Multiple sequence alignment - TraesCS7A01G272400

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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 TraesCS7A01G272400 chr7A 100.000 6329 0 0 1 6329 285691246 285697574 0.000000e+00 11688.0
1 TraesCS7A01G272400 chr7A 85.600 750 92 10 418 1164 691517451 691516715 0.000000e+00 773.0
2 TraesCS7A01G272400 chr7A 84.667 750 98 10 418 1164 514689266 514688531 0.000000e+00 732.0
3 TraesCS7A01G272400 chr7A 95.531 179 7 1 2323 2501 677738459 677738636 1.040000e-72 285.0
4 TraesCS7A01G272400 chr7A 96.667 90 0 3 5595 5683 80581355 80581442 5.110000e-31 147.0
5 TraesCS7A01G272400 chr7A 95.556 90 3 1 5595 5684 78420436 78420348 6.610000e-30 143.0
6 TraesCS7A01G272400 chr7A 95.506 89 4 0 5591 5679 733832398 733832310 6.610000e-30 143.0
7 TraesCS7A01G272400 chr7A 85.714 105 10 4 318 420 691517635 691517534 8.680000e-19 106.0
8 TraesCS7A01G272400 chr7D 95.781 3887 90 21 2488 6329 263034903 263038760 0.000000e+00 6202.0
9 TraesCS7A01G272400 chr7D 92.036 1783 64 33 597 2327 263033148 263034904 0.000000e+00 2435.0
10 TraesCS7A01G272400 chr7D 91.556 450 18 3 1 443 263024197 263024633 2.520000e-168 603.0
11 TraesCS7A01G272400 chr7D 97.778 90 1 1 5595 5684 74395372 74395284 3.060000e-33 154.0
12 TraesCS7A01G272400 chr7D 97.619 84 2 0 5595 5678 633248725 633248808 1.840000e-30 145.0
13 TraesCS7A01G272400 chr7D 90.826 109 7 3 493 598 263032969 263033077 6.610000e-30 143.0
14 TraesCS7A01G272400 chr7B 95.087 2117 73 18 3765 5851 240638046 240635931 0.000000e+00 3304.0
15 TraesCS7A01G272400 chr7B 94.672 1858 64 15 461 2296 240641198 240639354 0.000000e+00 2850.0
16 TraesCS7A01G272400 chr7B 95.923 1251 28 9 2519 3767 240639316 240638087 0.000000e+00 2006.0
17 TraesCS7A01G272400 chr7B 95.516 446 19 1 1 446 240641618 240641174 0.000000e+00 712.0
18 TraesCS7A01G272400 chr7B 90.971 443 20 6 5887 6327 240635926 240635502 4.250000e-161 579.0
19 TraesCS7A01G272400 chr7B 83.217 429 35 19 1 396 352534670 352535094 6.030000e-95 359.0
20 TraesCS7A01G272400 chr7B 96.809 94 0 3 5591 5684 17611701 17611611 3.060000e-33 154.0
21 TraesCS7A01G272400 chr7B 94.737 95 3 2 5591 5684 17517333 17517240 5.110000e-31 147.0
22 TraesCS7A01G272400 chr2A 85.067 750 96 10 418 1164 445577851 445577115 0.000000e+00 750.0
23 TraesCS7A01G272400 chr5A 84.041 589 63 15 1760 2327 533480443 533479865 7.220000e-149 538.0
24 TraesCS7A01G272400 chr5A 84.075 427 35 19 1 396 647700680 647700256 1.290000e-101 381.0
25 TraesCS7A01G272400 chr5A 89.855 69 7 0 1531 1599 533480563 533480495 8.740000e-14 89.8
26 TraesCS7A01G272400 chr2B 84.075 427 35 20 1 396 49512554 49512978 1.290000e-101 381.0
27 TraesCS7A01G272400 chr6B 83.607 427 36 21 1 396 666785652 666786075 2.790000e-98 370.0
28 TraesCS7A01G272400 chr1D 83.372 433 34 21 1 400 399804630 399804203 3.610000e-97 366.0
29 TraesCS7A01G272400 chr1D 95.556 180 6 2 2325 2503 366677272 366677450 2.890000e-73 287.0
30 TraesCS7A01G272400 chr1D 95.455 176 8 0 2321 2496 476231391 476231216 1.340000e-71 281.0
31 TraesCS7A01G272400 chr1D 92.857 42 3 0 295 336 355079570 355079611 1.910000e-05 62.1
32 TraesCS7A01G272400 chr4D 97.619 168 4 0 2326 2493 16666599 16666766 8.030000e-74 289.0
33 TraesCS7A01G272400 chr5D 97.059 170 5 0 2323 2492 447433769 447433600 2.890000e-73 287.0
34 TraesCS7A01G272400 chr5D 83.740 123 11 4 1849 1964 418868763 418868643 2.410000e-19 108.0
35 TraesCS7A01G272400 chr2D 97.059 170 5 0 2322 2491 330215231 330215062 2.890000e-73 287.0
36 TraesCS7A01G272400 chr2D 97.024 168 5 0 2327 2494 628554900 628554733 3.740000e-72 283.0
37 TraesCS7A01G272400 chrUn 97.041 169 5 0 2324 2492 318699531 318699363 1.040000e-72 285.0
38 TraesCS7A01G272400 chr1A 96.512 172 5 1 2323 2493 5595424 5595253 3.740000e-72 283.0
39 TraesCS7A01G272400 chr6D 94.048 84 3 2 338 420 112957543 112957625 6.660000e-25 126.0


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 TraesCS7A01G272400 chr7A 285691246 285697574 6328 False 11688.000000 11688 100.0000 1 6329 1 chr7A.!!$F2 6328
1 TraesCS7A01G272400 chr7A 514688531 514689266 735 True 732.000000 732 84.6670 418 1164 1 chr7A.!!$R2 746
2 TraesCS7A01G272400 chr7A 691516715 691517635 920 True 439.500000 773 85.6570 318 1164 2 chr7A.!!$R4 846
