Multiple sequence alignment - TraesCS4D01G134100

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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 TraesCS4D01G134100 chr4D 100.000 2635 0 0 1 2635 120885140 120887774 0.000000e+00 4867
1 TraesCS4D01G134100 chr4D 84.380 685 82 13 1001 1664 121073959 121074639 0.000000e+00 649
2 TraesCS4D01G134100 chr4A 95.059 931 31 8 897 1812 452358860 452359790 0.000000e+00 1450
3 TraesCS4D01G134100 chr4A 92.810 918 27 17 1 897 452349470 452350369 0.000000e+00 1293
4 TraesCS4D01G134100 chr4A 83.857 700 84 17 990 1664 452594115 452594810 7.950000e-180 640
5 TraesCS4D01G134100 chr4A 89.881 336 23 9 2016 2350 452402655 452402980 3.140000e-114 422
6 TraesCS4D01G134100 chr4A 89.583 336 24 9 2016 2350 452369672 452369997 1.460000e-112 416
7 TraesCS4D01G134100 chr4A 95.890 219 9 0 1807 2025 452360032 452360250 3.230000e-94 355
8 TraesCS4D01G134100 chr4B 92.765 1009 28 15 840 1812 183612330 183613329 0.000000e+00 1417
9 TraesCS4D01G134100 chr4B 94.620 539 22 6 1813 2349 183613576 183614109 0.000000e+00 828
10 TraesCS4D01G134100 chr4B 91.914 606 25 8 254 854 183611728 183612314 0.000000e+00 826
11 TraesCS4D01G134100 chr4B 83.846 650 85 11 984 1617 183672564 183673209 3.750000e-168 601
12 TraesCS4D01G134100 chr4B 92.941 170 12 0 3 172 183608599 183608768 5.630000e-62 248
13 TraesCS4D01G134100 chr2D 81.145 594 54 30 169 730 473100726 473101293 8.720000e-115 424
14 TraesCS4D01G134100 chr2D 92.580 283 12 4 2362 2635 206219168 206218886 5.280000e-107 398
15 TraesCS4D01G134100 chr2D 91.844 282 14 5 2362 2635 262950670 262950950 4.110000e-103 385
16 TraesCS4D01G134100 chr2D 77.581 678 98 33 169 820 547792760 547793409 6.930000e-96 361
17 TraesCS4D01G134100 chr2D 80.893 403 43 17 169 552 62386923 62386536 1.190000e-73 287
18 TraesCS4D01G134100 chr2B 80.862 580 71 33 169 730 552434132 552434689 1.130000e-113 420
19 TraesCS4D01G134100 chr6D 93.286 283 10 4 2362 2635 220031822 220032104 2.440000e-110 409
20 TraesCS4D01G134100 chr6D 94.488 254 12 2 2384 2635 222438601 222438854 8.840000e-105 390
21 TraesCS4D01G134100 chr6D 77.424 691 104 35 169 820 72223773 72223096 5.360000e-97 364
22 TraesCS4D01G134100 chr6D 84.746 236 26 9 423 654 436466012 436466241 7.340000e-56 228
23 TraesCS4D01G134100 chr1D 92.553 282 13 3 2362 2635 328829174 328828893 5.280000e-107 398
24 TraesCS4D01G134100 chrUn 94.862 253 12 1 2384 2635 109528251 109527999 6.840000e-106 394
25 TraesCS4D01G134100 chr7D 92.500 280 13 3 2364 2635 332990082 332990361 6.840000e-106 394
26 TraesCS4D01G134100 chr7D 92.199 282 14 3 2362 2635 296468529 296468810 2.460000e-105 392
27 TraesCS4D01G134100 chr5D 92.473 279 13 3 2365 2635 186344354 186344076 2.460000e-105 392
28 TraesCS4D01G134100 chr5D 79.002 581 93 20 169 741 347017673 347018232 1.150000e-98 370
29 TraesCS4D01G134100 chr2A 79.688 512 75 24 180 674 614584574 614585073 2.510000e-90 342
30 TraesCS4D01G134100 chr5A 77.701 435 74 17 169 587 112618650 112619077 7.290000e-61 244
31 TraesCS4D01G134100 chr6A 82.051 234 25 9 423 654 584687449 584687667 1.610000e-42 183


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 TraesCS4D01G134100 chr4D 120885140 120887774 2634 False 4867.00 4867 100.0000 1 2635 1 chr4D.!!$F1 2634
1 TraesCS4D01G134100 chr4D 121073959 121074639 680 False 649.00 649 84.3800 1001 1664 1 chr4D.!!$F2 663
2 TraesCS4D01G134100 chr4A 452349470 452350369 899 False 1293.00 1293 92.8100 1 897 1 chr4A.!!$F1 896
3 TraesCS4D01G134100 chr4A 452358860 452360250 1390 False 902.50 1450 95.4745 897 2025 2 chr4A.!!$F5 1128
4 TraesCS4D01G134100 chr4A 452594115 452594810 695 False 640.00 640 83.8570 990 1664 1 chr4A.!!$F4 674
5 TraesCS4D01G134100 chr4B 183608599 183614109 5510 False 829.75 1417 93.0600 3 2349 4 chr4B.!!$F2 2346
6 TraesCS4D01G134100 chr4B 183672564 183673209 645 False 601.00 601 83.8460 984 1617 1 chr4B.!!$F1 633
7 TraesCS4D01G134100 chr2D 473100726 473101293 567 False 424.00 424 81.1450 169 730 1 chr2D.!!$F2 561
8 TraesCS4D01G134100 chr2D 547792760 547793409 649 False 361.00 361 77.5810 169 820 1 chr2D.!!$F3 651
9 TraesCS4D01G134100 chr2B 552434132 552434689 557 False 420.00 420 80.8620 169 730 1 chr2B.!!$F1 561
10 TraesCS4D01G134100 chr6D 72223096 72223773 677 True 364.00 364 77.4240 169 820 1 chr6D.!!$R1 651
11 TraesCS4D01G134100 chr5D 347017673 347018232 559 False 370.00 370 79.0020 169 741 1 chr5D.!!$F1 572

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
137 144 0.105039 ATTCCATTCGCGGTCTCTCC 59.895 55.0 6.13 0.0 0.00 3.71 F
1108 4120 0.320683 CGCATCGGCATCCCTATCAA 60.321 55.0 0.00 0.0 41.24 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1114 4126 0.317436 CTCGGCGACAGATGAGTAGC 60.317 60.0 4.99 0.0 39.08 3.58 R
2478 5844 0.035458 AAAAGCTCAGACTGGTCCGG 59.965 55.0 1.81 0.0 0.00 5.14 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
115 122 1.957562 CTGCTGCTGCTGCTTCTTT 59.042 52.632 27.67 0.00 40.48 2.52
