Multiple sequence alignment - TraesCS6B01G297300

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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 TraesCS6B01G297300 chr6B 100.000 4351 0 0 1 4351 534087997 534092347 0.000000e+00 8035.0
1 TraesCS6B01G297300 chr6A 94.815 1755 53 9 594 2313 496467670 496469421 0.000000e+00 2702.0
2 TraesCS6B01G297300 chr6A 93.208 854 41 8 2534 3379 496469475 496470319 0.000000e+00 1240.0
3 TraesCS6B01G297300 chr6A 92.526 388 27 1 3964 4351 496471709 496472094 4.920000e-154 555.0
4 TraesCS6B01G297300 chr6A 86.036 222 23 8 371 591 191233911 191234125 9.410000e-57 231.0
5 TraesCS6B01G297300 chr6A 89.474 171 14 3 2331 2499 214179674 214179506 3.410000e-51 213.0
6 TraesCS6B01G297300 chr6A 90.000 140 11 2 3825 3962 496471528 496471666 1.240000e-40 178.0
7 TraesCS6B01G297300 chr6A 98.182 55 1 0 3786 3840 496470836 496470890 3.580000e-16 97.1
8 TraesCS6B01G297300 chr6A 94.545 55 2 1 3786 3839 496470920 496470974 2.790000e-12 84.2
9 TraesCS6B01G297300 chr6D 95.242 1366 29 5 768 2110 346961929 346960577 0.000000e+00 2130.0
10 TraesCS6B01G297300 chr6D 89.257 1117 75 19 2560 3640 346959081 346957974 0.000000e+00 1356.0
11 TraesCS6B01G297300 chr6D 92.105 380 21 3 3973 4351 346957645 346957274 1.070000e-145 527.0
12 TraesCS6B01G297300 chr6D 91.600 250 20 1 3713 3962 346957951 346957703 1.160000e-90 344.0
13 TraesCS6B01G297300 chr6D 88.393 224 12 9 2110 2333 346959346 346959137 1.550000e-64 257.0
14 TraesCS6B01G297300 chr6D 96.923 65 1 1 669 733 346961990 346961927 1.650000e-19 108.0
15 TraesCS6B01G297300 chr6D 85.106 94 14 0 2571 2664 96747893 96747800 3.580000e-16 97.1
16 TraesCS6B01G297300 chr5B 95.791 594 20 5 1 591 319897401 319897992 0.000000e+00 953.0
17 TraesCS6B01G297300 chr5B 91.231 593 35 6 1 592 237756223 237756799 0.000000e+00 791.0
18 TraesCS6B01G297300 chr2B 95.777 592 23 2 1 591 427875543 427876133 0.000000e+00 953.0
19 TraesCS6B01G297300 chr2B 90.672 268 23 1 1 268 464599432 464599167 5.350000e-94 355.0
20 TraesCS6B01G297300 chr2B 89.474 171 14 3 2330 2500 740563572 740563406 3.410000e-51 213.0
21 TraesCS6B01G297300 chr2B 78.859 298 43 13 306 591 776043716 776043427 2.670000e-42 183.0
22 TraesCS6B01G297300 chr2B 92.593 54 2 2 2236 2289 222229570 222229519 4.670000e-10 76.8
23 TraesCS6B01G297300 chr1B 93.167 600 20 10 1 594 169527323 169527907 0.000000e+00 861.0
24 TraesCS6B01G297300 chr1B 87.375 301 24 7 306 593 50970891 50970592 2.510000e-87 333.0
25 TraesCS6B01G297300 chr1B 87.500 88 11 0 2571 2658 328127455 328127542 7.700000e-18 102.0
26 TraesCS6B01G297300 chr3B 92.074 593 29 7 1 592 214071347 214071922 0.000000e+00 819.0
27 TraesCS6B01G297300 chr3B 88.645 273 24 7 4 274 428063765 428063498 4.200000e-85 326.0
28 TraesCS6B01G297300 chr3B 88.136 177 16 3 2321 2496 269252162 269251990 5.700000e-49 206.0
29 TraesCS6B01G297300 chr3B 91.837 49 2 2 2242 2290 675520491 675520445 2.810000e-07 67.6
30 TraesCS6B01G297300 chr3B 92.683 41 3 0 2569 2609 805685577 805685537 4.700000e-05 60.2
31 TraesCS6B01G297300 chr3B 100.000 29 0 0 599 627 666616687 666616659 2.000000e-03 54.7
32 TraesCS6B01G297300 chr3B 100.000 28 0 0 600 627 248245728 248245755 8.000000e-03 52.8
33 TraesCS6B01G297300 chr7B 93.917 411 18 7 1 409 662909699 662910104 8.000000e-172 614.0
34 TraesCS6B01G297300 chr7B 78.528 163 22 12 3480 3635 600446879 600446723 1.290000e-15 95.3
35 TraesCS6B01G297300 chr7B 93.182 44 2 1 3740 3782 674078360 674078403 3.630000e-06 63.9
36 TraesCS6B01G297300 chr5D 86.339 366 30 14 1 355 227455049 227455405 8.830000e-102 381.0
37 TraesCS6B01G297300 chr5D 77.431 288 39 17 3378 3646 364735869 364736149 9.750000e-32 148.0
38 TraesCS6B01G297300 chr3D 85.650 223 23 9 371 591 578898571 578898786 4.380000e-55 226.0
39 TraesCS6B01G297300 chr3D 89.266 177 15 2 2321 2496 187836481 187836308 7.330000e-53 219.0
40 TraesCS6B01G297300 chr3D 79.845 129 22 4 3471 3599 84023573 84023449 1.670000e-14 91.6
41 TraesCS6B01G297300 chr7D 90.476 168 13 2 2332 2496 525767962 525768129 7.330000e-53 219.0
42 TraesCS6B01G297300 chr7D 88.068 176 18 1 2326 2501 454079414 454079242 5.700000e-49 206.0
43 TraesCS6B01G297300 chr7D 93.750 48 3 0 2244 2291 399598041 399597994 6.040000e-09 73.1
44 TraesCS6B01G297300 chr3A 89.655 174 15 1 2326 2499 600920849 600921019 7.330000e-53 219.0