3 TraesCS7A01G272400 chr7D 263032969 263038760 5791 False 2926.666667 6202 92.8810 493 6329 3 chr7D.!!$F3 5836
4 TraesCS7A01G272400 chr7B 240635502 240641618 6116 True 1890.200000 3304 94.4338 1 6327 5 chr7B.!!$R3 6326
5 TraesCS7A01G272400 chr2A 445577115 445577851 736 True 750.000000 750 85.0670 418 1164 1 chr2A.!!$R1 746
6 TraesCS7A01G272400 chr5A 533479865 533480563 698 True 313.900000 538 86.9480 1531 2327 2 chr5A.!!$R2 796

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
470 558 1.663695 AGTTTCAGTGTTGGGTGTCG 58.336 50.000 0.00 0.00 0.00 4.35 F
1903 2117 0.032952 TGGTAACTGTCACGCACTCC 59.967 55.000 0.00 0.00 37.61 3.85 F
2387 2638 0.179020 ATGGCCACCACATACGGATG 60.179 55.000 8.16 5.94 35.80 3.51 F
2389 2640 0.466543 GGCCACCACATACGGATGTA 59.533 55.000 14.23 0.00 44.82 2.29 F
3747 4021 1.066787 GGCAAGCTCTACGAGGTTCTT 60.067 52.381 5.42 0.00 45.53 2.52 F
4178 4501 1.074405 ACCGACTACCTCTGGTACACA 59.926 52.381 0.00 0.00 37.09 3.72 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2368 2619 0.179020 CATCCGTATGTGGTGGCCAT 60.179 55.000 9.72 0.0 35.28 4.40 R
3255 3529 1.098129 CGGCAGATCTCTGAGACGGA 61.098 60.000 10.00 0.0 46.59 4.69 R
4249 4587 0.887387 CCACCCACCGTACAAACCAG 60.887 60.000 0.00 0.0 0.00 4.00 R
4437 4775 0.605319 GGTTGATGCCGACCTTGACA 60.605 55.000 0.00 0.0 42.50 3.58 R
4797 5135 2.100197 TGCTTGTACGAGCTCCAGTAT 58.900 47.619 30.54 0.0 43.11 2.12 R
5832 6188 3.293337 TGGCTCTTCGGTTAGTATAGCA 58.707 45.455 0.00 0.0 0.00 3.49 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
32 33 8.255206 TCTTTGTTTCAGTGTTTCTGTAGTCTA 58.745 33.333 0.00 0.00 43.97 2.59
131 132 5.663106 ACCTATTAATCTGACCTCAGCTCAA 59.337 40.000 0.00 0.00 43.46 3.02
150 151 7.167302 CAGCTCAATCTCTTTAATCAGTACTCG 59.833 40.741 0.00 0.00 0.00 4.18
204 205 7.086376 GCATCATTGTTCAGTCACACTAAATT 58.914 34.615 0.00 0.00 0.00 1.82
285 286 4.168101 TGTGATCCTTCCTCACCTAAGTT 58.832 43.478 1.37 0.00 41.87 2.66
295 296 5.611374 TCCTCACCTAAGTTCTTCAGTTTG 58.389 41.667 0.00 0.00 0.00 2.93
323 324 6.704937 TCTTAGTCTATGAGCTTGCATCATTG 59.295 38.462 6.60 5.43 38.36 2.82
449 537 8.564574 TGGTGTCATTTTCTTCAGTTATGTTAC 58.435 33.333 0.00 0.00 0.00 2.50
463 551 9.256477 TCAGTTATGTTACTAGTTTCAGTGTTG 57.744 33.333 0.00 0.63 0.00 3.33
470 558 1.663695 AGTTTCAGTGTTGGGTGTCG 58.336 50.000 0.00 0.00 0.00 4.35
475 563 2.011222 TCAGTGTTGGGTGTCGTTTTC 58.989 47.619 0.00 0.00 0.00 2.29
572 660 5.231702 TCATTGTTTCGATCGTAAGTCCAA 58.768 37.500 15.94 12.35 39.48 3.53
653 813 2.545946 GTGTTCAGACCTTCAGTTGCTC 59.454 50.000 0.00 0.00 0.00 4.26
675 835 4.838423 TCCAGTCCATGTTAAGTCTTCTCA 59.162 41.667 0.00 0.00 0.00 3.27
692 852 8.099537 AGTCTTCTCAAATAAAGCTCTCAATCA 58.900 33.333 0.00 0.00 0.00 2.57
697 857 9.896645 TCTCAAATAAAGCTCTCAATCATAGTT 57.103 29.630 0.00 0.00 0.00 2.24
721 885 5.003804 TCTAGTTTGTCAAGAAATCCCAGC 58.996 41.667 0.00 0.00 0.00 4.85
806 971 9.869844 CTTTAGCCTCATATTTATTTCTTCACG 57.130 33.333 0.00 0.00 0.00 4.35
899 1064 7.123098 ACCATGATCAGATACATGCTTTTGAAA 59.877 33.333 0.09 0.00 41.43 2.69
931 1096 9.360901 AGATACAACTCTCAGAGCAAGATAATA 57.639 33.333 0.00 0.00 32.04 0.98
1059 1225 5.277250 GCTTTTAGAAGATCATTGCTCTCGG 60.277 44.000 0.00 0.00 34.71 4.63
1145 1311 6.831727 TTGCATTTGTTTTCATCAGTCTTG 57.168 33.333 0.00 0.00 0.00 3.02
1186 1353 1.748403 GGAGGCGATGGTCATAGCA 59.252 57.895 15.69 0.00 40.53 3.49
1282 1482 3.532792 CGTGACGGCGTGACGATG 61.533 66.667 40.88 16.74 45.09 3.84
1469 1669 4.129737 ATGCGTGGACGGACGGAG 62.130 66.667 0.71 0.00 43.23 4.63
1535 1735 1.401905 CAGCGCCATCCCTTTAAACTC 59.598 52.381 2.29 0.00 0.00 3.01
1745 1959 1.906824 GTGGACGGACAGAGGGACA 60.907 63.158 0.00 0.00 0.00 4.02
1902 2116 1.137513 GTGGTAACTGTCACGCACTC 58.862 55.000 0.00 0.00 37.61 3.51
1903 2117 0.032952 TGGTAACTGTCACGCACTCC 59.967 55.000 0.00 0.00 37.61 3.85
2156 2391 3.001736 GTGTATTGCTCGATTTCTGGCTC 59.998 47.826 0.00 0.00 0.00 4.70
2170 2409 0.249955 TGGCTCATCTGCATTCACGA 59.750 50.000 0.00 0.00 34.04 4.35
2242 2481 3.143010 GGAGGTCCCCGACATCATA 57.857 57.895 8.51 0.00 43.88 2.15
2257 2496 4.454678 ACATCATATTCCGCACAGACAAT 58.545 39.130 0.00 0.00 0.00 2.71
2325 2576 2.561478 AGTTGCGGACATACCAAACT 57.439 45.000 0.00 0.00 39.12 2.66
2326 2577 3.688694 AGTTGCGGACATACCAAACTA 57.311 42.857 0.00 0.00 40.87 2.24
2327 2578 3.332034 AGTTGCGGACATACCAAACTAC 58.668 45.455 0.00 0.00 40.87 2.73
