Multiple sequence alignment - TraesCS3A01G132400

Loading Multiple Alignment...

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 TraesCS3A01G132400 chr3A 100.000 6260 0 0 1 6260 109148373 109154632 0.000000e+00 11561.0
1 TraesCS3A01G132400 chr3A 98.387 62 1 0 2357 2418 14062106 14062045 6.630000e-20 110.0
2 TraesCS3A01G132400 chr3A 90.411 73 4 2 308 380 699881925 699881856 6.680000e-15 93.5
3 TraesCS3A01G132400 chr3D 96.007 3055 97 13 2587 5632 113799412 113802450 0.000000e+00 4942.0
4 TraesCS3A01G132400 chr3D 94.653 2394 67 26 2 2355 113796971 113799343 0.000000e+00 3655.0
5 TraesCS3A01G132400 chr3D 93.344 631 32 4 5633 6258 113802528 113803153 0.000000e+00 924.0
6 TraesCS3A01G132400 chr3D 94.595 74 3 1 2420 2493 113799341 113799413 5.130000e-21 113.0
7 TraesCS3A01G132400 chr3B 89.013 3122 233 50 2760 5805 167246336 167243249 0.000000e+00 3764.0
8 TraesCS3A01G132400 chr3B 91.838 1997 109 30 382 2350 167248649 167246679 0.000000e+00 2736.0
9 TraesCS3A01G132400 chr3B 92.669 341 21 3 5842 6182 167243249 167242913 7.290000e-134 488.0
10 TraesCS3A01G132400 chr3B 93.678 174 8 3 2587 2760 167246605 167246435 2.240000e-64 257.0
11 TraesCS3A01G132400 chr5D 98.000 100 2 0 2490 2589 65990589 65990490 2.320000e-39 174.0
12 TraesCS3A01G132400 chr5D 94.545 110 4 1 2492 2599 328911558 328911667 1.080000e-37 169.0
13 TraesCS3A01G132400 chr4D 97.087 103 2 1 2487 2589 110081035 110080934 8.340000e-39 172.0
14 TraesCS3A01G132400 chr4D 96.190 105 4 0 2491 2595 323929572 323929676 8.340000e-39 172.0
15 TraesCS3A01G132400 chr7B 93.805 113 7 0 2485 2597 589348422 589348310 3.000000e-38 171.0
16 TraesCS3A01G132400 chr7B 98.387 62 1 0 2357 2418 741552048 741551987 6.630000e-20 110.0
17 TraesCS3A01G132400 chr7B 97.561 41 1 0 340 380 242718366 242718326 3.130000e-08 71.3
18 TraesCS3A01G132400 chr5B 93.805 113 6 1 2491 2603 537533147 537533258 1.080000e-37 169.0
19 TraesCS3A01G132400 chr7D 92.920 113 8 0 2485 2597 545397641 545397529 1.400000e-36 165.0
20 TraesCS3A01G132400 chr7D 100.000 64 0 0 2357 2420 140921192 140921255 1.100000e-22 119.0
21 TraesCS3A01G132400 chr7D 86.538 52 7 0 342 393 153130567 153130618 2.440000e-04 58.4
22 TraesCS3A01G132400 chr6A 92.105 114 8 1 2480 2593 155803743 155803855 6.500000e-35 159.0
23 TraesCS3A01G132400 chr6A 96.774 62 2 0 2357 2418 2489658 2489719 3.090000e-18 104.0
24 TraesCS3A01G132400 chr6A 93.617 47 3 0 334 380 346592126 346592172 3.130000e-08 71.3