45 TraesCS6B01G297300 chr3A 100.000 35 0 0 2242 2276 648480459 648480425 1.010000e-06 65.8
46 TraesCS6B01G297300 chr3A 82.857 70 8 2 561 629 669562690 669562756 4.700000e-05 60.2
47 TraesCS6B01G297300 chr3A 100.000 29 0 0 600 628 669562694 669562722 2.000000e-03 54.7
48 TraesCS6B01G297300 chr3A 94.286 35 2 0 600 634 693557322 693557356 2.000000e-03 54.7
49 TraesCS6B01G297300 chr5A 90.000 170 13 4 2327 2496 320214409 320214244 2.630000e-52 217.0
50 TraesCS6B01G297300 chr5A 90.000 50 3 2 3742 3791 321920409 321920456 3.630000e-06 63.9
51 TraesCS6B01G297300 chr4D 89.595 173 14 3 2332 2504 89423899 89424067 2.630000e-52 217.0
52 TraesCS6B01G297300 chr4A 76.779 267 36 17 3471 3733 459759499 459759255 4.570000e-25 126.0
53 TraesCS6B01G297300 chr4A 79.389 131 15 10 3471 3599 720377777 720377657 1.000000e-11 82.4
54 TraesCS6B01G297300 chr4A 94.872 39 0 1 2243 2281 673490537 673490573 4.700000e-05 60.2
55 TraesCS6B01G297300 chr2A 74.928 347 49 26 3373 3692 709597513 709597178 1.640000e-24 124.0
56 TraesCS6B01G297300 chr2A 78.191 188 30 8 3468 3649 194717359 194717541 4.600000e-20 110.0
57 TraesCS6B01G297300 chr2A 100.000 28 0 0 600 627 778137324 778137351 8.000000e-03 52.8
58 TraesCS6B01G297300 chr1A 88.636 88 10 0 2571 2658 296923070 296923157 1.650000e-19 108.0
59 TraesCS6B01G297300 chr1D 89.189 74 6 2 2238 2310 396889998 396889926 1.670000e-14 91.6
60 TraesCS6B01G297300 chr1D 100.000 28 0 0 600 627 736719 736692 8.000000e-03 52.8
61 TraesCS6B01G297300 chrUn 76.836 177 29 8 3471 3642 49987740 49987571 5.990000e-14 89.8
62 TraesCS6B01G297300 chr2D 79.545 132 20 7 3471 3600 14725744 14725618 2.160000e-13 87.9
63 TraesCS6B01G297300 chr2D 91.667 48 3 1 2242 2289 174446705 174446659 1.010000e-06 65.8
64 TraesCS6B01G297300 chr4B 100.000 29 0 0 600 628 7551603 7551631 2.000000e-03 54.7


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 TraesCS6B01G297300 chr6B 534087997 534092347 4350 False 8035.000000 8035 100.000000 1 4351 1 chr6B.!!$F1 4350
1 TraesCS6B01G297300 chr6A 496467670 496472094 4424 False 809.383333 2702 93.879333 594 4351 6 chr6A.!!$F2 3757
2 TraesCS6B01G297300 chr6D 346957274 346961990 4716 True 787.000000 2130 92.253333 669 4351 6 chr6D.!!$R2 3682
3 TraesCS6B01G297300 chr5B 319897401 319897992 591 False 953.000000 953 95.791000 1 591 1 chr5B.!!$F2 590
4 TraesCS6B01G297300 chr5B 237756223 237756799 576 False 791.000000 791 91.231000 1 592 1 chr5B.!!$F1 591
5 TraesCS6B01G297300 chr2B 427875543 427876133 590 False 953.000000 953 95.777000 1 591 1 chr2B.!!$F1 590
6 TraesCS6B01G297300 chr1B 169527323 169527907 584 False 861.000000 861 93.167000 1 594 1 chr1B.!!$F1 593
7 TraesCS6B01G297300 chr3B 214071347 214071922 575 False 819.000000 819 92.074000 1 592 1 chr3B.!!$F1 591

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
857 903 1.404843 GCCGTCCTAGATCTGAACCT 58.595 55.0 5.18 0.0 0.00 3.50 F
2536 3827 0.396001 GGAGCTACTCCCTCCGTTCT 60.396 60.0 1.98 0.0 44.36 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2639 3941 0.104304 CCCTCCGTTCGGACATAAGG 59.896 60.0 10.00 9.29 0.0 2.69 R
4091 6321 0.175760 GAGATGGAGTGGCGCAGTAA 59.824 55.0 10.83 0.00 0.0 2.24 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
69 70 7.708752 ACAAATTTGGAAGAGCGAACATTTTTA 59.291 29.630 21.74 0.00 0.00 1.52
344 357 7.610865 TCAAAAAGAAAGGAGCAAGAAGAAAA 58.389 30.769 0.00 0.00 0.00 2.29
435 451 6.749036 TCAGAAACCTTCTAGAAAGTTCCT 57.251 37.500 17.68 9.55 38.11 3.36
750 783 4.329545 ACCACTCGCGCACCCAAT 62.330 61.111 8.75 0.00 0.00 3.16
751 784 3.499737 CCACTCGCGCACCCAATC 61.500 66.667 8.75 0.00 0.00 2.67
765 800 1.821332 CAATCAAGCCCCTCCTCGC 60.821 63.158 0.00 0.00 0.00 5.03
766 801 3.391665 AATCAAGCCCCTCCTCGCG 62.392 63.158 0.00 0.00 0.00 5.87
857 903 1.404843 GCCGTCCTAGATCTGAACCT 58.595 55.000 5.18 0.00 0.00 3.50
969 1015 2.125912 CTCTTCACTCCACCGCCG 60.126 66.667 0.00 0.00 0.00 6.46
970 1016 4.373116 TCTTCACTCCACCGCCGC 62.373 66.667 0.00 0.00 0.00 6.53
1627 1673 6.005066 TCATGATGGGAGATAAAGCTCAAA 57.995 37.500 0.00 0.00 36.62 2.69
1870 1921 7.662604 TTAACTTACAATCTTCTTTCCCGTC 57.337 36.000 0.00 0.00 0.00 4.79
1939 1997 4.330944 AGATTGTGACACGGTTGAGTAA 57.669 40.909 0.22 0.00 0.00 2.24
2175 3464 0.959372 GCAAGCTGCACTGTCCTGAT 60.959 55.000 1.02 0.00 44.26 2.90
2185 3474 1.276421 ACTGTCCTGATGGAAGAACGG 59.724 52.381 0.00 0.00 45.18 4.44