137 144 0.105039 ATTCCATTCGCGGTCTCTCC 59.895 55.000 6.13 0.00 0.00 3.71
158 165 3.131046 CCTGGTCTTGTTGTTTTCTGCTT 59.869 43.478 0.00 0.00 0.00 3.91
256 3141 7.763172 CTGAAGCAATTCAGTAGTAACTAGG 57.237 40.000 9.35 0.00 42.53 3.02
375 3275 7.450634 ACAGACTTCAGGAGTGTAATACAGTAA 59.549 37.037 0.03 0.00 39.19 2.24
377 3277 9.036980 AGACTTCAGGAGTGTAATACAGTAAAT 57.963 33.333 0.03 0.00 39.19 1.40
415 3319 2.508526 AGGAACACAGCAAGCCTAAAG 58.491 47.619 0.00 0.00 0.00 1.85
442 3358 4.357947 GGTGGCAGCACGACGAGA 62.358 66.667 12.58 0.00 0.00 4.04
825 3787 1.460273 TTTCTTCCGGCCCAACTTGC 61.460 55.000 0.00 0.00 0.00 4.01
836 3798 1.345415 CCCAACTTGCTGGCTGATTTT 59.655 47.619 0.00 0.00 34.88 1.82
897 3889 1.227380 GAATCGATGCGGCTGGTCT 60.227 57.895 0.00 0.00 0.00 3.85
898 3890 1.218230 GAATCGATGCGGCTGGTCTC 61.218 60.000 0.00 0.00 0.00 3.36
1095 4101 4.637489 CTCTCCTCCGCCGCATCG 62.637 72.222 0.00 0.00 0.00 3.84
1108 4120 0.320683 CGCATCGGCATCCCTATCAA 60.321 55.000 0.00 0.00 41.24 2.57
1114 4126 1.961277 GCATCCCTATCAACGGCCG 60.961 63.158 26.86 26.86 0.00 6.13
1270 4295 5.185056 TCATCGATTTCACCTGTCTGTCTTA 59.815 40.000 0.00 0.00 0.00 2.10
1282 4312 2.102252 GTCTGTCTTATCCCAGCTGAGG 59.898 54.545 17.39 15.01 0.00 3.86
1427 4467 2.683933 ATGTCCGTCGCCTTCCCT 60.684 61.111 0.00 0.00 0.00 4.20
1530 4570 1.598130 GTGCTCTTCACCAACGCCT 60.598 57.895 0.00 0.00 39.79 5.52
1589 4650 5.462530 TCTTCGGTAACATGAAGAAGTCA 57.537 39.130 0.00 0.00 45.52 3.41
1655 4739 2.944409 GATGCCTCTGCCTGCTCCTG 62.944 65.000 0.00 0.00 36.33 3.86
1746 4831 4.525949 GAACGGGCGCCTACTCCC 62.526 72.222 28.56 7.30 37.48 4.30
1775 4860 9.256477 CTTATCAGTTCGGCTTGTATATGTAAA 57.744 33.333 0.00 0.00 0.00 2.01
1808 4893 4.363138 AGCAGTACGATGTATGATGTGTG 58.637 43.478 0.00 0.00 0.00 3.82
1870 5234 8.128582 TCCAAAAGCACGATTCATATATCAAAC 58.871 33.333 0.00 0.00 0.00 2.93
1881 5245 9.599322 GATTCATATATCAAACAATTGGTCGTC 57.401 33.333 10.83 0.00 37.15 4.20
1951 5316 6.902224 TGGTACTTCGTGTTGATATGATTG 57.098 37.500 0.00 0.00 0.00 2.67
2068 5433 6.260714 TCTCTCATATTTTTACATGCATGCGT 59.739 34.615 26.53 10.53 0.00 5.24
2087 5452 4.739228 TGCGTGAACAAATGAATTCAACAG 59.261 37.500 13.09 7.47 36.62 3.16
2092 5457 7.195646 GTGAACAAATGAATTCAACAGACTGA 58.804 34.615 13.09 0.00 36.62 3.41
2104 5469 4.580167 TCAACAGACTGAAAACTTGATGGG 59.420 41.667 10.08 0.00 0.00 4.00
2211 5577 8.902806 CATCTCAAAATTATAGGGTAAGCACAA 58.097 33.333 0.00 0.00 0.00 3.33
2224 5590 5.576774 GGGTAAGCACAAATTCATAGTTTGC 59.423 40.000 0.00 0.00 39.55 3.68
2231 5597 6.966632 GCACAAATTCATAGTTTGCGAGAATA 59.033 34.615 0.00 0.00 39.55 1.75
2265 5631 5.614308 TGTATACTCATCATGAAGCCTTGG 58.386 41.667 0.00 0.00 0.00 3.61
2336 5702 3.006752 ACTCTGCTCTCCTTCAGAAAGTG 59.993 47.826 0.00 0.00 38.68 3.16
2343 5709 2.370189 CTCCTTCAGAAAGTGTCACCCT 59.630 50.000 0.00 0.00 0.00 4.34
2344 5710 2.104792 TCCTTCAGAAAGTGTCACCCTG 59.895 50.000 0.00 5.44 0.00 4.45
2345 5711 2.104792 CCTTCAGAAAGTGTCACCCTGA 59.895 50.000 13.24 13.24 32.67 3.86
2346 5712 3.244700 CCTTCAGAAAGTGTCACCCTGAT 60.245 47.826 16.28 0.00 34.34 2.90
2347 5713 3.685139 TCAGAAAGTGTCACCCTGATC 57.315 47.619 13.24 0.00 0.00 2.92
2348 5714 2.972021 TCAGAAAGTGTCACCCTGATCA 59.028 45.455 13.24 0.00 0.00 2.92
2349 5715 3.584406 TCAGAAAGTGTCACCCTGATCAT 59.416 43.478 13.24 0.00 0.00 2.45
2350 5716 3.937706 CAGAAAGTGTCACCCTGATCATC 59.062 47.826 10.45 0.00 0.00 2.92
2351 5717 3.054802 AGAAAGTGTCACCCTGATCATCC 60.055 47.826 0.00 0.00 0.00 3.51
2352 5718 2.260639 AGTGTCACCCTGATCATCCT 57.739 50.000 0.00 0.00 0.00 3.24
2353 5719 2.114616 AGTGTCACCCTGATCATCCTC 58.885 52.381 0.00 0.00 0.00 3.71
2354 5720 1.139853 GTGTCACCCTGATCATCCTCC 59.860 57.143 0.00 0.00 0.00 4.30
2355 5721 0.761802 GTCACCCTGATCATCCTCCC 59.238 60.000 0.00 0.00 0.00 4.30
2356 5722 0.400525 TCACCCTGATCATCCTCCCC 60.401 60.000 0.00 0.00 0.00 4.81
2357 5723 0.401105 CACCCTGATCATCCTCCCCT 60.401 60.000 0.00 0.00 0.00 4.79
2358 5724 0.348370 ACCCTGATCATCCTCCCCTT 59.652 55.000 0.00 0.00 0.00 3.95
2359 5725 0.769873 CCCTGATCATCCTCCCCTTG 59.230 60.000 0.00 0.00 0.00 3.61
2360 5726 1.696965 CCCTGATCATCCTCCCCTTGA 60.697 57.143 0.00 0.00 0.00 3.02
2361 5727 2.130193 CCTGATCATCCTCCCCTTGAA 58.870 52.381 0.00 0.00 0.00 2.69
2362 5728 2.511218 CCTGATCATCCTCCCCTTGAAA 59.489 50.000 0.00 0.00 0.00 2.69
2363 5729 3.434739 CCTGATCATCCTCCCCTTGAAAG 60.435 52.174 0.00 0.00 0.00 2.62
2364 5730 3.192944 TGATCATCCTCCCCTTGAAAGT 58.807 45.455 0.00 0.00 0.00 2.66
2365 5731 3.054139 TGATCATCCTCCCCTTGAAAGTG 60.054 47.826 0.00 0.00 0.00 3.16
2366 5732 1.635487 TCATCCTCCCCTTGAAAGTGG 59.365 52.381 0.00 0.00 0.00 4.00
2367 5733 1.355720 CATCCTCCCCTTGAAAGTGGT 59.644 52.381 0.00 0.00 0.00 4.16
2368 5734 2.426431 TCCTCCCCTTGAAAGTGGTA 57.574 50.000 0.00 0.00 0.00 3.25
2369 5735 2.929301 TCCTCCCCTTGAAAGTGGTAT 58.071 47.619 0.00 0.00 0.00 2.73
2370 5736 2.844348 TCCTCCCCTTGAAAGTGGTATC 59.156 50.000 0.00 0.00 0.00 2.24