25 TraesCS3A01G132400 chr2A 89.231 130 7 7 2482 2609 596771376 596771252 8.400000e-34 156.0
26 TraesCS3A01G132400 chr1A 100.000 62 0 0 2357 2418 84177117 84177056 1.430000e-21 115.0
27 TraesCS3A01G132400 chr1A 98.387 62 1 0 2357 2418 502825968 502826029 6.630000e-20 110.0
28 TraesCS3A01G132400 chr5A 100.000 60 0 0 2357 2416 1759679 1759620 1.840000e-20 111.0
29 TraesCS3A01G132400 chr7A 96.825 63 2 0 2357 2419 508843624 508843562 8.580000e-19 106.0
30 TraesCS3A01G132400 chr7A 86.486 74 4 3 309 380 262465883 262465952 6.730000e-10 76.8
31 TraesCS3A01G132400 chr4B 96.774 62 2 0 2357 2418 657251153 657251214 3.090000e-18 104.0
32 TraesCS3A01G132400 chr2D 86.250 80 5 4 307 380 81657717 81657638 1.450000e-11 82.4
33 TraesCS3A01G132400 chr6B 95.349 43 2 0 341 383 95494815 95494857 1.130000e-07 69.4
34 TraesCS3A01G132400 chr4A 93.617 47 2 1 342 388 731396437 731396482 1.130000e-07 69.4
35 TraesCS3A01G132400 chr6D 100.000 31 0 0 308 338 358980206 358980176 2.440000e-04 58.4


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3A01G132400 chr3A 109148373 109154632 6259 False 11561.00 11561 100.00000 1 6260 1 chr3A.!!$F1 6259
1 TraesCS3A01G132400 chr3D 113796971 113803153 6182 False 2408.50 4942 94.64975 2 6258 4 chr3D.!!$F1 6256
2 TraesCS3A01G132400 chr3B 167242913 167248649 5736 True 1811.25 3764 91.79950 382 6182 4 chr3B.!!$R1 5800

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
164 166 0.170339 AAACTAATCTTTGCGGCGGC 59.830 50.000 9.78 9.68 40.52 6.53 F
919 959 1.337167 GGTTCAAAGGCATGGCAAGAC 60.337 52.381 22.64 11.60 0.00 3.01 F
2370 2428 1.549170 ACCGTGCAGACTAAGTTAGGG 59.451 52.381 14.36 6.26 0.00 3.53 F
2411 2469 0.103390 GGAGCGAAGTTAGAGGAGCC 59.897 60.000 0.00 0.00 0.00 4.70 F
2414 2472 0.533032 GCGAAGTTAGAGGAGCCAGT 59.467 55.000 0.00 0.00 0.00 4.00 F
2507 2565 0.635009 AGATACTCCCTCCGTCCCAA 59.365 55.000 0.00 0.00 0.00 4.12 F
2508 2566 1.007963 AGATACTCCCTCCGTCCCAAA 59.992 52.381 0.00 0.00 0.00 3.28 F
4101 4264 1.181786 GATATGGAGGGGCTCGAGAG 58.818 60.000 18.75 0.00 0.00 3.20 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1960 2018 1.486310 CAGGTTCTTGATGGATCGGGA 59.514 52.381 0.00 0.0 0.00 5.14 R
2392 2450 0.103390 GGCTCCTCTAACTTCGCTCC 59.897 60.000 0.00 0.0 0.00 4.70 R
3771 3934 1.184349 GTTGATCGAGCGTCTCTTCG 58.816 55.000 0.00 0.0 0.00 3.79 R
4117 4280 2.290641 GCCCTAATATTGTGTCTTGCCG 59.709 50.000 0.00 0.0 0.00 5.69 R
4300 4463 9.474920 CAGAGATTCTGGTAGATTTATGACTTC 57.525 37.037 0.00 0.0 40.71 3.01 R