2299 3589 8.680903 CATATATTGATAGGAGAAAATGGGTGC 58.319 37.037 0.00 0.00 0.00 5.01
2314 3604 2.203788 TGCGAGAACCCTCCACCT 60.204 61.111 0.00 0.00 36.04 4.00
2319 3609 0.836400 GAGAACCCTCCACCTGACCA 60.836 60.000 0.00 0.00 33.30 4.02
2331 3621 4.018506 TCCACCTGACCATGTACATTTCAT 60.019 41.667 5.37 0.00 0.00 2.57
2332 3622 5.190726 TCCACCTGACCATGTACATTTCATA 59.809 40.000 5.37 0.00 0.00 2.15
2333 3623 5.296780 CCACCTGACCATGTACATTTCATAC 59.703 44.000 5.37 0.00 0.00 2.39
2334 3624 6.115446 CACCTGACCATGTACATTTCATACT 58.885 40.000 5.37 0.00 0.00 2.12
2335 3625 6.258727 CACCTGACCATGTACATTTCATACTC 59.741 42.308 5.37 0.00 0.00 2.59
2336 3626 5.760253 CCTGACCATGTACATTTCATACTCC 59.240 44.000 5.37 0.00 0.00 3.85
2337 3627 5.680619 TGACCATGTACATTTCATACTCCC 58.319 41.667 5.37 0.00 0.00 4.30
2338 3628 5.428457 TGACCATGTACATTTCATACTCCCT 59.572 40.000 5.37 0.00 0.00 4.20
2339 3629 5.930135 ACCATGTACATTTCATACTCCCTC 58.070 41.667 5.37 0.00 0.00 4.30
2340 3630 5.428457 ACCATGTACATTTCATACTCCCTCA 59.572 40.000 5.37 0.00 0.00 3.86
2341 3631 5.994054 CCATGTACATTTCATACTCCCTCAG 59.006 44.000 5.37 0.00 0.00 3.35
2342 3632 6.408548 CCATGTACATTTCATACTCCCTCAGT 60.409 42.308 5.37 0.00 39.41 3.41
2343 3633 6.620877 TGTACATTTCATACTCCCTCAGTT 57.379 37.500 0.00 0.00 36.43 3.16
2344 3634 6.640518 TGTACATTTCATACTCCCTCAGTTC 58.359 40.000 0.00 0.00 36.43 3.01
2345 3635 5.104259 ACATTTCATACTCCCTCAGTTCC 57.896 43.478 0.00 0.00 36.43 3.62
2346 3636 4.785376 ACATTTCATACTCCCTCAGTTCCT 59.215 41.667 0.00 0.00 36.43 3.36
2347 3637 5.964477 ACATTTCATACTCCCTCAGTTCCTA 59.036 40.000 0.00 0.00 36.43 2.94
2348 3638 6.443849 ACATTTCATACTCCCTCAGTTCCTAA 59.556 38.462 0.00 0.00 36.43 2.69
2349 3639 6.945636 TTTCATACTCCCTCAGTTCCTAAA 57.054 37.500 0.00 0.00 36.43 1.85
2350 3640 7.510675 TTTCATACTCCCTCAGTTCCTAAAT 57.489 36.000 0.00 0.00 36.43 1.40
2351 3641 8.618240 TTTCATACTCCCTCAGTTCCTAAATA 57.382 34.615 0.00 0.00 36.43 1.40
2352 3642 7.841282 TCATACTCCCTCAGTTCCTAAATAG 57.159 40.000 0.00 0.00 36.43 1.73
2353 3643 7.363031 TCATACTCCCTCAGTTCCTAAATAGT 58.637 38.462 0.00 0.00 36.43 2.12
2354 3644 8.508601 TCATACTCCCTCAGTTCCTAAATAGTA 58.491 37.037 0.00 0.00 36.43 1.82
2355 3645 9.315363 CATACTCCCTCAGTTCCTAAATAGTAT 57.685 37.037 0.00 0.00 36.43 2.12
2358 3648 9.369672 ACTCCCTCAGTTCCTAAATAGTATAAG 57.630 37.037 0.00 0.00 26.56 1.73
2359 3649 9.369672 CTCCCTCAGTTCCTAAATAGTATAAGT 57.630 37.037 0.00 0.00 0.00 2.24
2360 3650 9.364653 TCCCTCAGTTCCTAAATAGTATAAGTC 57.635 37.037 0.00 0.00 0.00 3.01
2361 3651 9.369672 CCCTCAGTTCCTAAATAGTATAAGTCT 57.630 37.037 0.00 0.00 0.00 3.24
2379 3669 8.940768 ATAAGTCTTTCTAGAGATTTCTGTGC 57.059 34.615 0.00 0.00 34.79 4.57
2380 3670 5.406649 AGTCTTTCTAGAGATTTCTGTGCG 58.593 41.667 0.00 0.00 34.79 5.34
2381 3671 4.564769 GTCTTTCTAGAGATTTCTGTGCGG 59.435 45.833 0.00 0.00 34.79 5.69
2382 3672 4.462834 TCTTTCTAGAGATTTCTGTGCGGA 59.537 41.667 0.00 0.00 34.79 5.54
2383 3673 3.784701 TCTAGAGATTTCTGTGCGGAC 57.215 47.619 0.00 0.00 34.79 4.79
2384 3674 3.357203 TCTAGAGATTTCTGTGCGGACT 58.643 45.455 8.99 0.00 34.79 3.85
2385 3675 4.524053 TCTAGAGATTTCTGTGCGGACTA 58.476 43.478 8.99 0.00 34.79 2.59
2386 3676 3.512033 AGAGATTTCTGTGCGGACTAC 57.488 47.619 8.99 0.00 30.72 2.73
2387 3677 2.826128 AGAGATTTCTGTGCGGACTACA 59.174 45.455 8.99 0.00 30.72 2.74
2388 3678 3.449018 AGAGATTTCTGTGCGGACTACAT 59.551 43.478 8.99 0.00 30.72 2.29
2389 3679 4.645136 AGAGATTTCTGTGCGGACTACATA 59.355 41.667 8.99 0.00 30.72 2.29
2390 3680 4.683832 AGATTTCTGTGCGGACTACATAC 58.316 43.478 8.99 0.00 0.00 2.39
2391 3681 2.554806 TTCTGTGCGGACTACATACG 57.445 50.000 8.99 0.00 0.00 3.06
2392 3682 0.736636 TCTGTGCGGACTACATACGG 59.263 55.000 8.99 0.00 0.00 4.02
2393 3683 0.736636 CTGTGCGGACTACATACGGA 59.263 55.000 8.99 0.00 0.00 4.69
2394 3684 1.337071 CTGTGCGGACTACATACGGAT 59.663 52.381 8.99 0.00 0.00 4.18
2395 3685 1.066454 TGTGCGGACTACATACGGATG 59.934 52.381 5.94 5.94 39.16 3.51
2397 3687 2.291465 GTGCGGACTACATACGGATGTA 59.709 50.000 19.32 19.32 44.77 2.29
2398 3688 3.057736 GTGCGGACTACATACGGATGTAT 60.058 47.826 20.64 11.04 45.42 2.29
2399 3689 4.154737 GTGCGGACTACATACGGATGTATA 59.845 45.833 20.64 1.71 45.42 1.47
2400 3690 4.945543 TGCGGACTACATACGGATGTATAT 59.054 41.667 20.64 12.15 45.42 0.86
2401 3691 6.037500 GTGCGGACTACATACGGATGTATATA 59.962 42.308 20.64 0.52 45.42 0.86