2371 5737 2.576191 CCTCCCCTTGAAAGTGGTATCA 59.424 50.000 0.00 0.00 0.00 2.15
2372 5738 3.370953 CCTCCCCTTGAAAGTGGTATCAG 60.371 52.174 0.00 0.00 0.00 2.90
2373 5739 3.519510 CTCCCCTTGAAAGTGGTATCAGA 59.480 47.826 0.00 0.00 0.00 3.27
2374 5740 4.111577 TCCCCTTGAAAGTGGTATCAGAT 58.888 43.478 0.00 0.00 0.00 2.90
2375 5741 4.540099 TCCCCTTGAAAGTGGTATCAGATT 59.460 41.667 0.00 0.00 0.00 2.40
2376 5742 5.015178 TCCCCTTGAAAGTGGTATCAGATTT 59.985 40.000 0.00 0.00 0.00 2.17
2377 5743 5.716703 CCCCTTGAAAGTGGTATCAGATTTT 59.283 40.000 0.00 0.00 0.00 1.82
2378 5744 6.127619 CCCCTTGAAAGTGGTATCAGATTTTC 60.128 42.308 0.00 0.00 0.00 2.29
2379 5745 6.434028 CCCTTGAAAGTGGTATCAGATTTTCA 59.566 38.462 3.89 3.89 0.00 2.69
2380 5746 7.362401 CCCTTGAAAGTGGTATCAGATTTTCAG 60.362 40.741 7.10 3.77 0.00 3.02
2381 5747 7.362401 CCTTGAAAGTGGTATCAGATTTTCAGG 60.362 40.741 8.61 8.61 0.00 3.86
2382 5748 5.415701 TGAAAGTGGTATCAGATTTTCAGGC 59.584 40.000 3.89 0.00 0.00 4.85
2383 5749 4.851639 AGTGGTATCAGATTTTCAGGCT 57.148 40.909 0.00 0.00 0.00 4.58
2384 5750 4.521146 AGTGGTATCAGATTTTCAGGCTG 58.479 43.478 8.58 8.58 0.00 4.85
2385 5751 4.225942 AGTGGTATCAGATTTTCAGGCTGA 59.774 41.667 14.43 14.43 42.25 4.26
2386 5752 4.574013 GTGGTATCAGATTTTCAGGCTGAG 59.426 45.833 17.91 5.05 41.45 3.35
2387 5753 4.471025 TGGTATCAGATTTTCAGGCTGAGA 59.529 41.667 17.91 10.85 41.45 3.27
2388 5754 5.131642 TGGTATCAGATTTTCAGGCTGAGAT 59.868 40.000 17.91 16.77 41.45 2.75
2389 5755 6.060788 GGTATCAGATTTTCAGGCTGAGATT 58.939 40.000 17.91 9.69 41.45 2.40
2390 5756 6.545298 GGTATCAGATTTTCAGGCTGAGATTT 59.455 38.462 17.91 8.49 41.45 2.17
2391 5757 7.067981 GGTATCAGATTTTCAGGCTGAGATTTT 59.932 37.037 17.91 2.33 41.45 1.82
2392 5758 9.113838 GTATCAGATTTTCAGGCTGAGATTTTA 57.886 33.333 17.91 0.00 41.45 1.52
2393 5759 7.383102 TCAGATTTTCAGGCTGAGATTTTAC 57.617 36.000 17.91 7.06 34.02 2.01
2394 5760 6.942005 TCAGATTTTCAGGCTGAGATTTTACA 59.058 34.615 17.91 0.00 34.02 2.41
2395 5761 7.120285 TCAGATTTTCAGGCTGAGATTTTACAG 59.880 37.037 17.91 4.22 34.02 2.74
2396 5762 6.944862 AGATTTTCAGGCTGAGATTTTACAGT 59.055 34.615 17.91 0.00 36.62 3.55
2397 5763 6.959639 TTTTCAGGCTGAGATTTTACAGTT 57.040 33.333 17.91 0.00 36.62 3.16
2398 5764 6.959639 TTTCAGGCTGAGATTTTACAGTTT 57.040 33.333 17.91 0.00 36.62 2.66
2399 5765 6.959639 TTCAGGCTGAGATTTTACAGTTTT 57.040 33.333 17.91 0.00 36.62 2.43
2400 5766 6.959639 TCAGGCTGAGATTTTACAGTTTTT 57.040 33.333 14.43 0.00 36.62 1.94
2401 5767 6.970484 TCAGGCTGAGATTTTACAGTTTTTC 58.030 36.000 14.43 0.00 36.62 2.29
2402 5768 5.853282 CAGGCTGAGATTTTACAGTTTTTCG 59.147 40.000 9.42 0.00 36.62 3.46
2403 5769 5.531287 AGGCTGAGATTTTACAGTTTTTCGT 59.469 36.000 0.00 0.00 36.62 3.85
2404 5770 6.708949 AGGCTGAGATTTTACAGTTTTTCGTA 59.291 34.615 0.00 0.00 36.62 3.43
2405 5771 7.015877 GGCTGAGATTTTACAGTTTTTCGTAG 58.984 38.462 0.00 0.00 36.62 3.51
2406 5772 7.307811 GGCTGAGATTTTACAGTTTTTCGTAGT 60.308 37.037 0.00 0.00 36.62 2.73
2407 5773 8.068380 GCTGAGATTTTACAGTTTTTCGTAGTT 58.932 33.333 0.00 0.00 36.62 2.24
2408 5774 9.931210 CTGAGATTTTACAGTTTTTCGTAGTTT 57.069 29.630 0.00 0.00 0.00 2.66
2415 5781 9.462174 TTTACAGTTTTTCGTAGTTTAGATCGA 57.538 29.630 0.00 0.00 0.00 3.59
2416 5782 7.564044 ACAGTTTTTCGTAGTTTAGATCGAG 57.436 36.000 0.00 0.00 33.98 4.04
2417 5783 7.144000 ACAGTTTTTCGTAGTTTAGATCGAGT 58.856 34.615 0.00 0.00 33.98 4.18
2418 5784 8.292448 ACAGTTTTTCGTAGTTTAGATCGAGTA 58.708 33.333 0.00 0.00 33.98 2.59
2419 5785 9.286946 CAGTTTTTCGTAGTTTAGATCGAGTAT 57.713 33.333 0.00 0.00 33.98 2.12
2420 5786 9.286946 AGTTTTTCGTAGTTTAGATCGAGTATG 57.713 33.333 0.00 0.00 33.98 2.39
2421 5787 9.070149 GTTTTTCGTAGTTTAGATCGAGTATGT 57.930 33.333 0.00 0.00 33.98 2.29
2422 5788 9.630098 TTTTTCGTAGTTTAGATCGAGTATGTT 57.370 29.630 0.00 0.00 33.98 2.71
2423 5789 9.630098 TTTTCGTAGTTTAGATCGAGTATGTTT 57.370 29.630 0.00 0.00 33.98 2.83
2424 5790 9.630098 TTTCGTAGTTTAGATCGAGTATGTTTT 57.370 29.630 0.00 0.00 33.98 2.43
2425 5791 9.630098 TTCGTAGTTTAGATCGAGTATGTTTTT 57.370 29.630 0.00 0.00 33.98 1.94
2426 5792 9.282247 TCGTAGTTTAGATCGAGTATGTTTTTC 57.718 33.333 0.00 0.00 0.00 2.29
2427 5793 9.069078 CGTAGTTTAGATCGAGTATGTTTTTCA 57.931 33.333 0.00 0.00 0.00 2.69
2442 5808 4.992319 TGTTTTTCATACCTACAGTCCACG 59.008 41.667 0.00 0.00 0.00 4.94
2443 5809 5.221481 TGTTTTTCATACCTACAGTCCACGA 60.221 40.000 0.00 0.00 0.00 4.35
2444 5810 5.471556 TTTTCATACCTACAGTCCACGAA 57.528 39.130 0.00 0.00 0.00 3.85
2445 5811 5.471556 TTTCATACCTACAGTCCACGAAA 57.528 39.130 0.00 0.00 0.00 3.46
2446 5812 5.471556 TTCATACCTACAGTCCACGAAAA 57.528 39.130 0.00 0.00 0.00 2.29
2447 5813 5.068234 TCATACCTACAGTCCACGAAAAG 57.932 43.478 0.00 0.00 0.00 2.27
2448 5814 2.165319 ACCTACAGTCCACGAAAAGC 57.835 50.000 0.00 0.00 0.00 3.51
2449 5815 1.270678 ACCTACAGTCCACGAAAAGCC 60.271 52.381 0.00 0.00 0.00 4.35
2450 5816 1.270625 CCTACAGTCCACGAAAAGCCA 60.271 52.381 0.00 0.00 0.00 4.75
2451 5817 2.489971 CTACAGTCCACGAAAAGCCAA 58.510 47.619 0.00 0.00 0.00 4.52