2328 2579 3.007614 AGTTGCGGACATACCAAACTACT 59.992 43.478 0.00 0.00 40.87 2.57
2329 2580 3.241067 TGCGGACATACCAAACTACTC 57.759 47.619 0.00 0.00 38.90 2.59
2330 2581 2.093869 TGCGGACATACCAAACTACTCC 60.094 50.000 0.00 0.00 38.90 3.85
2331 2582 2.740904 GCGGACATACCAAACTACTCCC 60.741 54.545 0.00 0.00 38.90 4.30
2332 2583 2.764572 CGGACATACCAAACTACTCCCT 59.235 50.000 0.00 0.00 38.90 4.20
2333 2584 3.181478 CGGACATACCAAACTACTCCCTC 60.181 52.174 0.00 0.00 38.90 4.30
2334 2585 3.134262 GGACATACCAAACTACTCCCTCC 59.866 52.174 0.00 0.00 38.79 4.30
2335 2586 2.764572 ACATACCAAACTACTCCCTCCG 59.235 50.000 0.00 0.00 0.00 4.63
2336 2587 2.610438 TACCAAACTACTCCCTCCGT 57.390 50.000 0.00 0.00 0.00 4.69
2337 2588 1.725803 ACCAAACTACTCCCTCCGTT 58.274 50.000 0.00 0.00 0.00 4.44
2338 2589 1.622312 ACCAAACTACTCCCTCCGTTC 59.378 52.381 0.00 0.00 0.00 3.95
2339 2590 1.066358 CCAAACTACTCCCTCCGTTCC 60.066 57.143 0.00 0.00 0.00 3.62
2340 2591 1.900486 CAAACTACTCCCTCCGTTCCT 59.100 52.381 0.00 0.00 0.00 3.36
2341 2592 3.094572 CAAACTACTCCCTCCGTTCCTA 58.905 50.000 0.00 0.00 0.00 2.94
2342 2593 3.463048 AACTACTCCCTCCGTTCCTAA 57.537 47.619 0.00 0.00 0.00 2.69
2343 2594 3.463048 ACTACTCCCTCCGTTCCTAAA 57.537 47.619 0.00 0.00 0.00 1.85
2344 2595 3.991683 ACTACTCCCTCCGTTCCTAAAT 58.008 45.455 0.00 0.00 0.00 1.40
2345 2596 5.134725 ACTACTCCCTCCGTTCCTAAATA 57.865 43.478 0.00 0.00 0.00 1.40
2346 2597 5.713807 ACTACTCCCTCCGTTCCTAAATAT 58.286 41.667 0.00 0.00 0.00 1.28
2347 2598 6.141790 ACTACTCCCTCCGTTCCTAAATATT 58.858 40.000 0.00 0.00 0.00 1.28
2348 2599 5.970501 ACTCCCTCCGTTCCTAAATATTT 57.029 39.130 5.89 5.89 0.00 1.40
2349 2600 5.681639 ACTCCCTCCGTTCCTAAATATTTG 58.318 41.667 11.05 1.40 0.00 2.32
2350 2601 5.191124 ACTCCCTCCGTTCCTAAATATTTGT 59.809 40.000 11.05 0.00 0.00 2.83
2351 2602 5.677567 TCCCTCCGTTCCTAAATATTTGTC 58.322 41.667 11.05 0.00 0.00 3.18
2352 2603 5.427481 TCCCTCCGTTCCTAAATATTTGTCT 59.573 40.000 11.05 0.00 0.00 3.41
2353 2604 6.069847 TCCCTCCGTTCCTAAATATTTGTCTT 60.070 38.462 11.05 0.00 0.00 3.01
2354 2605 6.602009 CCCTCCGTTCCTAAATATTTGTCTTT 59.398 38.462 11.05 0.00 0.00 2.52
2355 2606 7.201705 CCCTCCGTTCCTAAATATTTGTCTTTC 60.202 40.741 11.05 0.00 0.00 2.62
2356 2607 7.553044 CCTCCGTTCCTAAATATTTGTCTTTCT 59.447 37.037 11.05 0.00 0.00 2.52
2357 2608 9.595823 CTCCGTTCCTAAATATTTGTCTTTCTA 57.404 33.333 11.05 0.00 0.00 2.10
2358 2609 9.595823 TCCGTTCCTAAATATTTGTCTTTCTAG 57.404 33.333 11.05 0.00 0.00 2.43
2359 2610 9.595823 CCGTTCCTAAATATTTGTCTTTCTAGA 57.404 33.333 11.05 0.00 0.00 2.43
2372 2623 7.383102 TGTCTTTCTAGAGATTTCAAATGGC 57.617 36.000 0.00 0.00 0.00 4.40
2373 2624 6.375455 TGTCTTTCTAGAGATTTCAAATGGCC 59.625 38.462 0.00 0.00 0.00 5.36
2374 2625 6.375455 GTCTTTCTAGAGATTTCAAATGGCCA 59.625 38.462 8.56 8.56 0.00 5.36
2375 2626 6.375455 TCTTTCTAGAGATTTCAAATGGCCAC 59.625 38.462 8.16 0.00 0.00 5.01
2376 2627 4.526970 TCTAGAGATTTCAAATGGCCACC 58.473 43.478 8.16 0.00 0.00 4.61
2377 2628 3.173953 AGAGATTTCAAATGGCCACCA 57.826 42.857 8.16 0.00 38.19 4.17
2378 2629 2.827921 AGAGATTTCAAATGGCCACCAC 59.172 45.455 8.16 0.00 35.80 4.16
2379 2630 2.562298 GAGATTTCAAATGGCCACCACA 59.438 45.455 8.16 0.00 35.80 4.17
2380 2631 3.175594 AGATTTCAAATGGCCACCACAT 58.824 40.909 8.16 0.00 35.80 3.21
2381 2632 4.352009 AGATTTCAAATGGCCACCACATA 58.648 39.130 8.16 0.00 35.80 2.29
2382 2633 3.951775 TTTCAAATGGCCACCACATAC 57.048 42.857 8.16 0.00 35.80 2.39
2383 2634 1.458398 TCAAATGGCCACCACATACG 58.542 50.000 8.16 0.00 35.80 3.06
2384 2635 0.455410 CAAATGGCCACCACATACGG 59.545 55.000 8.16 0.00 35.80 4.02
2385 2636 0.329931 AAATGGCCACCACATACGGA 59.670 50.000 8.16 0.00 35.80 4.69
2386 2637 0.550914 AATGGCCACCACATACGGAT 59.449 50.000 8.16 0.00 35.80 4.18
2387 2638 0.179020 ATGGCCACCACATACGGATG 60.179 55.000 8.16 5.94 35.80 3.51
2389 2640 0.466543 GGCCACCACATACGGATGTA 59.533 55.000 14.23 0.00 44.82 2.29
2390 2641 1.071699 GGCCACCACATACGGATGTAT 59.928 52.381 14.23 1.38 44.82 2.29
2391 2642 2.300723 GGCCACCACATACGGATGTATA 59.699 50.000 14.23 0.00 44.82 1.47
2392 2643 3.055385 GGCCACCACATACGGATGTATAT 60.055 47.826 14.23 0.00 44.82 0.86
2393 2644 4.160814 GGCCACCACATACGGATGTATATA 59.839 45.833 14.23 0.00 44.82 0.86
2394 2645 5.348986 GCCACCACATACGGATGTATATAG 58.651 45.833 14.23 0.00 44.82 1.31
2395 2646 5.126545 GCCACCACATACGGATGTATATAGA 59.873 44.000 14.23 0.00 44.82 1.98