2402 3692 6.259387 TGCGGACTACATACGGATGTATATAG 59.741 42.308 20.64 13.28 45.42 1.31
2403 3693 6.481313 GCGGACTACATACGGATGTATATAGA 59.519 42.308 20.64 0.00 45.42 1.98
2404 3694 7.518052 GCGGACTACATACGGATGTATATAGAC 60.518 44.444 20.64 10.95 45.42 2.59
2405 3695 7.306457 CGGACTACATACGGATGTATATAGACG 60.306 44.444 20.64 15.48 45.42 4.18
2406 3696 7.493971 GGACTACATACGGATGTATATAGACGT 59.506 40.741 20.64 12.85 45.42 4.34
2407 3697 9.521503 GACTACATACGGATGTATATAGACGTA 57.478 37.037 20.64 9.65 45.42 3.57
2425 3715 7.956420 AGACGTATTTTACTGTGTTGATTCA 57.044 32.000 0.00 0.00 0.00 2.57
2426 3716 7.793902 AGACGTATTTTACTGTGTTGATTCAC 58.206 34.615 0.00 0.00 38.63 3.18
2427 3717 7.656137 AGACGTATTTTACTGTGTTGATTCACT 59.344 33.333 0.00 0.00 38.90 3.41
2428 3718 7.793902 ACGTATTTTACTGTGTTGATTCACTC 58.206 34.615 0.00 0.00 38.90 3.51
2429 3719 7.439955 ACGTATTTTACTGTGTTGATTCACTCA 59.560 33.333 0.00 0.00 38.90 3.41
2430 3720 8.443160 CGTATTTTACTGTGTTGATTCACTCAT 58.557 33.333 0.00 0.00 38.90 2.90
2433 3723 7.566760 TTTACTGTGTTGATTCACTCATTGT 57.433 32.000 0.00 0.00 38.90 2.71
2435 3725 4.224433 CTGTGTTGATTCACTCATTGTGC 58.776 43.478 0.00 0.00 45.81 4.57
2436 3726 3.884693 TGTGTTGATTCACTCATTGTGCT 59.115 39.130 0.00 0.00 45.81 4.40
2437 3727 4.023792 TGTGTTGATTCACTCATTGTGCTC 60.024 41.667 0.00 0.00 45.81 4.26
2438 3728 3.503363 TGTTGATTCACTCATTGTGCTCC 59.497 43.478 0.00 0.00 45.81 4.70
2439 3729 2.349590 TGATTCACTCATTGTGCTCCG 58.650 47.619 0.00 0.00 45.81 4.63
2440 3730 2.289631 TGATTCACTCATTGTGCTCCGT 60.290 45.455 0.00 0.00 45.81 4.69
2441 3731 3.056179 TGATTCACTCATTGTGCTCCGTA 60.056 43.478 0.00 0.00 45.81 4.02
2442 3732 3.610040 TTCACTCATTGTGCTCCGTAT 57.390 42.857 0.00 0.00 45.81 3.06
2443 3733 2.892374 TCACTCATTGTGCTCCGTATG 58.108 47.619 0.00 0.00 45.81 2.39
2444 3734 2.233676 TCACTCATTGTGCTCCGTATGT 59.766 45.455 0.00 0.00 45.81 2.29
2445 3735 3.445805 TCACTCATTGTGCTCCGTATGTA 59.554 43.478 0.00 0.00 45.81 2.29
2446 3736 3.798878 CACTCATTGTGCTCCGTATGTAG 59.201 47.826 0.00 0.00 40.06 2.74
2447 3737 3.447586 ACTCATTGTGCTCCGTATGTAGT 59.552 43.478 0.00 0.00 0.00 2.73
2448 3738 4.041740 TCATTGTGCTCCGTATGTAGTC 57.958 45.455 0.00 0.00 0.00 2.59
2449 3739 2.953466 TTGTGCTCCGTATGTAGTCC 57.047 50.000 0.00 0.00 0.00 3.85
2450 3740 1.842052 TGTGCTCCGTATGTAGTCCA 58.158 50.000 0.00 0.00 0.00 4.02
2451 3741 2.384828 TGTGCTCCGTATGTAGTCCAT 58.615 47.619 0.00 0.00 37.58 3.41
2452 3742 3.558033 TGTGCTCCGTATGTAGTCCATA 58.442 45.455 0.00 0.00 34.86 2.74
2453 3743 4.149598 TGTGCTCCGTATGTAGTCCATAT 58.850 43.478 0.00 0.00 38.29 1.78
2454 3744 4.587262 TGTGCTCCGTATGTAGTCCATATT 59.413 41.667 0.00 0.00 38.29 1.28
2455 3745 4.923871 GTGCTCCGTATGTAGTCCATATTG 59.076 45.833 0.00 0.00 38.29 1.90
2456 3746 4.021456 TGCTCCGTATGTAGTCCATATTGG 60.021 45.833 0.00 0.00 38.29 3.16
2457 3747 4.219944 GCTCCGTATGTAGTCCATATTGGA 59.780 45.833 0.00 0.00 45.98 3.53
2472 3762 8.337118 TCCATATTGGAATCTCTAAAAGGACT 57.663 34.615 0.00 0.00 45.00 3.85
2473 3763 8.781951 TCCATATTGGAATCTCTAAAAGGACTT 58.218 33.333 0.00 0.00 45.00 3.01
2489 3779 8.959705 AAAAGGACTTATATTTAGGAACGGAG 57.040 34.615 0.00 0.00 0.00 4.63
2490 3780 6.667558 AGGACTTATATTTAGGAACGGAGG 57.332 41.667 0.00 0.00 0.00 4.30
2491 3781 5.543020 AGGACTTATATTTAGGAACGGAGGG 59.457 44.000 0.00 0.00 0.00 4.30
2507 3797 4.015084 CGGAGGGAGTAGTTCTTAACAGA 58.985 47.826 0.00 0.00 0.00 3.41
2512 3803 4.285260 GGGAGTAGTTCTTAACAGACCCAA 59.715 45.833 0.00 0.00 34.94 4.12
2534 3825 4.358810 GGAGCTACTCCCTCCGTT 57.641 61.111 1.98 0.00 44.36 4.44
2535 3826 2.117257 GGAGCTACTCCCTCCGTTC 58.883 63.158 1.98 0.00 44.36 3.95
2536 3827 0.396001 GGAGCTACTCCCTCCGTTCT 60.396 60.000 1.98 0.00 44.36 3.01
2538 3829 0.684805 AGCTACTCCCTCCGTTCTGG 60.685 60.000 0.00 0.00 40.09 3.86
2639 3941 6.872920 TCAAATTTGAACTATAACCATGCCC 58.127 36.000 18.45 0.00 33.55 5.36
2664 3966 1.684983 TGTCCGAACGGAGGGAATATC 59.315 52.381 16.35 3.05 46.16 1.63
2748 4051 2.601481 GTGAAACTGAAGCATGACGG 57.399 50.000 0.00 0.00 0.00 4.79
3098 4401 0.777446 AAAGCCCAAACTAGCCCTGA 59.223 50.000 0.00 0.00 0.00 3.86
3155 4465 7.014230 ACCAATAATGTACATTGTTATCCCTGC 59.986 37.037 27.62 0.00 32.12 4.85
3179 4489 6.464222 CACTGAATGTATATCCCGGTTGTAT 58.536 40.000 0.00 0.00 0.00 2.29
3266 4577 7.280356 ACACTTGTACTGGACAGAAAGTTAAT 58.720 34.615 6.29 0.06 39.88 1.40