2452 5818 1.757682 ACAGTCCACGAAAAGCCAAA 58.242 45.000 0.00 0.00 0.00 3.28
2453 5819 2.096248 ACAGTCCACGAAAAGCCAAAA 58.904 42.857 0.00 0.00 0.00 2.44
2454 5820 2.494073 ACAGTCCACGAAAAGCCAAAAA 59.506 40.909 0.00 0.00 0.00 1.94
2479 5845 8.870075 AAAAATAGGGCTAGTTCATCATATCC 57.130 34.615 0.00 0.00 0.00 2.59
2480 5846 5.860941 ATAGGGCTAGTTCATCATATCCG 57.139 43.478 0.00 0.00 0.00 4.18
2481 5847 2.834549 AGGGCTAGTTCATCATATCCGG 59.165 50.000 0.00 0.00 0.00 5.14
2482 5848 2.832129 GGGCTAGTTCATCATATCCGGA 59.168 50.000 6.61 6.61 0.00 5.14
2483 5849 3.368531 GGGCTAGTTCATCATATCCGGAC 60.369 52.174 6.12 0.00 0.00 4.79
2484 5850 3.368531 GGCTAGTTCATCATATCCGGACC 60.369 52.174 6.12 0.00 0.00 4.46
2485 5851 3.258372 GCTAGTTCATCATATCCGGACCA 59.742 47.826 6.12 0.00 0.00 4.02
2486 5852 4.619394 GCTAGTTCATCATATCCGGACCAG 60.619 50.000 6.12 0.00 0.00 4.00
2487 5853 3.309296 AGTTCATCATATCCGGACCAGT 58.691 45.455 6.12 0.00 0.00 4.00
2488 5854 3.322254 AGTTCATCATATCCGGACCAGTC 59.678 47.826 6.12 0.00 0.00 3.51
2489 5855 3.244887 TCATCATATCCGGACCAGTCT 57.755 47.619 6.12 0.00 0.00 3.24
2490 5856 2.893489 TCATCATATCCGGACCAGTCTG 59.107 50.000 6.12 0.32 35.77 3.51
2491 5857 2.748209 TCATATCCGGACCAGTCTGA 57.252 50.000 6.12 0.00 38.21 3.27
2492 5858 2.587522 TCATATCCGGACCAGTCTGAG 58.412 52.381 6.12 0.00 38.21 3.35
2493 5859 1.000283 CATATCCGGACCAGTCTGAGC 60.000 57.143 6.12 0.00 38.21 4.26
2494 5860 0.259065 TATCCGGACCAGTCTGAGCT 59.741 55.000 6.12 0.00 38.21 4.09
2495 5861 0.616111 ATCCGGACCAGTCTGAGCTT 60.616 55.000 6.12 0.00 38.21 3.74
2496 5862 0.832135 TCCGGACCAGTCTGAGCTTT 60.832 55.000 0.00 0.00 38.21 3.51
2497 5863 0.035458 CCGGACCAGTCTGAGCTTTT 59.965 55.000 8.22 0.00 38.21 2.27
2498 5864 1.151668 CGGACCAGTCTGAGCTTTTG 58.848 55.000 0.00 0.00 38.21 2.44
2535 5901 9.591404 TTAATATTTTGCTTTGTTGAATTTGCG 57.409 25.926 0.00 0.00 0.00 4.85
2536 5902 3.940657 TTTGCTTTGTTGAATTTGCGG 57.059 38.095 0.00 0.00 0.00 5.69
2537 5903 2.593346 TGCTTTGTTGAATTTGCGGT 57.407 40.000 0.00 0.00 0.00 5.68
2538 5904 2.898705 TGCTTTGTTGAATTTGCGGTT 58.101 38.095 0.00 0.00 0.00 4.44
2539 5905 2.606725 TGCTTTGTTGAATTTGCGGTTG 59.393 40.909 0.00 0.00 0.00 3.77
2540 5906 2.599612 GCTTTGTTGAATTTGCGGTTGC 60.600 45.455 0.00 0.00 43.20 4.17
2550 5916 3.411351 GCGGTTGCATCGTCGTGT 61.411 61.111 10.83 0.00 42.15 4.49
2551 5917 2.769617 CGGTTGCATCGTCGTGTC 59.230 61.111 0.00 0.00 0.00 3.67
2552 5918 2.019408 CGGTTGCATCGTCGTGTCA 61.019 57.895 0.00 0.00 0.00 3.58
2553 5919 1.553195 CGGTTGCATCGTCGTGTCAA 61.553 55.000 0.00 0.00 0.00 3.18
2554 5920 0.163788 GGTTGCATCGTCGTGTCAAG 59.836 55.000 0.00 0.00 0.00 3.02
2555 5921 0.859232 GTTGCATCGTCGTGTCAAGT 59.141 50.000 0.00 0.00 0.00 3.16
2556 5922 1.260561 GTTGCATCGTCGTGTCAAGTT 59.739 47.619 0.00 0.00 0.00 2.66
2557 5923 0.858583 TGCATCGTCGTGTCAAGTTG 59.141 50.000 0.00 0.00 0.00 3.16
2558 5924 0.451135 GCATCGTCGTGTCAAGTTGC 60.451 55.000 0.00 0.00 0.00 4.17
2559 5925 1.139989 CATCGTCGTGTCAAGTTGCT 58.860 50.000 0.00 0.00 0.00 3.91
2560 5926 1.136529 CATCGTCGTGTCAAGTTGCTG 60.137 52.381 0.00 0.00 0.00 4.41
2561 5927 0.874175 TCGTCGTGTCAAGTTGCTGG 60.874 55.000 0.00 0.00 0.00 4.85
2562 5928 1.151777 CGTCGTGTCAAGTTGCTGGT 61.152 55.000 0.00 0.00 0.00 4.00
2563 5929 0.582005 GTCGTGTCAAGTTGCTGGTC 59.418 55.000 0.00 0.00 0.00 4.02
2564 5930 0.464036 TCGTGTCAAGTTGCTGGTCT 59.536 50.000 0.00 0.00 0.00 3.85
2565 5931 1.134521 TCGTGTCAAGTTGCTGGTCTT 60.135 47.619 0.00 0.00 0.00 3.01
2566 5932 2.101750 TCGTGTCAAGTTGCTGGTCTTA 59.898 45.455 0.00 0.00 0.00 2.10
2567 5933 2.476619 CGTGTCAAGTTGCTGGTCTTAG 59.523 50.000 0.00 0.00 0.00 2.18
2568 5934 2.224314 GTGTCAAGTTGCTGGTCTTAGC 59.776 50.000 0.00 0.00 43.95 3.09
2569 5935 1.461127 GTCAAGTTGCTGGTCTTAGCG 59.539 52.381 0.00 0.00 46.61 4.26
2570 5936 1.070134 TCAAGTTGCTGGTCTTAGCGT 59.930 47.619 0.00 0.00 46.61 5.07
2571 5937 1.461127 CAAGTTGCTGGTCTTAGCGTC 59.539 52.381 0.00 0.00 46.61 5.19
2572 5938 0.969894 AGTTGCTGGTCTTAGCGTCT 59.030 50.000 0.00 0.00 46.61 4.18
2573 5939 2.168496 AGTTGCTGGTCTTAGCGTCTA 58.832 47.619 0.00 0.00 46.61 2.59
2574 5940 2.164624 AGTTGCTGGTCTTAGCGTCTAG 59.835 50.000 0.00 0.00 46.61 2.43
2575 5941 1.835494 TGCTGGTCTTAGCGTCTAGT 58.165 50.000 0.00 0.00 46.61 2.57
2576 5942 2.168496 TGCTGGTCTTAGCGTCTAGTT 58.832 47.619 0.00 0.00 46.61 2.24
2577 5943 2.561419 TGCTGGTCTTAGCGTCTAGTTT 59.439 45.455 0.00 0.00 46.61 2.66
2578 5944 3.180613 GCTGGTCTTAGCGTCTAGTTTC 58.819 50.000 0.00 0.00 33.46 2.78
2579 5945 3.771798 CTGGTCTTAGCGTCTAGTTTCC 58.228 50.000 0.00 0.00 0.00 3.13
2580 5946 2.494870 TGGTCTTAGCGTCTAGTTTCCC 59.505 50.000 0.00 0.00 0.00 3.97
2581 5947 2.759535 GGTCTTAGCGTCTAGTTTCCCT 59.240 50.000 0.00 0.00 0.00 4.20
2582 5948 3.195182 GGTCTTAGCGTCTAGTTTCCCTT 59.805 47.826 0.00 0.00 0.00 3.95
2583 5949 4.400567 GGTCTTAGCGTCTAGTTTCCCTTA 59.599 45.833 0.00 0.00 0.00 2.69
2584 5950 5.450274 GGTCTTAGCGTCTAGTTTCCCTTAG 60.450 48.000 0.00 0.00 0.00 2.18