2396 2647 6.561614 CCACCACATACGGATGTATATAGAC 58.438 44.000 14.23 0.00 44.82 2.59
2397 2648 6.152154 CCACCACATACGGATGTATATAGACA 59.848 42.308 14.23 2.07 44.82 3.41
2398 2649 7.147897 CCACCACATACGGATGTATATAGACAT 60.148 40.741 14.23 12.70 44.82 3.06
2399 2650 8.899771 CACCACATACGGATGTATATAGACATA 58.100 37.037 14.23 0.00 44.82 2.29
2400 2651 9.642343 ACCACATACGGATGTATATAGACATAT 57.358 33.333 14.23 5.08 44.82 1.78
2427 2678 9.677567 TTTAAAGTGTAGATTCACTCATTTTGC 57.322 29.630 0.00 0.00 46.25 3.68
2428 2679 7.516198 AAAGTGTAGATTCACTCATTTTGCT 57.484 32.000 0.00 0.00 46.25 3.91
2429 2680 6.734104 AGTGTAGATTCACTCATTTTGCTC 57.266 37.500 0.00 0.00 44.07 4.26
2430 2681 5.645497 AGTGTAGATTCACTCATTTTGCTCC 59.355 40.000 0.00 0.00 44.07 4.70
2431 2682 4.631377 TGTAGATTCACTCATTTTGCTCCG 59.369 41.667 0.00 0.00 0.00 4.63
2432 2683 3.679389 AGATTCACTCATTTTGCTCCGT 58.321 40.909 0.00 0.00 0.00 4.69
2433 2684 4.832248 AGATTCACTCATTTTGCTCCGTA 58.168 39.130 0.00 0.00 0.00 4.02
2434 2685 5.431765 AGATTCACTCATTTTGCTCCGTAT 58.568 37.500 0.00 0.00 0.00 3.06
2435 2686 4.944962 TTCACTCATTTTGCTCCGTATG 57.055 40.909 0.00 0.00 0.00 2.39
2436 2687 3.937814 TCACTCATTTTGCTCCGTATGT 58.062 40.909 0.00 0.00 0.00 2.29
2437 2688 5.079689 TCACTCATTTTGCTCCGTATGTA 57.920 39.130 0.00 0.00 0.00 2.29
2438 2689 5.109210 TCACTCATTTTGCTCCGTATGTAG 58.891 41.667 0.00 0.00 0.00 2.74
2439 2690 4.870426 CACTCATTTTGCTCCGTATGTAGT 59.130 41.667 0.00 0.00 0.00 2.73
2440 2691 5.005779 CACTCATTTTGCTCCGTATGTAGTC 59.994 44.000 0.00 0.00 0.00 2.59
2441 2692 5.079689 TCATTTTGCTCCGTATGTAGTCA 57.920 39.130 0.00 0.00 0.00 3.41
2442 2693 4.868171 TCATTTTGCTCCGTATGTAGTCAC 59.132 41.667 0.00 0.00 0.00 3.67
2443 2694 2.953466 TTGCTCCGTATGTAGTCACC 57.047 50.000 0.00 0.00 0.00 4.02
2444 2695 1.842052 TGCTCCGTATGTAGTCACCA 58.158 50.000 0.00 0.00 0.00 4.17
2445 2696 2.384828 TGCTCCGTATGTAGTCACCAT 58.615 47.619 0.00 0.00 0.00 3.55
2446 2697 2.764010 TGCTCCGTATGTAGTCACCATT 59.236 45.455 0.00 0.00 0.00 3.16
2447 2698 3.196901 TGCTCCGTATGTAGTCACCATTT 59.803 43.478 0.00 0.00 0.00 2.32
2448 2699 4.403113 TGCTCCGTATGTAGTCACCATTTA 59.597 41.667 0.00 0.00 0.00 1.40
2449 2700 5.105269 TGCTCCGTATGTAGTCACCATTTAA 60.105 40.000 0.00 0.00 0.00 1.52
2450 2701 5.813672 GCTCCGTATGTAGTCACCATTTAAA 59.186 40.000 0.00 0.00 0.00 1.52
2451 2702 6.314400 GCTCCGTATGTAGTCACCATTTAAAA 59.686 38.462 0.00 0.00 0.00 1.52
2452 2703 7.599630 TCCGTATGTAGTCACCATTTAAAAC 57.400 36.000 0.00 0.00 0.00 2.43
2453 2704 6.594937 TCCGTATGTAGTCACCATTTAAAACC 59.405 38.462 0.00 0.00 0.00 3.27
2454 2705 6.596497 CCGTATGTAGTCACCATTTAAAACCT 59.404 38.462 0.00 0.00 0.00 3.50
2455 2706 7.201582 CCGTATGTAGTCACCATTTAAAACCTC 60.202 40.741 0.00 0.00 0.00 3.85
2456 2707 7.548075 CGTATGTAGTCACCATTTAAAACCTCT 59.452 37.037 0.00 0.00 0.00 3.69
2457 2708 9.880157 GTATGTAGTCACCATTTAAAACCTCTA 57.120 33.333 0.00 0.00 0.00 2.43
2459 2710 9.802039 ATGTAGTCACCATTTAAAACCTCTAAA 57.198 29.630 0.00 0.00 0.00 1.85
2460 2711 9.629878 TGTAGTCACCATTTAAAACCTCTAAAA 57.370 29.630 0.00 0.00 0.00 1.52
2463 2714 9.416284 AGTCACCATTTAAAACCTCTAAAAAGA 57.584 29.630 0.00 0.00 0.00 2.52
2464 2715 9.459640 GTCACCATTTAAAACCTCTAAAAAGAC 57.540 33.333 0.00 0.00 0.00 3.01
2465 2716 9.191479 TCACCATTTAAAACCTCTAAAAAGACA 57.809 29.630 0.00 0.00 0.00 3.41
2466 2717 9.810545 CACCATTTAAAACCTCTAAAAAGACAA 57.189 29.630 0.00 0.00 0.00 3.18
2483 2734 7.625828 AAAGACAAATATTTAGGAACGGAGG 57.374 36.000 0.00 0.00 0.00 4.30
2484 2735 5.681639 AGACAAATATTTAGGAACGGAGGG 58.318 41.667 0.00 0.00 0.00 4.30
2485 2736 5.427481 AGACAAATATTTAGGAACGGAGGGA 59.573 40.000 0.00 0.00 0.00 4.20
2486 2737 5.681639 ACAAATATTTAGGAACGGAGGGAG 58.318 41.667 0.00 0.00 0.00 4.30
2503 2754 5.298026 GGAGGGAGTAGATGCATTTCTTTTC 59.702 44.000 0.00 0.00 0.00 2.29
2513 2764 7.150640 AGATGCATTTCTTTTCCTTTCTCAAC 58.849 34.615 0.00 0.00 0.00 3.18
2610 2865 3.735591 CGTCCTCACCTTGGTTTTTCTA 58.264 45.455 0.00 0.00 0.00 2.10
2615 2870 7.572539 CGTCCTCACCTTGGTTTTTCTATTTAC 60.573 40.741 0.00 0.00 0.00 2.01
2644 2899 3.501445 AGAAGCTCATGCAGAAGTTTGTC 59.499 43.478 5.17 0.00 42.74 3.18
2671 2926 2.989840 CGTAGTGAACAAGCTCAAGGAG 59.010 50.000 0.00 0.00 0.00 3.69
2713 2968 1.205893 GGAGGCCCTATCATTCTAGCG 59.794 57.143 0.00 0.00 0.00 4.26