3268 4579 8.926710 CACTTGTACTGGACAGAAAGTTAATAG 58.073 37.037 6.29 0.00 39.88 1.73
3287 4598 0.673985 GTCCCCTTTTGCCTGTGTTC 59.326 55.000 0.00 0.00 0.00 3.18
3304 4615 9.162764 GCCTGTGTTCTAATCTTTCTGTTATTA 57.837 33.333 0.00 0.00 0.00 0.98
3362 4673 7.072076 AGGTAAAGGAATAAATATGGACGAGGT 59.928 37.037 0.00 0.00 0.00 3.85
3376 4701 1.635663 CGAGGTGTTTTGGCTAGCCG 61.636 60.000 28.28 8.71 39.42 5.52
3391 4716 0.822121 AGCCGGGGAGTGAACAAAAC 60.822 55.000 2.18 0.00 0.00 2.43
3396 4722 2.621055 CGGGGAGTGAACAAAACAATCA 59.379 45.455 0.00 0.00 34.66 2.57
3469 4796 2.462456 TGACTGAGTGCTTGATGTCC 57.538 50.000 0.00 0.00 0.00 4.02
3491 4841 3.752222 CCATTTGGATATCTGAGCTGCTC 59.248 47.826 22.38 22.38 37.39 4.26
3493 4843 4.333913 TTTGGATATCTGAGCTGCTCTC 57.666 45.455 28.04 17.26 42.23 3.20
3494 4844 2.246469 TGGATATCTGAGCTGCTCTCC 58.754 52.381 28.04 24.45 41.18 3.71
3548 4898 7.539366 GTGAAAAAGTTTACTGTTTGTGCACTA 59.461 33.333 19.41 7.83 33.75 2.74
3550 4900 8.996024 AAAAAGTTTACTGTTTGTGCACTATT 57.004 26.923 19.41 0.00 32.45 1.73
3553 4903 7.328277 AGTTTACTGTTTGTGCACTATTTGA 57.672 32.000 19.41 0.00 0.00 2.69
3554 4904 7.767261 AGTTTACTGTTTGTGCACTATTTGAA 58.233 30.769 19.41 0.00 0.00 2.69
3556 4906 8.690840 GTTTACTGTTTGTGCACTATTTGAATC 58.309 33.333 19.41 2.67 0.00 2.52
3557 4907 6.639632 ACTGTTTGTGCACTATTTGAATCT 57.360 33.333 19.41 0.00 0.00 2.40
3558 4908 6.441274 ACTGTTTGTGCACTATTTGAATCTG 58.559 36.000 19.41 8.23 0.00 2.90
3559 4909 6.262944 ACTGTTTGTGCACTATTTGAATCTGA 59.737 34.615 19.41 0.00 0.00 3.27
3565 4915 8.523523 TGTGCACTATTTGAATCTGATTTTTG 57.476 30.769 19.41 0.00 0.00 2.44
3618 4972 1.994779 GCAAATTTGGCATCCACTTCG 59.005 47.619 19.47 0.00 30.78 3.79
3637 4991 0.373716 GCGCCCTCAAACATCTTACG 59.626 55.000 0.00 0.00 0.00 3.18
3640 4994 1.130561 GCCCTCAAACATCTTACGTGC 59.869 52.381 0.00 0.00 0.00 5.34
3643 4997 3.252215 CCCTCAAACATCTTACGTGCAAA 59.748 43.478 0.00 0.00 0.00 3.68
3645 4999 5.277825 CCTCAAACATCTTACGTGCAAAAA 58.722 37.500 0.00 0.00 0.00 1.94
3664 5019 2.625695 AAAAGTCGGGGTTCTTCGAA 57.374 45.000 0.00 0.00 37.14 3.71
3674 5029 4.436986 CGGGGTTCTTCGAATTTTTCTAGC 60.437 45.833 0.00 0.00 0.00 3.42
3679 5037 7.652105 GGGTTCTTCGAATTTTTCTAGCTTTTT 59.348 33.333 0.00 0.00 0.00 1.94
3728 5086 1.139654 TCTCGGGCTCAGAATTGGATG 59.860 52.381 0.00 0.00 0.00 3.51
3782 5140 5.104859 TCCTACATATAAGACGTTTGGGCAA 60.105 40.000 0.00 0.00 0.00 4.52
3842 6025 6.790285 AAATGAAAAATGCATCCACAGTTC 57.210 33.333 0.00 0.00 0.00 3.01
3878 6061 6.002082 TGAGGCAAAATCCATGATATCTGAG 58.998 40.000 3.98 0.00 0.00 3.35
3880 6063 5.075493 GGCAAAATCCATGATATCTGAGGT 58.925 41.667 3.98 0.00 0.00 3.85
3922 6105 3.186909 TGCTGTGGATCGTCGAAATAAG 58.813 45.455 0.00 0.00 0.00 1.73
3944 6127 3.323403 GGATCGATGGAGGAGATCACTTT 59.677 47.826 0.54 0.00 41.71 2.66
3946 6129 2.432146 TCGATGGAGGAGATCACTTTGG 59.568 50.000 0.00 0.00 0.00 3.28
3947 6130 2.484417 CGATGGAGGAGATCACTTTGGG 60.484 54.545 0.00 0.00 0.00 4.12
3950 6133 1.065126 GGAGGAGATCACTTTGGGTGG 60.065 57.143 0.00 0.00 45.38 4.61
3954 6137 1.142688 AGATCACTTTGGGTGGCCCT 61.143 55.000 0.00 0.00 45.70 5.19
3956 6139 2.445492 ATCACTTTGGGTGGCCCTGG 62.445 60.000 0.00 0.00 45.70 4.45
3958 6141 2.399607 ACTTTGGGTGGCCCTGGAA 61.400 57.895 0.00 0.00 45.70 3.53
3977 6206 2.772691 GGTACCAGTCCTCGCTCCG 61.773 68.421 7.15 0.00 0.00 4.63
3996 6225 1.445582 CGGAGAGGTACACGGCAAC 60.446 63.158 0.00 0.00 0.00 4.17
4091 6321 2.693864 CCCATGGCCTCCACCTCT 60.694 66.667 6.09 0.00 35.80 3.69
4113 6343 4.899239 GCGCCACTCCATCTCCGG 62.899 72.222 0.00 0.00 0.00 5.14
4115 6345 3.785859 GCCACTCCATCTCCGGCA 61.786 66.667 0.00 0.00 42.50 5.69
4166 6396 4.083862 GCTTCTCCGCCTCCCGTT 62.084 66.667 0.00 0.00 34.38 4.44
4320 6550 3.676324 CGAGTCTGGTATGTTCAAGGACC 60.676 52.174 0.00 0.00 0.00 4.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
531 550 2.355986 TTCCGCACACCCTATCGCT 61.356 57.895 0.00 0.00 0.00 4.93
751 784 4.821589 GACGCGAGGAGGGGCTTG 62.822 72.222 15.93 0.00 37.90 4.01
857 903 1.006571 GAAAGGTCGTCGCCTGACA 60.007 57.895 8.66 0.00 45.80 3.58
866 912 0.830866 AACGGAGGAGGAAAGGTCGT 60.831 55.000 0.00 0.00 0.00 4.34
969 1015 1.227973 CTAGGGCCTGGATTTCGGC 60.228 63.158 18.53 0.00 45.55 5.54
970 1016 1.227973 GCTAGGGCCTGGATTTCGG 60.228 63.158 22.50 0.00 0.00 4.30
1062 1108 3.068691 CGGGTCAGGAAGGCGAGA 61.069 66.667 0.00 0.00 0.00 4.04