2585 5951 5.356470 GTCTTAGCGTCTAGTTTCCCTTAGA 59.644 44.000 0.00 0.00 0.00 2.10
2586 5952 5.589452 TCTTAGCGTCTAGTTTCCCTTAGAG 59.411 44.000 0.00 0.00 0.00 2.43
2587 5953 3.699413 AGCGTCTAGTTTCCCTTAGAGT 58.301 45.455 0.00 0.00 0.00 3.24
2588 5954 4.087907 AGCGTCTAGTTTCCCTTAGAGTT 58.912 43.478 0.00 0.00 0.00 3.01
2589 5955 4.527427 AGCGTCTAGTTTCCCTTAGAGTTT 59.473 41.667 0.00 0.00 0.00 2.66
2590 5956 4.863689 GCGTCTAGTTTCCCTTAGAGTTTC 59.136 45.833 0.00 0.00 0.00 2.78
2591 5957 5.094134 CGTCTAGTTTCCCTTAGAGTTTCG 58.906 45.833 0.00 0.00 0.00 3.46
2592 5958 5.106396 CGTCTAGTTTCCCTTAGAGTTTCGA 60.106 44.000 0.00 0.00 0.00 3.71
2593 5959 6.324042 GTCTAGTTTCCCTTAGAGTTTCGAG 58.676 44.000 0.00 0.00 0.00 4.04
2594 5960 6.008960 TCTAGTTTCCCTTAGAGTTTCGAGT 58.991 40.000 0.00 0.00 0.00 4.18
2595 5961 5.548181 AGTTTCCCTTAGAGTTTCGAGTT 57.452 39.130 0.00 0.00 0.00 3.01
2596 5962 5.539979 AGTTTCCCTTAGAGTTTCGAGTTC 58.460 41.667 0.00 0.00 0.00 3.01
2597 5963 5.304871 AGTTTCCCTTAGAGTTTCGAGTTCT 59.695 40.000 0.00 0.00 0.00 3.01
2598 5964 4.785511 TCCCTTAGAGTTTCGAGTTCTG 57.214 45.455 5.87 0.00 0.00 3.02
2599 5965 3.056749 TCCCTTAGAGTTTCGAGTTCTGC 60.057 47.826 5.87 0.00 0.00 4.26
2600 5966 3.056465 CCCTTAGAGTTTCGAGTTCTGCT 60.056 47.826 5.87 0.00 0.00 4.24
2601 5967 4.170256 CCTTAGAGTTTCGAGTTCTGCTC 58.830 47.826 5.87 0.00 40.77 4.26
2602 5968 4.321304 CCTTAGAGTTTCGAGTTCTGCTCA 60.321 45.833 5.87 0.00 44.33 4.26
2603 5969 3.019933 AGAGTTTCGAGTTCTGCTCAC 57.980 47.619 0.00 0.00 44.33 3.51
2604 5970 2.362397 AGAGTTTCGAGTTCTGCTCACA 59.638 45.455 0.00 0.00 44.33 3.58
2605 5971 3.123804 GAGTTTCGAGTTCTGCTCACAA 58.876 45.455 0.00 0.00 44.33 3.33
2606 5972 3.126831 AGTTTCGAGTTCTGCTCACAAG 58.873 45.455 0.00 0.00 44.33 3.16
2607 5973 2.866762 GTTTCGAGTTCTGCTCACAAGT 59.133 45.455 0.00 0.00 44.33 3.16
2608 5974 2.890808 TCGAGTTCTGCTCACAAGTT 57.109 45.000 0.00 0.00 44.33 2.66
2609 5975 2.473816 TCGAGTTCTGCTCACAAGTTG 58.526 47.619 0.00 0.00 44.33 3.16
2610 5976 1.070309 CGAGTTCTGCTCACAAGTTGC 60.070 52.381 1.81 0.00 44.33 4.17
2611 5977 1.265365 GAGTTCTGCTCACAAGTTGCC 59.735 52.381 1.81 0.00 43.58 4.52
2612 5978 1.024271 GTTCTGCTCACAAGTTGCCA 58.976 50.000 1.81 0.00 0.00 4.92
2613 5979 1.024271 TTCTGCTCACAAGTTGCCAC 58.976 50.000 1.81 0.00 0.00 5.01
2614 5980 1.159713 TCTGCTCACAAGTTGCCACG 61.160 55.000 1.81 0.00 0.00 4.94
2615 5981 2.050985 GCTCACAAGTTGCCACGC 60.051 61.111 1.81 0.00 0.00 5.34
2616 5982 2.639286 CTCACAAGTTGCCACGCC 59.361 61.111 1.81 0.00 0.00 5.68
2617 5983 3.240606 CTCACAAGTTGCCACGCCG 62.241 63.158 1.81 0.00 0.00 6.46
2618 5984 4.980903 CACAAGTTGCCACGCCGC 62.981 66.667 1.81 0.00 0.00 6.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
115 122 0.248907 GAGACCGCGAATGGAATCGA 60.249 55.000 8.23 0.00 45.48 3.59
137 144 4.376340 AAGCAGAAAACAACAAGACCAG 57.624 40.909 0.00 0.00 0.00 4.00
158 165 6.718912 TGTCATTGTCATATTGGTTTGAGGAA 59.281 34.615 0.00 0.00 0.00 3.36
256 3141 3.760684 AGCTGTGATTTCCAGGAATGTTC 59.239 43.478 1.58 1.76 0.00 3.18
380 3280 7.717875 TGCTGTGTTCCTTTGTAGTAAATTACT 59.282 33.333 10.75 10.75 42.68 2.24
381 3281 7.867752 TGCTGTGTTCCTTTGTAGTAAATTAC 58.132 34.615 0.00 0.00 0.00 1.89
382 3282 8.453238 TTGCTGTGTTCCTTTGTAGTAAATTA 57.547 30.769 0.00 0.00 0.00 1.40
383 3283 6.952773 TGCTGTGTTCCTTTGTAGTAAATT 57.047 33.333 0.00 0.00 0.00 1.82
384 3284 6.515035 GCTTGCTGTGTTCCTTTGTAGTAAAT 60.515 38.462 0.00 0.00 0.00 1.40
385 3285 5.220970 GCTTGCTGTGTTCCTTTGTAGTAAA 60.221 40.000 0.00 0.00 0.00 2.01
386 3286 4.274950 GCTTGCTGTGTTCCTTTGTAGTAA 59.725 41.667 0.00 0.00 0.00 2.24
387 3287 3.813166 GCTTGCTGTGTTCCTTTGTAGTA 59.187 43.478 0.00 0.00 0.00 1.82
388 3288 2.618709 GCTTGCTGTGTTCCTTTGTAGT 59.381 45.455 0.00 0.00 0.00 2.73
389 3289 2.030805 GGCTTGCTGTGTTCCTTTGTAG 60.031 50.000 0.00 0.00 0.00 2.74
399 3303 1.202651 ACGACTTTAGGCTTGCTGTGT 60.203 47.619 0.00 0.00 0.00 3.72
415 3319 2.391389 GCTGCCACCTGCTTACGAC 61.391 63.158 0.00 0.00 42.00 4.34
836 3798 5.896073 ACAAAAGAGAGGGAGAGAGAAAA 57.104 39.130 0.00 0.00 0.00 2.29
838 3800 4.040952 CCAACAAAAGAGAGGGAGAGAGAA 59.959 45.833 0.00 0.00 0.00 2.87
847 3839 2.654863 ACCACACCAACAAAAGAGAGG 58.345 47.619 0.00 0.00 0.00 3.69
897 3889 2.338620 CACGCGACCAAGGTCTGA 59.661 61.111 15.93 0.00 42.54 3.27
898 3890 2.738521 CCACGCGACCAAGGTCTG 60.739 66.667 15.93 11.29 42.54 3.51
1095 4101 1.600916 GGCCGTTGATAGGGATGCC 60.601 63.158 0.00 0.00 0.00 4.40
1108 4120 2.005960 GACAGATGAGTAGCGGCCGT 62.006 60.000 28.70 16.08 0.00 5.68
1114 4126 0.317436 CTCGGCGACAGATGAGTAGC 60.317 60.000 4.99 0.00 39.08 3.58
1270 4295 1.066143 CGTGTTTACCTCAGCTGGGAT 60.066 52.381 17.43 0.00 0.00 3.85
1282 4312 2.789723 GCGTGCGTGCGTGTTTAC 60.790 61.111 3.11 0.00 0.00 2.01
1427 4467 2.444706 CGGGCCTGGGAGAGATCA 60.445 66.667 2.57 0.00 0.00 2.92
1589 4650 4.603535 GCTGGCTTGGGTGGTGGT 62.604 66.667 0.00 0.00 0.00 4.16
1655 4739 6.478344 CAGAATACAGAACAGAATAGTGGAGC 59.522 42.308 0.00 0.00 0.00 4.70
