10368 1.425428 GCATCGCCACTTTCCTTCG 59.575 57.895 0.00 0.00 0.00 3.79
6657 10380 3.453070 GAGGGAGTCCTGGCATCGC 62.453 68.421 9.58 6.85 45.05 4.58
6658 10381 1.333636 AAGAGGGAGTCCTGGCATCG 61.334 60.000 9.58 0.00 45.05 3.84
6659 10382 0.467804 GAAGAGGGAGTCCTGGCATC 59.532 60.000 9.58 0.33 45.05 3.91
6660 10383 0.252881 TGAAGAGGGAGTCCTGGCAT 60.253 55.000 9.58 0.00 45.05 4.40
6661 10384 0.906756 CTGAAGAGGGAGTCCTGGCA 60.907 60.000 9.58 0.27 45.05 4.92
6662 10385 0.907230 ACTGAAGAGGGAGTCCTGGC 60.907 60.000 9.58 0.00 45.05 4.85
6663 10386 1.190643 GACTGAAGAGGGAGTCCTGG 58.809 60.000 9.58 0.00 45.05 4.45
6664 10387 1.930251 TGACTGAAGAGGGAGTCCTG 58.070 55.000 9.58 0.00 45.05 3.86
6666 10389 1.066502 GCTTGACTGAAGAGGGAGTCC 60.067 57.143 0.00 0.00 38.28 3.85
6667 10390 1.066502 GGCTTGACTGAAGAGGGAGTC 60.067 57.143 0.00 0.00 39.31 3.36
6668 10391 0.980423 GGCTTGACTGAAGAGGGAGT 59.020 55.000 0.00 0.00 32.82 3.85
6669 10392 0.979665 TGGCTTGACTGAAGAGGGAG 59.020 55.000 0.00 0.00 32.82 4.30
6670 10393 0.687354 GTGGCTTGACTGAAGAGGGA 59.313 55.000 0.00 0.00 32.82 4.20
6671 10394 0.397941 TGTGGCTTGACTGAAGAGGG 59.602 55.000 0.00 0.00 32.82 4.30
6672 10395 1.071385 ACTGTGGCTTGACTGAAGAGG 59.929 52.381 0.00 0.00 32.82 3.69
6673 10396 2.540265 ACTGTGGCTTGACTGAAGAG 57.460 50.000 0.00 0.00 32.82 2.85
6674 10397 2.485479 GGAACTGTGGCTTGACTGAAGA 60.485 50.000 0.00 0.00 32.82 2.87
6675 10398 1.876156 GGAACTGTGGCTTGACTGAAG 59.124 52.381 0.00 0.00 34.41 3.02
6676 10399 1.211703 TGGAACTGTGGCTTGACTGAA 59.788 47.619 0.00 0.00 0.00 3.02
6677 10400 0.836606 TGGAACTGTGGCTTGACTGA 59.163 50.000 0.00 0.00 0.00 3.41
6678 10401 1.233019 CTGGAACTGTGGCTTGACTG 58.767 55.000 0.00 0.00 0.00 3.51
6679 10402 0.536006 GCTGGAACTGTGGCTTGACT 60.536 55.000 0.00 0.00 0.00 3.41
6680 10403 1.845809 CGCTGGAACTGTGGCTTGAC 61.846 60.000 0.00 0.00 34.11 3.18
6681 10404 1.597854 CGCTGGAACTGTGGCTTGA 60.598 57.895 0.00 0.00 34.11 3.02
6682 10405 0.602638 TACGCTGGAACTGTGGCTTG 60.603 55.000 0.00 0.00 42.13 4.01
6683 10406 0.602905 GTACGCTGGAACTGTGGCTT 60.603 55.000 0.00 0.00 42.13 4.35
6684 10407 1.004918 GTACGCTGGAACTGTGGCT 60.005 57.895 0.00 0.00 42.13 4.75
6685 10408 2.033194 GGTACGCTGGAACTGTGGC 61.033 63.158 0.00 0.00 42.13 5.01
6686 10409 1.369692 TGGTACGCTGGAACTGTGG 59.630 57.895 0.00 0.00 42.13 4.17


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

AutoCloner maintained by Alex Coulton.