1627 1673 5.824624 CACCAACCTACAGCAAAGATATCAT 59.175 40.000 5.32 0.00 0.00 2.45
1816 1862 8.976986 ATAATTCAGCAATCACTTCAAAGTTC 57.023 30.769 0.00 0.00 37.08 3.01
1846 1892 6.366877 CGACGGGAAAGAAGATTGTAAGTTAA 59.633 38.462 0.00 0.00 0.00 2.01
1939 1997 3.402628 AAGCGTCTCAACTACACCAAT 57.597 42.857 0.00 0.00 0.00 3.16
2299 3589 1.592223 GTCAGGTGGAGGGTTCTCG 59.408 63.158 0.00 0.00 40.85 4.04
2314 3604 5.428457 AGGGAGTATGAAATGTACATGGTCA 59.572 40.000 19.46 19.46 0.00 4.02
2319 3609 6.814954 ACTGAGGGAGTATGAAATGTACAT 57.185 37.500 1.41 1.41 30.86 2.29
2332 3622 9.369672 CTTATACTATTTAGGAACTGAGGGAGT 57.630 37.037 0.00 0.00 41.52 3.85
2333 3623 9.369672 ACTTATACTATTTAGGAACTGAGGGAG 57.630 37.037 0.00 0.00 41.52 4.30
2334 3624 9.364653 GACTTATACTATTTAGGAACTGAGGGA 57.635 37.037 0.00 0.00 41.52 4.20
2335 3625 9.369672 AGACTTATACTATTTAGGAACTGAGGG 57.630 37.037 0.00 0.00 41.52 4.30
2354 3644 7.704472 CGCACAGAAATCTCTAGAAAGACTTAT 59.296 37.037 0.00 0.00 0.00 1.73
2355 3645 7.030165 CGCACAGAAATCTCTAGAAAGACTTA 58.970 38.462 0.00 0.00 0.00 2.24
2356 3646 5.866633 CGCACAGAAATCTCTAGAAAGACTT 59.133 40.000 0.00 0.00 0.00 3.01
2357 3647 5.406649 CGCACAGAAATCTCTAGAAAGACT 58.593 41.667 0.00 0.00 0.00 3.24
2358 3648 4.564769 CCGCACAGAAATCTCTAGAAAGAC 59.435 45.833 0.00 0.00 0.00 3.01
2359 3649 4.462834 TCCGCACAGAAATCTCTAGAAAGA 59.537 41.667 0.00 0.00 0.00 2.52
2360 3650 4.564769 GTCCGCACAGAAATCTCTAGAAAG 59.435 45.833 0.00 0.00 0.00 2.62
2361 3651 4.220821 AGTCCGCACAGAAATCTCTAGAAA 59.779 41.667 0.00 0.00 0.00 2.52
2362 3652 3.764434 AGTCCGCACAGAAATCTCTAGAA 59.236 43.478 0.00 0.00 0.00 2.10
2363 3653 3.357203 AGTCCGCACAGAAATCTCTAGA 58.643 45.455 0.00 0.00 0.00 2.43
2364 3654 3.791973 AGTCCGCACAGAAATCTCTAG 57.208 47.619 0.00 0.00 0.00 2.43
2365 3655 4.014406 TGTAGTCCGCACAGAAATCTCTA 58.986 43.478 0.00 0.00 0.00 2.43
2366 3656 2.826128 TGTAGTCCGCACAGAAATCTCT 59.174 45.455 0.00 0.00 0.00 3.10
2367 3657 3.232213 TGTAGTCCGCACAGAAATCTC 57.768 47.619 0.00 0.00 0.00 2.75
2368 3658 3.895232 ATGTAGTCCGCACAGAAATCT 57.105 42.857 0.00 0.00 0.00 2.40
2369 3659 3.486108 CGTATGTAGTCCGCACAGAAATC 59.514 47.826 0.00 0.00 0.00 2.17
2370 3660 3.444916 CGTATGTAGTCCGCACAGAAAT 58.555 45.455 0.00 0.00 0.00 2.17
2371 3661 2.416296 CCGTATGTAGTCCGCACAGAAA 60.416 50.000 0.00 0.00 0.00 2.52
2372 3662 1.133598 CCGTATGTAGTCCGCACAGAA 59.866 52.381 0.00 0.00 0.00 3.02
2373 3663 0.736636 CCGTATGTAGTCCGCACAGA 59.263 55.000 0.00 0.00 0.00 3.41
2374 3664 0.736636 TCCGTATGTAGTCCGCACAG 59.263 55.000 0.00 0.00 0.00 3.66
2375 3665 1.066454 CATCCGTATGTAGTCCGCACA 59.934 52.381 0.00 0.00 0.00 4.57
2376 3666 1.066605 ACATCCGTATGTAGTCCGCAC 59.933 52.381 0.00 0.00 44.66 5.34
2377 3667 1.395635 ACATCCGTATGTAGTCCGCA 58.604 50.000 0.00 0.00 44.66 5.69
2399 3689 9.647797 TGAATCAACACAGTAAAATACGTCTAT 57.352 29.630 0.00 0.00 0.00 1.98
2400 3690 8.918658 GTGAATCAACACAGTAAAATACGTCTA 58.081 33.333 0.00 0.00 40.11 2.59
2401 3691 7.656137 AGTGAATCAACACAGTAAAATACGTCT 59.344 33.333 0.00 0.00 42.45 4.18
2402 3692 7.793902 AGTGAATCAACACAGTAAAATACGTC 58.206 34.615 0.00 0.00 42.45 4.34
2403 3693 7.439955 TGAGTGAATCAACACAGTAAAATACGT 59.560 33.333 0.00 0.00 42.45 3.57
2404 3694 7.792925 TGAGTGAATCAACACAGTAAAATACG 58.207 34.615 0.00 0.00 42.45 3.06
2407 3697 8.632679 ACAATGAGTGAATCAACACAGTAAAAT 58.367 29.630 0.00 0.00 42.53 1.82
2408 3698 7.995289 ACAATGAGTGAATCAACACAGTAAAA 58.005 30.769 0.00 0.00 42.53 1.52
2409 3699 7.566760 ACAATGAGTGAATCAACACAGTAAA 57.433 32.000 0.00 0.00 42.53 2.01
2425 3715 3.447586 ACTACATACGGAGCACAATGAGT 59.552 43.478 0.00 0.00 0.00 3.41
2426 3716 4.045104 GACTACATACGGAGCACAATGAG 58.955 47.826 0.00 0.00 0.00 2.90
2427 3717 3.181479 GGACTACATACGGAGCACAATGA 60.181 47.826 0.00 0.00 0.00 2.57
2428 3718 3.123804 GGACTACATACGGAGCACAATG 58.876 50.000 0.00 0.00 0.00 2.82
2429 3719 2.764010 TGGACTACATACGGAGCACAAT 59.236 45.455 0.00 0.00 0.00 2.71
2430 3720 2.172679 TGGACTACATACGGAGCACAA 58.827 47.619 0.00 0.00 0.00 3.33
2431 3721 1.842052 TGGACTACATACGGAGCACA 58.158 50.000 0.00 0.00 0.00 4.57
2432 3722 4.785511 ATATGGACTACATACGGAGCAC 57.214 45.455 0.00 0.00 44.41 4.40
2433 3723 4.021456 CCAATATGGACTACATACGGAGCA 60.021 45.833 0.00 0.00 44.41 4.26
2434 3724 4.219944 TCCAATATGGACTACATACGGAGC 59.780 45.833 0.00 0.00 42.67 4.70