1746 4831 3.252974 ACAAGCCGAACTGATAAGAGG 57.747 47.619 0.00 0.00 0.00 3.69
1775 4860 4.081972 ACATCGTACTGCTCTGAATCAAGT 60.082 41.667 0.00 0.00 0.00 3.16
1808 4893 3.916776 CCCGAGTTCTAGTTTCACGTAAC 59.083 47.826 0.00 0.00 0.00 2.50
1870 5234 4.921470 AATGTTAGACGACGACCAATTG 57.079 40.909 0.00 0.00 0.00 2.32
1951 5316 6.567050 TGAATAGAATTGCAGCTTTCATTCC 58.433 36.000 18.03 7.23 0.00 3.01
2068 5433 7.332213 TCAGTCTGTTGAATTCATTTGTTCA 57.668 32.000 9.40 2.17 32.86 3.18
2087 5452 4.219288 AGCATTCCCATCAAGTTTTCAGTC 59.781 41.667 0.00 0.00 0.00 3.51
2092 5457 5.549742 TTTCAGCATTCCCATCAAGTTTT 57.450 34.783 0.00 0.00 0.00 2.43
2104 5469 9.846248 AGTTAATCAAGTGTAATTTCAGCATTC 57.154 29.630 0.00 0.00 0.00 2.67
2181 5547 9.120538 GCTTACCCTATAATTTTGAGATGTTGA 57.879 33.333 0.00 0.00 0.00 3.18
2195 5561 9.914834 AACTATGAATTTGTGCTTACCCTATAA 57.085 29.630 0.00 0.00 0.00 0.98
2196 5562 9.914834 AAACTATGAATTTGTGCTTACCCTATA 57.085 29.630 0.00 0.00 0.00 1.31
2197 5563 8.686334 CAAACTATGAATTTGTGCTTACCCTAT 58.314 33.333 0.00 0.00 33.27 2.57
2198 5564 7.362574 GCAAACTATGAATTTGTGCTTACCCTA 60.363 37.037 0.00 0.00 38.93 3.53
2211 5577 8.893219 TCTCATATTCTCGCAAACTATGAATT 57.107 30.769 0.00 0.00 30.69 2.17
2259 5625 0.322456 TGCACATGTACTCCCAAGGC 60.322 55.000 0.00 0.00 0.00 4.35
2265 5631 4.049186 CGGTAAGTATGCACATGTACTCC 58.951 47.826 0.00 0.00 31.10 3.85
2336 5702 0.761802 GGGAGGATGATCAGGGTGAC 59.238 60.000 0.09 0.00 0.00 3.67
2343 5709 3.054139 CACTTTCAAGGGGAGGATGATCA 60.054 47.826 0.00 0.00 0.00 2.92
2344 5710 3.549794 CACTTTCAAGGGGAGGATGATC 58.450 50.000 0.00 0.00 0.00 2.92
2345 5711 3.659183 CACTTTCAAGGGGAGGATGAT 57.341 47.619 0.00 0.00 0.00 2.45
2354 5720 6.434028 TGAAAATCTGATACCACTTTCAAGGG 59.566 38.462 10.46 0.00 31.70 3.95
2355 5721 7.362401 CCTGAAAATCTGATACCACTTTCAAGG 60.362 40.741 12.78 12.03 33.68 3.61
2356 5722 7.533426 CCTGAAAATCTGATACCACTTTCAAG 58.467 38.462 12.78 6.15 33.68 3.02
2357 5723 6.071952 GCCTGAAAATCTGATACCACTTTCAA 60.072 38.462 12.78 2.24 33.68 2.69
2358 5724 5.415701 GCCTGAAAATCTGATACCACTTTCA 59.584 40.000 11.73 11.73 33.19 2.69
2359 5725 5.649831 AGCCTGAAAATCTGATACCACTTTC 59.350 40.000 5.29 5.29 0.00 2.62
2360 5726 5.416952 CAGCCTGAAAATCTGATACCACTTT 59.583 40.000 0.00 0.00 0.00 2.66
2361 5727 4.946157 CAGCCTGAAAATCTGATACCACTT 59.054 41.667 0.00 0.00 0.00 3.16
2362 5728 4.225942 TCAGCCTGAAAATCTGATACCACT 59.774 41.667 0.00 0.00 32.48 4.00
2363 5729 4.517285 TCAGCCTGAAAATCTGATACCAC 58.483 43.478 0.00 0.00 32.48 4.16
2364 5730 4.471025 TCTCAGCCTGAAAATCTGATACCA 59.529 41.667 0.00 0.00 36.41 3.25
2365 5731 5.028549 TCTCAGCCTGAAAATCTGATACC 57.971 43.478 0.00 0.00 36.41 2.73
2366 5732 7.565323 AAATCTCAGCCTGAAAATCTGATAC 57.435 36.000 0.00 0.00 36.41 2.24
2367 5733 9.113838 GTAAAATCTCAGCCTGAAAATCTGATA 57.886 33.333 0.00 0.00 36.41 2.15
2368 5734 7.613022 TGTAAAATCTCAGCCTGAAAATCTGAT 59.387 33.333 0.00 0.00 36.41 2.90
2369 5735 6.942005 TGTAAAATCTCAGCCTGAAAATCTGA 59.058 34.615 0.00 0.00 35.74 3.27
2370 5736 7.094463 ACTGTAAAATCTCAGCCTGAAAATCTG 60.094 37.037 0.00 0.00 35.37 2.90
2371 5737 6.944862 ACTGTAAAATCTCAGCCTGAAAATCT 59.055 34.615 0.00 0.00 35.37 2.40
2372 5738 7.150783 ACTGTAAAATCTCAGCCTGAAAATC 57.849 36.000 0.00 0.00 35.37 2.17
2373 5739 7.530426 AACTGTAAAATCTCAGCCTGAAAAT 57.470 32.000 0.00 0.00 35.37 1.82
2374 5740 6.959639 AACTGTAAAATCTCAGCCTGAAAA 57.040 33.333 0.00 0.00 35.37 2.29
2375 5741 6.959639 AAACTGTAAAATCTCAGCCTGAAA 57.040 33.333 0.00 0.00 35.37 2.69
2376 5742 6.959639 AAAACTGTAAAATCTCAGCCTGAA 57.040 33.333 0.00 0.00 35.37 3.02
2377 5743 6.293407 CGAAAAACTGTAAAATCTCAGCCTGA 60.293 38.462 0.00 0.00 35.37 3.86
2378 5744 5.853282 CGAAAAACTGTAAAATCTCAGCCTG 59.147 40.000 0.00 0.00 35.37 4.85
2379 5745 5.531287 ACGAAAAACTGTAAAATCTCAGCCT 59.469 36.000 0.00 0.00 35.37 4.58
2380 5746 5.758924 ACGAAAAACTGTAAAATCTCAGCC 58.241 37.500 0.00 0.00 35.37 4.85
2381 5747 7.573627 ACTACGAAAAACTGTAAAATCTCAGC 58.426 34.615 0.00 0.00 35.37 4.26
2382 5748 9.931210 AAACTACGAAAAACTGTAAAATCTCAG 57.069 29.630 0.00 0.00 37.65 3.35
2389 5755 9.462174 TCGATCTAAACTACGAAAAACTGTAAA 57.538 29.630 0.00 0.00 0.00 2.01
2390 5756 9.121517 CTCGATCTAAACTACGAAAAACTGTAA 57.878 33.333 0.00 0.00 34.50 2.41
2391 5757 8.292448 ACTCGATCTAAACTACGAAAAACTGTA 58.708 33.333 0.00 0.00 34.50 2.74
2392 5758 7.144000 ACTCGATCTAAACTACGAAAAACTGT 58.856 34.615 0.00 0.00 34.50 3.55
2393 5759 7.564044 ACTCGATCTAAACTACGAAAAACTG 57.436 36.000 0.00 0.00 34.50 3.16
2394 5760 9.286946 CATACTCGATCTAAACTACGAAAAACT 57.713 33.333 0.00 0.00 34.50 2.66
2395 5761 9.070149 ACATACTCGATCTAAACTACGAAAAAC 57.930 33.333 0.00 0.00 34.50 2.43
2396 5762 9.630098 AACATACTCGATCTAAACTACGAAAAA 57.370 29.630 0.00 0.00 34.50 1.94
2397 5763 9.630098 AAACATACTCGATCTAAACTACGAAAA 57.370 29.630 0.00 0.00 34.50 2.29
2398 5764 9.630098 AAAACATACTCGATCTAAACTACGAAA 57.370 29.630 0.00 0.00 34.50 3.46