2909 3166 1.913951 AAGATGGCCATCAGCACCGA 61.914 55.000 40.05 0.90 46.50 4.69
2912 3169 2.124570 GGCCATCAGCACCGACAT 60.125 61.111 0.00 0.00 46.50 3.06
2974 3231 3.805971 AGCGGACGTGGTAATTTATTAGC 59.194 43.478 0.00 5.05 40.24 3.09
3049 3321 8.545420 CATGCTTAAGCCATAATCATGTTTTTC 58.455 33.333 24.30 0.00 40.65 2.29
3255 3529 5.475220 CAGATACAGAGTATTCGGTGATCCT 59.525 44.000 1.31 0.00 33.65 3.24
3363 3637 1.232119 CGTCCAGTAACCAACCAACC 58.768 55.000 0.00 0.00 0.00 3.77
3364 3638 1.475392 CGTCCAGTAACCAACCAACCA 60.475 52.381 0.00 0.00 0.00 3.67
3365 3639 2.657143 GTCCAGTAACCAACCAACCAA 58.343 47.619 0.00 0.00 0.00 3.67
3486 3760 2.730382 ACAAACTTTGGAAGAACGGGT 58.270 42.857 6.47 0.00 34.12 5.28
3555 3829 4.744795 ATTCGGTAAAGCAGAGACAGAT 57.255 40.909 0.00 0.00 0.00 2.90
3747 4021 1.066787 GGCAAGCTCTACGAGGTTCTT 60.067 52.381 5.42 0.00 45.53 2.52
3748 4022 2.263945 GCAAGCTCTACGAGGTTCTTC 58.736 52.381 5.42 0.00 45.53 2.87
3749 4023 2.094442 GCAAGCTCTACGAGGTTCTTCT 60.094 50.000 5.42 0.00 45.53 2.85
4178 4501 1.074405 ACCGACTACCTCTGGTACACA 59.926 52.381 0.00 0.00 37.09 3.72
4249 4587 1.236628 TGCCAATGCCAATGTTTTGC 58.763 45.000 0.00 0.00 36.33 3.68
4437 4775 2.049627 GCCTGGAGAAGCCCATCGAT 62.050 60.000 0.00 0.00 35.33 3.59
4638 4976 1.795170 GCAAGCAGGCTTTCACGGAA 61.795 55.000 3.30 0.00 33.42 4.30
4718 5056 3.869272 GCGCTTCGACATGCCCAG 61.869 66.667 0.00 0.00 0.00 4.45
5414 5760 5.798125 TTTCATGCTTGTTGTTTGGGATA 57.202 34.783 0.00 0.00 0.00 2.59
5416 5762 4.148079 TCATGCTTGTTGTTTGGGATACA 58.852 39.130 0.00 0.00 39.74 2.29
5486 5840 0.373024 GCGCTGAGATGAGAAGCAAC 59.627 55.000 0.00 0.00 36.73 4.17
5678 6034 0.899720 CCACTAGACCAAACGCCCTA 59.100 55.000 0.00 0.00 0.00 3.53
5688 6044 4.816392 ACCAAACGCCCTAATTGAAATTC 58.184 39.130 0.00 0.00 0.00 2.17
5689 6045 3.857093 CCAAACGCCCTAATTGAAATTCG 59.143 43.478 0.00 0.00 0.00 3.34
5702 6058 5.521906 TTGAAATTCGGTGTCATTGGAAA 57.478 34.783 0.00 0.00 0.00 3.13
5703 6059 5.720371 TGAAATTCGGTGTCATTGGAAAT 57.280 34.783 0.00 0.00 0.00 2.17
5737 6093 2.422479 TCTTTCTCGATGAACGGACGAT 59.578 45.455 0.00 0.00 42.82 3.73
5829 6185 2.042831 GCTAGCCTGGTGCCACAAG 61.043 63.158 2.29 0.00 42.71 3.16
5832 6188 0.698238 TAGCCTGGTGCCACAAGAAT 59.302 50.000 0.00 0.00 42.71 2.40
5835 6191 0.896940 CCTGGTGCCACAAGAATGCT 60.897 55.000 0.00 0.00 0.00 3.79
5872 6228 5.473039 AGCCATTTTGTTTTGCAGATAGAC 58.527 37.500 0.00 0.00 0.00 2.59
5990 6346 4.801330 ATATCAGTTCGTCAGTCCAACA 57.199 40.909 0.00 0.00 0.00 3.33
6174 6532 6.382919 AGATAAAACCCTACACCTTGCTTA 57.617 37.500 0.00 0.00 0.00 3.09
6192 6550 8.024285 CCTTGCTTATGTTTTATTACGTTGGAA 58.976 33.333 0.00 0.00 0.00 3.53
6202 6560 6.971527 TTATTACGTTGGAATGTGTACAGG 57.028 37.500 0.00 0.00 0.00 4.00
6225 6583 5.416947 GGTACATGTAAACGACCAAGAGAT 58.583 41.667 7.25 0.00 0.00 2.75
6230 6588 8.385898 ACATGTAAACGACCAAGAGATTTTTA 57.614 30.769 0.00 0.00 0.00 1.52
6256 6614 6.887545 AGATATATCTACGAGCCTAGCAAACT 59.112 38.462 13.76 0.00 34.85 2.66
6279 6637 1.580059 GGAGGTCCTTGGGTACATGA 58.420 55.000 0.00 0.00 0.00 3.07
6291 6649 2.963782 GGGTACATGAATCCTAGTCCGT 59.036 50.000 0.00 0.00 0.00 4.69
6301 6659 3.057969 TCCTAGTCCGTTTCGTACAGA 57.942 47.619 0.00 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
118 119 5.745312 TTAAAGAGATTGAGCTGAGGTCA 57.255 39.130 10.72 10.72 38.32 4.02
131 132 6.458232 AGCACGAGTACTGATTAAAGAGAT 57.542 37.500 0.00 0.00 0.00 2.75
150 151 6.864342 TCACAGACTAAGGAAATACTAGCAC 58.136 40.000 0.00 0.00 0.00 4.40
249 250 8.212995 AGGAAGGATCACAATTGACAAAAATTT 58.787 29.630 13.59 0.00 33.38 1.82
251 252 7.015487 TGAGGAAGGATCACAATTGACAAAAAT 59.985 33.333 13.59 0.00 33.38 1.82
285 286 9.698309 CTCATAGACTAAGAAACAAACTGAAGA 57.302 33.333 0.00 0.00 0.00 2.87
295 296 6.536582 TGATGCAAGCTCATAGACTAAGAAAC 59.463 38.462 0.00 0.00 0.00 2.78
323 324 7.722285 AGGGACTTATAGACTGATAGACTGAAC 59.278 40.741 0.00 0.00 27.25 3.18
449 537 2.800544 CGACACCCAACACTGAAACTAG 59.199 50.000 0.00 0.00 0.00 2.57
463 551 4.102649 CAAAACTGAAGAAAACGACACCC 58.897 43.478 0.00 0.00 0.00 4.61
470 558 6.864165 TGGTAACACACAAAACTGAAGAAAAC 59.136 34.615 0.00 0.00 46.17 2.43
475 563 5.560966 ACTGGTAACACACAAAACTGAAG 57.439 39.130 0.00 0.00 46.17 3.02
563 651 3.396260 TGTAGGCTGTGTTGGACTTAC 57.604 47.619 0.00 0.00 0.00 2.34
572 660 2.632996 TCTTAGTGCTTGTAGGCTGTGT 59.367 45.455 0.00 0.00 0.00 3.72