2435 3725 5.977489 TCCAATATGGACTACATACGGAG 57.023 43.478 0.00 0.00 42.67 4.63
2447 3737 8.337118 AGTCCTTTTAGAGATTCCAATATGGA 57.663 34.615 0.00 0.00 46.61 3.41
2448 3738 8.986929 AAGTCCTTTTAGAGATTCCAATATGG 57.013 34.615 0.00 0.00 39.43 2.74
2464 3754 7.991460 CCTCCGTTCCTAAATATAAGTCCTTTT 59.009 37.037 0.00 0.00 0.00 2.27
2465 3755 7.419865 CCCTCCGTTCCTAAATATAAGTCCTTT 60.420 40.741 0.00 0.00 0.00 3.11
2466 3756 6.042897 CCCTCCGTTCCTAAATATAAGTCCTT 59.957 42.308 0.00 0.00 0.00 3.36
2467 3757 5.543020 CCCTCCGTTCCTAAATATAAGTCCT 59.457 44.000 0.00 0.00 0.00 3.85
2468 3758 5.541484 TCCCTCCGTTCCTAAATATAAGTCC 59.459 44.000 0.00 0.00 0.00 3.85
2469 3759 6.267242 ACTCCCTCCGTTCCTAAATATAAGTC 59.733 42.308 0.00 0.00 0.00 3.01
2470 3760 6.141790 ACTCCCTCCGTTCCTAAATATAAGT 58.858 40.000 0.00 0.00 0.00 2.24
2471 3761 6.667558 ACTCCCTCCGTTCCTAAATATAAG 57.332 41.667 0.00 0.00 0.00 1.73
2472 3762 7.300658 ACTACTCCCTCCGTTCCTAAATATAA 58.699 38.462 0.00 0.00 0.00 0.98
2473 3763 6.856757 ACTACTCCCTCCGTTCCTAAATATA 58.143 40.000 0.00 0.00 0.00 0.86
2474 3764 5.713807 ACTACTCCCTCCGTTCCTAAATAT 58.286 41.667 0.00 0.00 0.00 1.28
2475 3765 5.134725 ACTACTCCCTCCGTTCCTAAATA 57.865 43.478 0.00 0.00 0.00 1.40
2476 3766 3.991683 ACTACTCCCTCCGTTCCTAAAT 58.008 45.455 0.00 0.00 0.00 1.40
2477 3767 3.463048 ACTACTCCCTCCGTTCCTAAA 57.537 47.619 0.00 0.00 0.00 1.85
2478 3768 3.011032 AGAACTACTCCCTCCGTTCCTAA 59.989 47.826 0.00 0.00 37.15 2.69
2479 3769 2.579860 AGAACTACTCCCTCCGTTCCTA 59.420 50.000 0.00 0.00 37.15 2.94
2480 3770 1.358445 AGAACTACTCCCTCCGTTCCT 59.642 52.381 0.00 0.00 37.15 3.36
2481 3771 1.849977 AGAACTACTCCCTCCGTTCC 58.150 55.000 0.00 0.00 37.15 3.62
2482 3772 4.219288 TGTTAAGAACTACTCCCTCCGTTC 59.781 45.833 0.00 0.00 36.81 3.95
2483 3773 4.154942 TGTTAAGAACTACTCCCTCCGTT 58.845 43.478 0.00 0.00 0.00 4.44
2484 3774 3.762823 CTGTTAAGAACTACTCCCTCCGT 59.237 47.826 0.00 0.00 0.00 4.69
2485 3775 4.015084 TCTGTTAAGAACTACTCCCTCCG 58.985 47.826 0.00 0.00 0.00 4.63
2486 3776 4.160065 GGTCTGTTAAGAACTACTCCCTCC 59.840 50.000 0.00 0.00 37.15 4.30
2487 3777 4.160065 GGGTCTGTTAAGAACTACTCCCTC 59.840 50.000 0.00 0.00 40.30 4.30
2488 3778 4.095211 GGGTCTGTTAAGAACTACTCCCT 58.905 47.826 0.00 0.00 40.30 4.20
2489 3779 3.836562 TGGGTCTGTTAAGAACTACTCCC 59.163 47.826 0.00 0.00 40.30 4.30
2490 3780 5.479124 TTGGGTCTGTTAAGAACTACTCC 57.521 43.478 0.00 0.00 40.30 3.85
2491 3781 7.332182 CAGAATTGGGTCTGTTAAGAACTACTC 59.668 40.741 0.00 0.00 40.30 2.59
2530 3821 0.468648 GGTCCCCTAATCCAGAACGG 59.531 60.000 0.00 0.00 0.00 4.44
2531 3822 1.200519 TGGTCCCCTAATCCAGAACG 58.799 55.000 0.00 0.00 0.00 3.95
2536 3827 0.253160 ACAGCTGGTCCCCTAATCCA 60.253 55.000 19.93 0.00 0.00 3.41
2538 3829 0.464554 GCACAGCTGGTCCCCTAATC 60.465 60.000 19.93 0.00 0.00 1.75
2544 3846 0.322456 TAATGTGCACAGCTGGTCCC 60.322 55.000 25.84 3.70 0.00 4.46
2639 3941 0.104304 CCCTCCGTTCGGACATAAGG 59.896 60.000 10.00 9.29 0.00 2.69
2664 3966 5.443185 AGTGTGAAATGAATGTGAACTGG 57.557 39.130 0.00 0.00 0.00 4.00
2712 4015 7.278646 TCAGTTTCACTGTATGAATATGCACTC 59.721 37.037 3.87 0.00 46.80 3.51
2748 4051 5.243060 ACCAATAAGAAAACAGCCAAGTACC 59.757 40.000 0.00 0.00 0.00 3.34
3098 4401 6.838401 AGTCCTATGAAAATCTGGGAATCT 57.162 37.500 0.00 0.00 0.00 2.40
3155 4465 4.703897 ACAACCGGGATATACATTCAGTG 58.296 43.478 6.32 0.00 0.00 3.66
3266 4577 1.145571 ACACAGGCAAAAGGGGACTA 58.854 50.000 0.00 0.00 42.68 2.59
3268 4579 0.673985 GAACACAGGCAAAAGGGGAC 59.326 55.000 0.00 0.00 0.00 4.46
3341 4652 6.248569 ACACCTCGTCCATATTTATTCCTT 57.751 37.500 0.00 0.00 0.00 3.36
3347 4658 4.396790 GCCAAAACACCTCGTCCATATTTA 59.603 41.667 0.00 0.00 0.00 1.40
3362 4673 2.034999 CCCCGGCTAGCCAAAACA 59.965 61.111 32.47 0.00 35.37 2.83
3376 4701 4.280677 TCATGATTGTTTTGTTCACTCCCC 59.719 41.667 0.00 0.00 0.00 4.81
3422 4748 8.879342 TTTCTCCGCAAAAATAATTCTGAAAA 57.121 26.923 0.00 0.00 0.00 2.29
3423 4749 8.356657 TCTTTCTCCGCAAAAATAATTCTGAAA 58.643 29.630 0.00 0.00 0.00 2.69
3427 4753 7.970614 GTCATCTTTCTCCGCAAAAATAATTCT 59.029 33.333 0.00 0.00 0.00 2.40
3430 4756 7.121168 TCAGTCATCTTTCTCCGCAAAAATAAT 59.879 33.333 0.00 0.00 0.00 1.28
3433 4760 4.761739 TCAGTCATCTTTCTCCGCAAAAAT 59.238 37.500 0.00 0.00 0.00 1.82
3440 4767 2.094286 AGCACTCAGTCATCTTTCTCCG 60.094 50.000 0.00 0.00 0.00 4.63
3469 4796 3.752222 GAGCAGCTCAGATATCCAAATGG 59.248 47.826 18.17 0.00 0.00 3.16