2399 5765 9.630098 AAAAACATACTCGATCTAAACTACGAA 57.370 29.630 0.00 0.00 34.50 3.85
2400 5766 9.282247 GAAAAACATACTCGATCTAAACTACGA 57.718 33.333 0.00 0.00 0.00 3.43
2401 5767 9.069078 TGAAAAACATACTCGATCTAAACTACG 57.931 33.333 0.00 0.00 0.00 3.51
2417 5783 6.814644 CGTGGACTGTAGGTATGAAAAACATA 59.185 38.462 0.00 0.00 40.07 2.29
2418 5784 5.642063 CGTGGACTGTAGGTATGAAAAACAT 59.358 40.000 0.00 0.00 42.39 2.71
2419 5785 4.992319 CGTGGACTGTAGGTATGAAAAACA 59.008 41.667 0.00 0.00 0.00 2.83
2420 5786 5.232463 TCGTGGACTGTAGGTATGAAAAAC 58.768 41.667 0.00 0.00 0.00 2.43
2421 5787 5.471556 TCGTGGACTGTAGGTATGAAAAA 57.528 39.130 0.00 0.00 0.00 1.94
2422 5788 5.471556 TTCGTGGACTGTAGGTATGAAAA 57.528 39.130 0.00 0.00 0.00 2.29
2423 5789 5.471556 TTTCGTGGACTGTAGGTATGAAA 57.528 39.130 0.00 0.00 0.00 2.69
2424 5790 5.471556 TTTTCGTGGACTGTAGGTATGAA 57.528 39.130 0.00 0.00 0.00 2.57
2425 5791 4.619863 GCTTTTCGTGGACTGTAGGTATGA 60.620 45.833 0.00 0.00 0.00 2.15
2426 5792 3.617263 GCTTTTCGTGGACTGTAGGTATG 59.383 47.826 0.00 0.00 0.00 2.39
2427 5793 3.369157 GGCTTTTCGTGGACTGTAGGTAT 60.369 47.826 0.00 0.00 0.00 2.73
2428 5794 2.028748 GGCTTTTCGTGGACTGTAGGTA 60.029 50.000 0.00 0.00 0.00 3.08
2429 5795 1.270678 GGCTTTTCGTGGACTGTAGGT 60.271 52.381 0.00 0.00 0.00 3.08
2430 5796 1.270625 TGGCTTTTCGTGGACTGTAGG 60.271 52.381 0.00 0.00 0.00 3.18
2431 5797 2.163818 TGGCTTTTCGTGGACTGTAG 57.836 50.000 0.00 0.00 0.00 2.74
2432 5798 2.623878 TTGGCTTTTCGTGGACTGTA 57.376 45.000 0.00 0.00 0.00 2.74
2433 5799 1.757682 TTTGGCTTTTCGTGGACTGT 58.242 45.000 0.00 0.00 0.00 3.55
2434 5800 2.861462 TTTTGGCTTTTCGTGGACTG 57.139 45.000 0.00 0.00 0.00 3.51
2454 5820 7.607991 CGGATATGATGAACTAGCCCTATTTTT 59.392 37.037 0.00 0.00 0.00 1.94
2455 5821 7.106239 CGGATATGATGAACTAGCCCTATTTT 58.894 38.462 0.00 0.00 0.00 1.82
2456 5822 6.352222 CCGGATATGATGAACTAGCCCTATTT 60.352 42.308 0.00 0.00 0.00 1.40
2457 5823 5.129485 CCGGATATGATGAACTAGCCCTATT 59.871 44.000 0.00 0.00 0.00 1.73
2458 5824 4.651503 CCGGATATGATGAACTAGCCCTAT 59.348 45.833 0.00 0.00 0.00 2.57
2459 5825 4.023980 CCGGATATGATGAACTAGCCCTA 58.976 47.826 0.00 0.00 0.00 3.53
2460 5826 2.834549 CCGGATATGATGAACTAGCCCT 59.165 50.000 0.00 0.00 0.00 5.19
2461 5827 2.832129 TCCGGATATGATGAACTAGCCC 59.168 50.000 0.00 0.00 0.00 5.19
2462 5828 3.368531 GGTCCGGATATGATGAACTAGCC 60.369 52.174 7.81 0.00 0.00 3.93
2463 5829 3.258372 TGGTCCGGATATGATGAACTAGC 59.742 47.826 7.81 0.00 0.00 3.42
2464 5830 4.524714 ACTGGTCCGGATATGATGAACTAG 59.475 45.833 7.81 1.23 0.00 2.57
2465 5831 4.480115 ACTGGTCCGGATATGATGAACTA 58.520 43.478 7.81 0.00 0.00 2.24
2466 5832 3.309296 ACTGGTCCGGATATGATGAACT 58.691 45.455 7.81 0.00 0.00 3.01
2467 5833 3.322254 AGACTGGTCCGGATATGATGAAC 59.678 47.826 7.81 0.00 0.00 3.18
2468 5834 3.321968 CAGACTGGTCCGGATATGATGAA 59.678 47.826 7.81 0.00 0.00 2.57
2469 5835 2.893489 CAGACTGGTCCGGATATGATGA 59.107 50.000 7.81 0.00 0.00 2.92
2470 5836 2.893489 TCAGACTGGTCCGGATATGATG 59.107 50.000 7.81 3.17 0.00 3.07
2471 5837 3.161067 CTCAGACTGGTCCGGATATGAT 58.839 50.000 7.81 0.00 0.00 2.45
2472 5838 2.587522 CTCAGACTGGTCCGGATATGA 58.412 52.381 7.81 3.33 0.00 2.15
2473 5839 1.000283 GCTCAGACTGGTCCGGATATG 60.000 57.143 7.81 0.00 0.00 1.78
2474 5840 1.133325 AGCTCAGACTGGTCCGGATAT 60.133 52.381 7.81 0.00 0.00 1.63
2475 5841 0.259065 AGCTCAGACTGGTCCGGATA 59.741 55.000 7.81 0.00 0.00 2.59
2476 5842 0.616111 AAGCTCAGACTGGTCCGGAT 60.616 55.000 7.81 0.00 0.00 4.18
2477 5843 0.832135 AAAGCTCAGACTGGTCCGGA 60.832 55.000 0.00 0.00 0.00 5.14
2478 5844 0.035458 AAAAGCTCAGACTGGTCCGG 59.965 55.000 1.81 0.00 0.00 5.14
2479 5845 1.151668 CAAAAGCTCAGACTGGTCCG 58.848 55.000 1.81 0.00 0.00 4.79
2480 5846 0.877743 GCAAAAGCTCAGACTGGTCC 59.122 55.000 1.81 0.00 0.00 4.46
2481 5847 1.597742 TGCAAAAGCTCAGACTGGTC 58.402 50.000 1.81 0.00 0.00 4.02
2482 5848 2.283145 ATGCAAAAGCTCAGACTGGT 57.717 45.000 1.81 0.00 0.00 4.00
2483 5849 3.341823 ACTATGCAAAAGCTCAGACTGG 58.658 45.455 1.81 0.00 0.00 4.00
2484 5850 4.252073 AGACTATGCAAAAGCTCAGACTG 58.748 43.478 0.00 0.00 0.00 3.51
2485 5851 4.550076 AGACTATGCAAAAGCTCAGACT 57.450 40.909 0.00 0.00 0.00 3.24
2486 5852 5.619625 AAAGACTATGCAAAAGCTCAGAC 57.380 39.130 0.00 0.00 0.00 3.51
2487 5853 6.639632 AAAAAGACTATGCAAAAGCTCAGA 57.360 33.333 0.00 0.00 0.00 3.27
2488 5854 8.976986 ATTAAAAAGACTATGCAAAAGCTCAG 57.023 30.769 0.00 0.00 0.00 3.35
2509 5875 9.591404 CGCAAATTCAACAAAGCAAAATATTAA 57.409 25.926 0.00 0.00 0.00 1.40
2510 5876 8.226448 CCGCAAATTCAACAAAGCAAAATATTA 58.774 29.630 0.00 0.00 0.00 0.98
2511 5877 7.076983 CCGCAAATTCAACAAAGCAAAATATT 58.923 30.769 0.00 0.00 0.00 1.28
2512 5878 6.204495 ACCGCAAATTCAACAAAGCAAAATAT 59.796 30.769 0.00 0.00 0.00 1.28
2513 5879 5.525378 ACCGCAAATTCAACAAAGCAAAATA 59.475 32.000 0.00 0.00 0.00 1.40
2514 5880 4.335037 ACCGCAAATTCAACAAAGCAAAAT 59.665 33.333 0.00 0.00 0.00 1.82
2515 5881 3.686726 ACCGCAAATTCAACAAAGCAAAA 59.313 34.783 0.00 0.00 0.00 2.44