653 813 5.152623 TGAGAAGACTTAACATGGACTGG 57.847 43.478 0.00 0.00 0.00 4.00
692 852 9.232473 GGGATTTCTTGACAAACTAGAAACTAT 57.768 33.333 0.00 0.00 46.52 2.12
697 857 5.473504 GCTGGGATTTCTTGACAAACTAGAA 59.526 40.000 0.00 0.00 38.24 2.10
698 858 5.003804 GCTGGGATTTCTTGACAAACTAGA 58.996 41.667 0.00 0.00 0.00 2.43
699 859 5.006386 AGCTGGGATTTCTTGACAAACTAG 58.994 41.667 0.00 0.00 0.00 2.57
721 885 8.774586 ACTGTATGAACAAACTTGCTAAACTAG 58.225 33.333 0.00 0.00 34.49 2.57
842 1007 2.100631 CACTGACGCCCCATTCGAC 61.101 63.158 0.00 0.00 0.00 4.20
843 1008 2.264480 CACTGACGCCCCATTCGA 59.736 61.111 0.00 0.00 0.00 3.71
931 1096 3.023119 TGTTGGCGCAGATCCATAAAAT 58.977 40.909 10.83 0.00 32.92 1.82
1000 1165 2.996734 CCCCGCAAAACAGGCCAT 60.997 61.111 5.01 0.00 0.00 4.40
1059 1225 5.009210 ACAGAGATCTTACTGGAATAGCGTC 59.991 44.000 14.17 0.00 38.30 5.19
1119 1285 7.473027 AGACTGATGAAAACAAATGCAAAAG 57.527 32.000 0.00 0.00 0.00 2.27
1145 1311 2.964740 TCACTGATGCTACTTGTGCTC 58.035 47.619 0.00 0.00 0.00 4.26
1186 1353 2.048127 GAGCTCCGGACGTGCTTT 60.048 61.111 16.94 0.00 37.16 3.51
1265 1459 3.532792 CATCGTCACGCCGTCACG 61.533 66.667 7.52 7.52 39.50 4.35
1535 1735 2.420058 AAAATAGGAGGGAGGCGTTG 57.580 50.000 0.00 0.00 0.00 4.10
1745 1959 1.691434 GATGGAGCCGGAGAAGAAGAT 59.309 52.381 5.05 0.00 0.00 2.40
1902 2116 3.007723 ACGATGAGATGAATGAGATGGGG 59.992 47.826 0.00 0.00 0.00 4.96
1903 2117 4.268797 ACGATGAGATGAATGAGATGGG 57.731 45.455 0.00 0.00 0.00 4.00
2156 2391 1.791204 CGGAGATCGTGAATGCAGATG 59.209 52.381 0.00 0.00 0.00 2.90
2170 2409 7.112779 AGGAAAATCACAGATTAAACGGAGAT 58.887 34.615 0.00 0.00 0.00 2.75
2242 2481 1.089920 GCTCATTGTCTGTGCGGAAT 58.910 50.000 0.00 0.00 34.93 3.01
2281 2520 4.589216 AATTCTGTGTGGTTTGATGGTG 57.411 40.909 0.00 0.00 0.00 4.17
2325 2576 6.384886 ACAAATATTTAGGAACGGAGGGAGTA 59.615 38.462 0.00 0.00 0.00 2.59
2326 2577 5.191124 ACAAATATTTAGGAACGGAGGGAGT 59.809 40.000 0.00 0.00 0.00 3.85
2327 2578 5.681639 ACAAATATTTAGGAACGGAGGGAG 58.318 41.667 0.00 0.00 0.00 4.30
2328 2579 5.427481 AGACAAATATTTAGGAACGGAGGGA 59.573 40.000 0.00 0.00 0.00 4.20
2329 2580 5.681639 AGACAAATATTTAGGAACGGAGGG 58.318 41.667 0.00 0.00 0.00 4.30
2330 2581 7.553044 AGAAAGACAAATATTTAGGAACGGAGG 59.447 37.037 0.00 0.00 0.00 4.30
2331 2582 8.494016 AGAAAGACAAATATTTAGGAACGGAG 57.506 34.615 0.00 0.00 0.00 4.63
2332 2583 9.595823 CTAGAAAGACAAATATTTAGGAACGGA 57.404 33.333 0.00 0.00 0.00 4.69
2333 2584 9.595823 TCTAGAAAGACAAATATTTAGGAACGG 57.404 33.333 0.00 0.00 0.00 4.44
2346 2597 8.299570 GCCATTTGAAATCTCTAGAAAGACAAA 58.700 33.333 0.00 4.41 0.00 2.83
2347 2598 7.094205 GGCCATTTGAAATCTCTAGAAAGACAA 60.094 37.037 0.00 0.00 0.00 3.18
2348 2599 6.375455 GGCCATTTGAAATCTCTAGAAAGACA 59.625 38.462 0.00 0.00 0.00 3.41
2349 2600 6.375455 TGGCCATTTGAAATCTCTAGAAAGAC 59.625 38.462 0.00 0.00 0.00 3.01
2350 2601 6.375455 GTGGCCATTTGAAATCTCTAGAAAGA 59.625 38.462 9.72 0.00 0.00 2.52
2351 2602 6.405176 GGTGGCCATTTGAAATCTCTAGAAAG 60.405 42.308 9.72 0.00 0.00 2.62
2352 2603 5.418840 GGTGGCCATTTGAAATCTCTAGAAA 59.581 40.000 9.72 0.00 0.00 2.52
2353 2604 4.949856 GGTGGCCATTTGAAATCTCTAGAA 59.050 41.667 9.72 0.00 0.00 2.10
2354 2605 4.018506 TGGTGGCCATTTGAAATCTCTAGA 60.019 41.667 9.72 0.00 0.00 2.43
2355 2606 4.096984 GTGGTGGCCATTTGAAATCTCTAG 59.903 45.833 9.72 0.00 35.28 2.43
2356 2607 4.016444 GTGGTGGCCATTTGAAATCTCTA 58.984 43.478 9.72 0.00 35.28 2.43
2357 2608 2.827921 GTGGTGGCCATTTGAAATCTCT 59.172 45.455 9.72 0.00 35.28 3.10
2358 2609 2.562298 TGTGGTGGCCATTTGAAATCTC 59.438 45.455 9.72 0.00 35.28 2.75
2359 2610 2.607499 TGTGGTGGCCATTTGAAATCT 58.393 42.857 9.72 0.00 35.28 2.40
2360 2611 3.615224 ATGTGGTGGCCATTTGAAATC 57.385 42.857 9.72 0.00 35.28 2.17
2361 2612 3.119173 CGTATGTGGTGGCCATTTGAAAT 60.119 43.478 9.72 1.02 35.28 2.17
2362 2613 2.230025 CGTATGTGGTGGCCATTTGAAA 59.770 45.455 9.72 0.00 35.28 2.69
2363 2614 1.815613 CGTATGTGGTGGCCATTTGAA 59.184 47.619 9.72 0.00 35.28 2.69
2364 2615 1.458398 CGTATGTGGTGGCCATTTGA 58.542 50.000 9.72 0.00 35.28 2.69
2365 2616 0.455410 CCGTATGTGGTGGCCATTTG 59.545 55.000 9.72 0.00 35.28 2.32
2366 2617 0.329931 TCCGTATGTGGTGGCCATTT 59.670 50.000 9.72 0.00 35.28 2.32
2367 2618 0.550914 ATCCGTATGTGGTGGCCATT 59.449 50.000 9.72 0.00 35.28 3.16
2368 2619 0.179020 CATCCGTATGTGGTGGCCAT 60.179 55.000 9.72 0.00 35.28 4.40