3491 4841 9.831737 CCTAAATTTGATATATTCTTTGCGGAG 57.168 33.333 0.00 0.00 0.00 4.63
3493 4843 8.576442 ACCCTAAATTTGATATATTCTTTGCGG 58.424 33.333 0.00 0.00 0.00 5.69
3515 4865 7.891498 AACAGTAAACTTTTTCACATACCCT 57.109 32.000 0.00 0.00 0.00 4.34
3527 4877 8.247562 TCAAATAGTGCACAAACAGTAAACTTT 58.752 29.630 21.04 0.00 0.00 2.66
3535 4885 6.671190 TCAGATTCAAATAGTGCACAAACAG 58.329 36.000 21.04 5.94 0.00 3.16
3572 4922 2.294074 GACATCCGAGTAGCTCTCAGT 58.706 52.381 11.93 5.95 42.88 3.41
3610 4964 3.171828 TTTGAGGGCGCGAAGTGGA 62.172 57.895 12.10 0.00 39.19 4.02
3611 4965 2.668212 TTTGAGGGCGCGAAGTGG 60.668 61.111 12.10 0.00 39.19 4.00
3618 4972 0.373716 CGTAAGATGTTTGAGGGCGC 59.626 55.000 0.00 0.00 43.02 6.53
3622 4976 4.481930 TTTGCACGTAAGATGTTTGAGG 57.518 40.909 0.00 0.00 43.62 3.86
3645 4999 2.625695 TTCGAAGAACCCCGACTTTT 57.374 45.000 0.00 0.00 45.90 2.27
3648 5002 2.853235 AAATTCGAAGAACCCCGACT 57.147 45.000 3.35 0.00 45.90 4.18
3649 5003 3.501062 AGAAAAATTCGAAGAACCCCGAC 59.499 43.478 3.35 0.00 45.90 4.79
3650 5004 3.746940 AGAAAAATTCGAAGAACCCCGA 58.253 40.909 3.35 0.00 45.90 5.14
3651 5005 4.436986 GCTAGAAAAATTCGAAGAACCCCG 60.437 45.833 3.35 0.00 45.90 5.73
3654 5008 8.575565 AAAAAGCTAGAAAAATTCGAAGAACC 57.424 30.769 3.35 0.00 45.90 3.62
3693 5051 1.202222 CCGAGAACATCTGCATTTGGC 60.202 52.381 0.00 0.00 45.13 4.52
3697 5055 0.254178 AGCCCGAGAACATCTGCATT 59.746 50.000 0.00 0.00 0.00 3.56
3698 5056 0.179062 GAGCCCGAGAACATCTGCAT 60.179 55.000 0.00 0.00 0.00 3.96
3703 5061 2.611225 ATTCTGAGCCCGAGAACATC 57.389 50.000 0.00 0.00 32.30 3.06
3704 5062 2.636830 CAATTCTGAGCCCGAGAACAT 58.363 47.619 0.00 0.00 32.30 2.71
3705 5063 1.339055 CCAATTCTGAGCCCGAGAACA 60.339 52.381 0.00 0.00 32.30 3.18
3706 5064 1.066143 TCCAATTCTGAGCCCGAGAAC 60.066 52.381 0.00 0.00 32.30 3.01
3707 5065 1.275666 TCCAATTCTGAGCCCGAGAA 58.724 50.000 0.00 0.00 34.00 2.87
3708 5066 1.139654 CATCCAATTCTGAGCCCGAGA 59.860 52.381 0.00 0.00 0.00 4.04
3709 5067 1.134280 ACATCCAATTCTGAGCCCGAG 60.134 52.381 0.00 0.00 0.00 4.63
3710 5068 0.911769 ACATCCAATTCTGAGCCCGA 59.088 50.000 0.00 0.00 0.00 5.14
3711 5069 1.672881 GAACATCCAATTCTGAGCCCG 59.327 52.381 0.00 0.00 0.00 6.13
3842 6025 1.522668 TTGCCTCATCAAACAGACGG 58.477 50.000 0.00 0.00 0.00 4.79
3878 6061 4.547406 AACTTCTGCTGTTTACGAAACC 57.453 40.909 0.00 0.00 40.67 3.27
3880 6063 4.796312 GCAAAACTTCTGCTGTTTACGAAA 59.204 37.500 0.00 0.00 36.72 3.46
3922 6105 2.524306 AGTGATCTCCTCCATCGATCC 58.476 52.381 0.00 0.00 34.17 3.36
3929 6112 2.044793 ACCCAAAGTGATCTCCTCCA 57.955 50.000 0.00 0.00 0.00 3.86
3946 6129 2.675371 GTACCTTCCAGGGCCACC 59.325 66.667 6.18 0.00 40.58 4.61
3947 6130 2.228480 TGGTACCTTCCAGGGCCAC 61.228 63.158 14.36 0.00 40.58 5.01
3954 6137 1.255667 GCGAGGACTGGTACCTTCCA 61.256 60.000 26.25 3.14 37.93 3.53
3956 6139 0.456628 GAGCGAGGACTGGTACCTTC 59.543 60.000 14.36 9.41 37.93 3.46
3958 6141 1.380112 GGAGCGAGGACTGGTACCT 60.380 63.158 14.36 0.00 40.80 3.08
3960 6143 2.799371 CGGAGCGAGGACTGGTAC 59.201 66.667 0.00 0.00 0.00 3.34
3977 6206 3.291101 TTGCCGTGTACCTCTCCGC 62.291 63.158 0.00 0.00 0.00 5.54
3996 6225 3.227276 CCTCATCGTCTCCCCGGG 61.227 72.222 15.80 15.80 0.00 5.73
4000 6230 2.107953 GCTGCCTCATCGTCTCCC 59.892 66.667 0.00 0.00 0.00 4.30
4068 6298 0.753111 GTGGAGGCCATGGGTGAATC 60.753 60.000 15.13 0.00 35.28 2.52
4069 6299 1.307647 GTGGAGGCCATGGGTGAAT 59.692 57.895 15.13 0.00 35.28 2.57
4070 6300 2.763215 GTGGAGGCCATGGGTGAA 59.237 61.111 15.13 0.00 35.28 3.18
4071 6301 3.338250 GGTGGAGGCCATGGGTGA 61.338 66.667 15.13 0.00 35.28 4.02
4073 6303 3.017581 GAGGTGGAGGCCATGGGT 61.018 66.667 15.13 0.00 35.28 4.51
4074 6304 0.988145 TAAGAGGTGGAGGCCATGGG 60.988 60.000 15.13 0.00 35.28 4.00
4075 6305 0.181350 GTAAGAGGTGGAGGCCATGG 59.819 60.000 7.63 7.63 35.28 3.66
4091 6321 0.175760 GAGATGGAGTGGCGCAGTAA 59.824 55.000 10.83 0.00 0.00 2.24
4113 6343 2.233654 CGGCAGAGCATCGTAGTGC 61.234 63.158 2.75 2.75 45.38 4.40
4115 6345 2.105128 GCGGCAGAGCATCGTAGT 59.895 61.111 0.00 0.00 42.67 2.73
4250 6480 0.324738 CCTGCACTAGGGACTCCAGA 60.325 60.000 0.00 0.00 43.33 3.86
4307 6537 0.981183 ACGCCTGGTCCTTGAACATA 59.019 50.000 0.00 0.00 0.00 2.29
4308 6538 0.606401 CACGCCTGGTCCTTGAACAT 60.606 55.000 0.00 0.00 0.00 2.71


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

AutoCloner maintained by Alex Coulton.