2516 5882 3.265791 ACCGCAAATTCAACAAAGCAAA 58.734 36.364 0.00 0.00 0.00 3.68
2517 5883 2.898705 ACCGCAAATTCAACAAAGCAA 58.101 38.095 0.00 0.00 0.00 3.91
2518 5884 2.593346 ACCGCAAATTCAACAAAGCA 57.407 40.000 0.00 0.00 0.00 3.91
2519 5885 2.599612 GCAACCGCAAATTCAACAAAGC 60.600 45.455 0.00 0.00 38.36 3.51
2520 5886 3.237466 GCAACCGCAAATTCAACAAAG 57.763 42.857 0.00 0.00 38.36 2.77
2533 5899 3.348967 GACACGACGATGCAACCGC 62.349 63.158 0.00 4.58 39.24 5.68
2534 5900 1.553195 TTGACACGACGATGCAACCG 61.553 55.000 0.00 9.84 0.00 4.44
2535 5901 0.163788 CTTGACACGACGATGCAACC 59.836 55.000 0.00 0.00 0.00 3.77
2536 5902 0.859232 ACTTGACACGACGATGCAAC 59.141 50.000 0.00 0.00 0.00 4.17
2537 5903 1.260297 CAACTTGACACGACGATGCAA 59.740 47.619 0.00 1.43 0.00 4.08
2538 5904 0.858583 CAACTTGACACGACGATGCA 59.141 50.000 0.00 0.00 0.00 3.96
2539 5905 0.451135 GCAACTTGACACGACGATGC 60.451 55.000 0.00 0.00 0.00 3.91
2540 5906 1.136529 CAGCAACTTGACACGACGATG 60.137 52.381 0.00 0.00 0.00 3.84
2541 5907 1.139989 CAGCAACTTGACACGACGAT 58.860 50.000 0.00 0.00 0.00 3.73
2542 5908 0.874175 CCAGCAACTTGACACGACGA 60.874 55.000 0.00 0.00 0.00 4.20
2543 5909 1.151777 ACCAGCAACTTGACACGACG 61.152 55.000 0.00 0.00 0.00 5.12
2544 5910 0.582005 GACCAGCAACTTGACACGAC 59.418 55.000 0.00 0.00 0.00 4.34
2545 5911 0.464036 AGACCAGCAACTTGACACGA 59.536 50.000 0.00 0.00 0.00 4.35
2546 5912 1.299541 AAGACCAGCAACTTGACACG 58.700 50.000 0.00 0.00 0.00 4.49
2547 5913 2.224314 GCTAAGACCAGCAACTTGACAC 59.776 50.000 0.00 0.00 41.40 3.67
2548 5914 2.494059 GCTAAGACCAGCAACTTGACA 58.506 47.619 0.00 0.00 41.40 3.58
2549 5915 1.461127 CGCTAAGACCAGCAACTTGAC 59.539 52.381 0.00 0.00 41.88 3.18
2550 5916 1.070134 ACGCTAAGACCAGCAACTTGA 59.930 47.619 0.00 0.00 41.88 3.02
2551 5917 1.461127 GACGCTAAGACCAGCAACTTG 59.539 52.381 0.00 0.00 41.88 3.16
2552 5918 1.344763 AGACGCTAAGACCAGCAACTT 59.655 47.619 0.00 0.00 41.88 2.66
2553 5919 0.969894 AGACGCTAAGACCAGCAACT 59.030 50.000 0.00 0.00 41.88 3.16
2554 5920 2.094649 ACTAGACGCTAAGACCAGCAAC 60.095 50.000 0.00 0.00 41.88 4.17
2555 5921 2.168496 ACTAGACGCTAAGACCAGCAA 58.832 47.619 0.00 0.00 41.88 3.91
2556 5922 1.835494 ACTAGACGCTAAGACCAGCA 58.165 50.000 0.00 0.00 41.88 4.41
2557 5923 2.943449 AACTAGACGCTAAGACCAGC 57.057 50.000 0.00 0.00 38.23 4.85
2558 5924 3.429135 GGGAAACTAGACGCTAAGACCAG 60.429 52.174 0.00 0.00 0.00 4.00
2559 5925 2.494870 GGGAAACTAGACGCTAAGACCA 59.505 50.000 0.00 0.00 0.00 4.02
2560 5926 2.759535 AGGGAAACTAGACGCTAAGACC 59.240 50.000 0.00 0.00 0.00 3.85
2561 5927 4.453177 AAGGGAAACTAGACGCTAAGAC 57.547 45.455 0.00 0.00 0.00 3.01
2562 5928 5.503927 TCTAAGGGAAACTAGACGCTAAGA 58.496 41.667 0.00 0.00 0.00 2.10
2563 5929 5.357596 ACTCTAAGGGAAACTAGACGCTAAG 59.642 44.000 0.00 3.67 0.00 2.18
2564 5930 5.259632 ACTCTAAGGGAAACTAGACGCTAA 58.740 41.667 0.00 0.00 0.00 3.09
2565 5931 4.853007 ACTCTAAGGGAAACTAGACGCTA 58.147 43.478 0.00 0.00 0.00 4.26
2566 5932 3.699413 ACTCTAAGGGAAACTAGACGCT 58.301 45.455 0.00 0.00 0.00 5.07
2567 5933 4.453177 AACTCTAAGGGAAACTAGACGC 57.547 45.455 0.00 0.00 0.00 5.19
2568 5934 5.094134 CGAAACTCTAAGGGAAACTAGACG 58.906 45.833 0.00 0.00 0.00 4.18
2569 5935 6.072008 ACTCGAAACTCTAAGGGAAACTAGAC 60.072 42.308 0.00 0.00 0.00 2.59
2570 5936 6.008960 ACTCGAAACTCTAAGGGAAACTAGA 58.991 40.000 0.00 0.00 0.00 2.43
2571 5937 6.270156 ACTCGAAACTCTAAGGGAAACTAG 57.730 41.667 0.00 0.00 0.00 2.57
2572 5938 6.492772 AGAACTCGAAACTCTAAGGGAAACTA 59.507 38.462 0.00 0.00 0.00 2.24
2573 5939 5.304871 AGAACTCGAAACTCTAAGGGAAACT 59.695 40.000 0.00 0.00 0.00 2.66
2574 5940 5.405873 CAGAACTCGAAACTCTAAGGGAAAC 59.594 44.000 0.00 0.00 0.00 2.78
2575 5941 5.539048 CAGAACTCGAAACTCTAAGGGAAA 58.461 41.667 0.00 0.00 0.00 3.13
2576 5942 4.560919 GCAGAACTCGAAACTCTAAGGGAA 60.561 45.833 0.00 0.00 0.00 3.97
2577 5943 3.056749 GCAGAACTCGAAACTCTAAGGGA 60.057 47.826 0.00 0.00 0.00 4.20
2578 5944 3.056465 AGCAGAACTCGAAACTCTAAGGG 60.056 47.826 0.00 0.00 0.00 3.95
2579 5945 4.170256 GAGCAGAACTCGAAACTCTAAGG 58.830 47.826 0.00 0.00 35.18 2.69
2591 5957 1.265365 GGCAACTTGTGAGCAGAACTC 59.735 52.381 0.00 0.00 46.45 3.01
2592 5958 1.312815 GGCAACTTGTGAGCAGAACT 58.687 50.000 0.00 0.00 0.00 3.01
2593 5959 1.024271 TGGCAACTTGTGAGCAGAAC 58.976 50.000 0.00 0.00 37.61 3.01
2594 5960 1.024271 GTGGCAACTTGTGAGCAGAA 58.976 50.000 0.00 0.00 37.61 3.02
2595 5961 1.159713 CGTGGCAACTTGTGAGCAGA 61.160 55.000 0.00 0.00 37.61 4.26
2596 5962 1.280746 CGTGGCAACTTGTGAGCAG 59.719 57.895 0.00 0.00 37.61 4.24
2597 5963 2.833533 GCGTGGCAACTTGTGAGCA 61.834 57.895 0.00 0.00 37.61 4.26
2598 5964 2.050985 GCGTGGCAACTTGTGAGC 60.051 61.111 0.00 0.00 37.61 4.26
2599 5965 2.639286 GGCGTGGCAACTTGTGAG 59.361 61.111 0.00 0.00 37.61 3.51
2600 5966 3.276091 CGGCGTGGCAACTTGTGA 61.276 61.111 0.00 0.00 37.61 3.58
2601 5967 4.980903 GCGGCGTGGCAACTTGTG 62.981 66.667 9.37 0.00 37.61 3.33


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

AutoCloner maintained by Alex Coulton.