2369 2620 1.223211 CATCCGTATGTGGTGGCCA 59.777 57.895 0.00 0.00 0.00 5.36
2370 2621 0.466543 TACATCCGTATGTGGTGGCC 59.533 55.000 3.56 0.00 45.99 5.36
2371 2622 2.543777 ATACATCCGTATGTGGTGGC 57.456 50.000 3.56 0.00 45.99 5.01
2372 2623 6.152154 TGTCTATATACATCCGTATGTGGTGG 59.848 42.308 3.56 0.00 45.99 4.61
2373 2624 7.153217 TGTCTATATACATCCGTATGTGGTG 57.847 40.000 3.56 0.00 45.99 4.17
2374 2625 7.956328 ATGTCTATATACATCCGTATGTGGT 57.044 36.000 3.56 0.00 45.99 4.16
2407 2658 5.446473 CGGAGCAAAATGAGTGAATCTACAC 60.446 44.000 0.00 0.00 40.60 2.90
2408 2659 4.631377 CGGAGCAAAATGAGTGAATCTACA 59.369 41.667 0.00 0.00 0.00 2.74
2409 2660 4.631813 ACGGAGCAAAATGAGTGAATCTAC 59.368 41.667 0.00 0.00 0.00 2.59
2410 2661 4.832248 ACGGAGCAAAATGAGTGAATCTA 58.168 39.130 0.00 0.00 0.00 1.98
2411 2662 3.679389 ACGGAGCAAAATGAGTGAATCT 58.321 40.909 0.00 0.00 0.00 2.40
2412 2663 5.065218 ACATACGGAGCAAAATGAGTGAATC 59.935 40.000 0.00 0.00 0.00 2.52
2413 2664 4.943705 ACATACGGAGCAAAATGAGTGAAT 59.056 37.500 0.00 0.00 0.00 2.57
2414 2665 4.323417 ACATACGGAGCAAAATGAGTGAA 58.677 39.130 0.00 0.00 0.00 3.18
2415 2666 3.937814 ACATACGGAGCAAAATGAGTGA 58.062 40.909 0.00 0.00 0.00 3.41
2416 2667 4.870426 ACTACATACGGAGCAAAATGAGTG 59.130 41.667 0.00 0.00 0.00 3.51
2417 2668 5.086104 ACTACATACGGAGCAAAATGAGT 57.914 39.130 0.00 0.00 0.00 3.41
2418 2669 5.005779 GTGACTACATACGGAGCAAAATGAG 59.994 44.000 0.00 0.00 0.00 2.90
2419 2670 4.868171 GTGACTACATACGGAGCAAAATGA 59.132 41.667 0.00 0.00 0.00 2.57
2420 2671 4.034048 GGTGACTACATACGGAGCAAAATG 59.966 45.833 0.00 0.00 0.00 2.32
2421 2672 4.189231 GGTGACTACATACGGAGCAAAAT 58.811 43.478 0.00 0.00 0.00 1.82
2422 2673 3.007074 TGGTGACTACATACGGAGCAAAA 59.993 43.478 0.00 0.00 0.00 2.44
2423 2674 2.563620 TGGTGACTACATACGGAGCAAA 59.436 45.455 0.00 0.00 0.00 3.68
2424 2675 2.172679 TGGTGACTACATACGGAGCAA 58.827 47.619 0.00 0.00 0.00 3.91
2425 2676 1.842052 TGGTGACTACATACGGAGCA 58.158 50.000 0.00 0.00 0.00 4.26
2426 2677 3.454371 AATGGTGACTACATACGGAGC 57.546 47.619 0.00 0.00 0.00 4.70
2427 2678 7.201582 GGTTTTAAATGGTGACTACATACGGAG 60.202 40.741 0.00 0.00 0.00 4.63
2428 2679 6.594937 GGTTTTAAATGGTGACTACATACGGA 59.405 38.462 0.00 0.00 0.00 4.69
2429 2680 6.596497 AGGTTTTAAATGGTGACTACATACGG 59.404 38.462 0.00 0.00 0.00 4.02
2430 2681 7.548075 AGAGGTTTTAAATGGTGACTACATACG 59.452 37.037 0.00 0.00 0.00 3.06
2431 2682 8.788325 AGAGGTTTTAAATGGTGACTACATAC 57.212 34.615 0.00 0.00 0.00 2.39
2433 2684 9.802039 TTTAGAGGTTTTAAATGGTGACTACAT 57.198 29.630 0.00 0.00 0.00 2.29
2434 2685 9.629878 TTTTAGAGGTTTTAAATGGTGACTACA 57.370 29.630 0.00 0.00 0.00 2.74
2437 2688 9.416284 TCTTTTTAGAGGTTTTAAATGGTGACT 57.584 29.630 0.00 0.00 0.00 3.41
2438 2689 9.459640 GTCTTTTTAGAGGTTTTAAATGGTGAC 57.540 33.333 0.00 0.00 0.00 3.67
2439 2690 9.191479 TGTCTTTTTAGAGGTTTTAAATGGTGA 57.809 29.630 0.00 0.00 0.00 4.02
2440 2691 9.810545 TTGTCTTTTTAGAGGTTTTAAATGGTG 57.189 29.630 0.00 0.00 0.00 4.17
2457 2708 8.520351 CCTCCGTTCCTAAATATTTGTCTTTTT 58.480 33.333 11.05 0.00 0.00 1.94
2458 2709 7.122204 CCCTCCGTTCCTAAATATTTGTCTTTT 59.878 37.037 11.05 0.00 0.00 2.27
2459 2710 6.602009 CCCTCCGTTCCTAAATATTTGTCTTT 59.398 38.462 11.05 0.00 0.00 2.52
2460 2711 6.069847 TCCCTCCGTTCCTAAATATTTGTCTT 60.070 38.462 11.05 0.00 0.00 3.01
2461 2712 5.427481 TCCCTCCGTTCCTAAATATTTGTCT 59.573 40.000 11.05 0.00 0.00 3.41
2462 2713 5.677567 TCCCTCCGTTCCTAAATATTTGTC 58.322 41.667 11.05 0.00 0.00 3.18
2463 2714 5.191124 ACTCCCTCCGTTCCTAAATATTTGT 59.809 40.000 11.05 0.00 0.00 2.83
2464 2715 5.681639 ACTCCCTCCGTTCCTAAATATTTG 58.318 41.667 11.05 1.40 0.00 2.32
2465 2716 5.970501 ACTCCCTCCGTTCCTAAATATTT 57.029 39.130 5.89 5.89 0.00 1.40
2466 2717 6.379579 TCTACTCCCTCCGTTCCTAAATATT 58.620 40.000 0.00 0.00 0.00 1.28
2467 2718 5.961897 TCTACTCCCTCCGTTCCTAAATAT 58.038 41.667 0.00 0.00 0.00 1.28
2468 2719 5.393068 TCTACTCCCTCCGTTCCTAAATA 57.607 43.478 0.00 0.00 0.00 1.40
2469 2720 4.261411 TCTACTCCCTCCGTTCCTAAAT 57.739 45.455 0.00 0.00 0.00 1.40
2470 2721 3.744940 TCTACTCCCTCCGTTCCTAAA 57.255 47.619 0.00 0.00 0.00 1.85
2471 2722 3.563223 CATCTACTCCCTCCGTTCCTAA 58.437 50.000 0.00 0.00 0.00 2.69
2472 2723 2.752154 GCATCTACTCCCTCCGTTCCTA 60.752 54.545 0.00 0.00 0.00 2.94
2473 2724 2.030045 GCATCTACTCCCTCCGTTCCT 61.030 57.143 0.00 0.00 0.00 3.36
2474 2725 0.389757 GCATCTACTCCCTCCGTTCC 59.610 60.000 0.00 0.00 0.00 3.62
2475 2726 1.112113 TGCATCTACTCCCTCCGTTC 58.888 55.000 0.00 0.00 0.00 3.95
2476 2727 1.794714 ATGCATCTACTCCCTCCGTT 58.205 50.000 0.00 0.00 0.00 4.44
2477 2728 1.794714 AATGCATCTACTCCCTCCGT 58.205 50.000 0.00 0.00 0.00 4.69
2478 2729 2.366916 AGAAATGCATCTACTCCCTCCG 59.633 50.000 0.00 0.00 0.00 4.63
2479 2730 4.429854 AAGAAATGCATCTACTCCCTCC 57.570 45.455 0.00 0.00 0.00 4.30
2480 2731 5.298026 GGAAAAGAAATGCATCTACTCCCTC 59.702 44.000 0.00 0.00 29.84 4.30
2481 2732 5.044550 AGGAAAAGAAATGCATCTACTCCCT 60.045 40.000 0.00 0.00 33.66 4.20
2482 2733 5.196695 AGGAAAAGAAATGCATCTACTCCC 58.803 41.667 0.00 0.00 33.66 4.30
2483 2734 6.765915 AAGGAAAAGAAATGCATCTACTCC 57.234 37.500 0.00 4.71 33.50 3.85
2484 2735 8.049655 AGAAAGGAAAAGAAATGCATCTACTC 57.950 34.615 0.00 0.00 0.00 2.59
2485 2736 7.667219 TGAGAAAGGAAAAGAAATGCATCTACT 59.333 33.333 0.00 0.00 0.00 2.57
2486 2737 7.820648 TGAGAAAGGAAAAGAAATGCATCTAC 58.179 34.615 0.00 0.00 0.00 2.59
2503 2754 6.402226 GCATCTAGTTTTACCGTTGAGAAAGG 60.402 42.308 0.00 0.00 36.01 3.11
2513 2764 5.518847 TCTCGAAATGCATCTAGTTTTACCG 59.481 40.000 0.00 0.00 0.00 4.02
2610 2865 5.533528 TGCATGAGCTTCTGCATATGTAAAT 59.466 36.000 17.30 0.00 43.11 1.40
2615 2870 3.139077 TCTGCATGAGCTTCTGCATATG 58.861 45.455 20.34 11.78 46.48 1.78
2815 3072 4.276183 GTGCTGGTACTCATTCTCGATCTA 59.724 45.833 0.00 0.00 0.00 1.98
2909 3166 2.343475 GATCCATGGCACCCCGATGT 62.343 60.000 6.96 0.00 0.00 3.06
2912 3169 2.078044 ATGATCCATGGCACCCCGA 61.078 57.895 6.96 0.00 0.00 5.14
3049 3321 3.161866 GCAGGTAGGAATCTAGAGAGGG 58.838 54.545 0.00 0.00 0.00 4.30
3255 3529 1.098129 CGGCAGATCTCTGAGACGGA 61.098 60.000 10.00 0.00 46.59 4.69
3363 3637 2.615869 CAACAACAGGTTGGTTGGTTG 58.384 47.619 15.84 7.40 46.03 3.77
3486 3760 1.741401 CGGCATCACGAAAGAGGCA 60.741 57.895 13.60 0.00 46.34 4.75
3555 3829 6.765036 GCATATTCAGAGTTTGAGAGGATTCA 59.235 38.462 0.00 0.00 37.07 2.57
3596 3870 3.243704 ACCAACCAAAACGTTCATCCATG 60.244 43.478 0.00 0.00 0.00 3.66
3747 4021 4.679373 AGCAACAAGAGAACTGAAGAGA 57.321 40.909 0.00 0.00 0.00 3.10
3748 4022 6.397272 AGATAGCAACAAGAGAACTGAAGAG 58.603 40.000 0.00 0.00 0.00 2.85
3749 4023 6.352016 AGATAGCAACAAGAGAACTGAAGA 57.648 37.500 0.00 0.00 0.00 2.87
4178 4501 1.355043 AGAGGAGAGACGTACCTGGTT 59.645 52.381 3.84 0.00 33.89 3.67
4209 4540 4.143030 GCATTCGCATTCGCAAGATACTAT 60.143 41.667 0.00 0.00 42.52 2.12
4249 4587 0.887387 CCACCCACCGTACAAACCAG 60.887 60.000 0.00 0.00 0.00 4.00
4437 4775 0.605319 GGTTGATGCCGACCTTGACA 60.605 55.000 0.00 0.00 42.50 3.58
4593 4931 2.606213 TCCAGGCCCACGATGTGA 60.606 61.111 0.00 0.00 35.23 3.58
4797 5135 2.100197 TGCTTGTACGAGCTCCAGTAT 58.900 47.619 30.54 0.00 43.11 2.12
5414 5760 4.776349 TCAACAACCTGAGTACAACATGT 58.224 39.130 0.00 0.00 0.00 3.21
5416 5762 5.473504 GGAATCAACAACCTGAGTACAACAT 59.526 40.000 0.00 0.00 0.00 2.71
5486 5840 4.763279 TGGATCGATTGATTTCCATCCATG 59.237 41.667 0.00 0.00 35.85 3.66
5678 6034 5.720371 TCCAATGACACCGAATTTCAATT 57.280 34.783 0.00 0.00 0.00 2.32
5713 6069 3.314553 GTCCGTTCATCGAGAAAGAACA 58.685 45.455 17.30 2.90 41.17 3.18
5737 6093 3.765432 TCCCCTTCATCTCTTCTCTCA 57.235 47.619 0.00 0.00 0.00 3.27
5829 6185 4.924462 GGCTCTTCGGTTAGTATAGCATTC 59.076 45.833 0.00 0.00 0.00 2.67
5832 6188 3.293337 TGGCTCTTCGGTTAGTATAGCA 58.707 45.455 0.00 0.00 0.00 3.49
5835 6191 6.646267 ACAAAATGGCTCTTCGGTTAGTATA 58.354 36.000 0.00 0.00 0.00 1.47
5872 6228 7.535139 TCTAACAAAATAGGATTTTGCTTCCG 58.465 34.615 19.59 8.28 41.66 4.30
5936 6292 5.543507 ATGTTTTCATGCCAACTGGTTAA 57.456 34.783 7.95 0.00 39.30 2.01
6053 6411 4.508861 CCACCAACTTGAGAATTTGCTTTG 59.491 41.667 0.00 0.00 0.00 2.77
6174 6532 8.784994 TGTACACATTCCAACGTAATAAAACAT 58.215 29.630 0.00 0.00 0.00 2.71
6192 6550 5.047164 TCGTTTACATGTACCCTGTACACAT 60.047 40.000 4.68 3.91 32.06 3.21
6202 6560 4.813027 TCTCTTGGTCGTTTACATGTACC 58.187 43.478 4.68 6.42 0.00 3.34
6230 6588 7.394923 AGTTTGCTAGGCTCGTAGATATATCTT 59.605 37.037 20.13 3.53 38.32 2.40
6256 6614 2.502905 TACCCAAGGACCTCCCCCA 61.503 63.158 0.00 0.00 36.42 4.96
6279 6637 4.012374 TCTGTACGAAACGGACTAGGATT 58.988 43.478 7.96 0.00 41.83 3.01


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

AutoCloner maintained by Alex Coulton.