4537 4705 4.471025 TCTGGTCATGATCCCGCATTATAT 59.529 41.667 2.86 0.0 0.00 0.86 R
4569 4737 7.812648 GTTTGCTAACCAATACTGTGTGATAA 58.187 34.615 0.00 0.0 32.49 1.75 R
6170 6484 0.028110 GGAACTTCGGATCGCATTGC 59.972 55.000 0.00 0.0 0.00 3.56 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
50 52 7.859325 TTAAGCTCACTTCAGTTGTTACTTT 57.141 32.000 0.00 0.00 37.33 2.66
114 116 1.673033 GCTACGCAGCCAAAGAGAAGA 60.673 52.381 0.00 0.00 42.37 2.87
117 119 3.334583 ACGCAGCCAAAGAGAAGAATA 57.665 42.857 0.00 0.00 0.00 1.75
118 120 3.878778 ACGCAGCCAAAGAGAAGAATAT 58.121 40.909 0.00 0.00 0.00 1.28
120 122 5.428253 ACGCAGCCAAAGAGAAGAATATTA 58.572 37.500 0.00 0.00 0.00 0.98
121 123 6.058183 ACGCAGCCAAAGAGAAGAATATTAT 58.942 36.000 0.00 0.00 0.00 1.28
122 124 6.543831 ACGCAGCCAAAGAGAAGAATATTATT 59.456 34.615 0.00 0.00 0.00 1.40
123 125 6.854892 CGCAGCCAAAGAGAAGAATATTATTG 59.145 38.462 0.00 0.00 0.00 1.90
164 166 0.170339 AAACTAATCTTTGCGGCGGC 59.830 50.000 9.78 9.68 40.52 6.53
186 188 7.235777 CGGCACAAGATTTTAATTTTCCAATG 58.764 34.615 0.00 0.00 0.00 2.82
215 217 3.002348 GGACCCTTGCGAGAAATTAATCG 59.998 47.826 1.22 7.63 41.79 3.34
223 225 7.373441 CCTTGCGAGAAATTAATCGTAACAATC 59.627 37.037 1.22 0.00 38.35 2.67
305 308 3.938963 TCCAATTACTTCACGGCAAGATC 59.061 43.478 2.85 0.00 0.00 2.75
317 320 1.414550 GGCAAGATCAGTACTCCCTCC 59.585 57.143 0.00 0.00 0.00 4.30
319 322 2.656002 CAAGATCAGTACTCCCTCCGA 58.344 52.381 0.00 0.00 0.00 4.55
338 366 4.819088 TCCGATCCGAATTAAATGATGCAA 59.181 37.500 0.00 0.00 0.00 4.08
352 380 5.954296 ATGATGCAATGTATAGAGGTTGC 57.046 39.130 0.00 2.14 45.27 4.17
426 454 5.291858 GGCAGCAAAGCATATTCTTTTTACC 59.708 40.000 0.00 0.00 34.31 2.85
427 455 6.101997 GCAGCAAAGCATATTCTTTTTACCT 58.898 36.000 0.00 0.00 34.31 3.08
429 457 7.412237 GCAGCAAAGCATATTCTTTTTACCTTG 60.412 37.037 0.00 0.00 34.31 3.61
577 613 6.932356 ATAATTCTGCATAACCTGTCTGTG 57.068 37.500 0.00 0.00 0.00 3.66
618 654 2.942804 TCCAAAGGACTGCAAACATCA 58.057 42.857 0.00 0.00 0.00 3.07
641 677 3.170717 CTCCTAAACCCTGACCACACTA 58.829 50.000 0.00 0.00 0.00 2.74
652 688 4.468510 CCTGACCACACTAGGTAATGGTAA 59.531 45.833 8.85 2.73 45.55 2.85
706 742 5.313712 ACCTACCAAAACCATGAACAGTAG 58.686 41.667 0.00 0.00 0.00 2.57
913 952 2.093869 CCATGAAGGTTCAAAGGCATGG 60.094 50.000 0.00 0.00 44.47 3.66
919 959 1.337167 GGTTCAAAGGCATGGCAAGAC 60.337 52.381 22.64 11.60 0.00 3.01
968 1008 2.548904 CCTGTAGGAACTAGGATCGACG 59.451 54.545 0.00 0.00 44.14 5.12
1441 1484 1.607148 GTTGGTACTTGCACCTCAACC 59.393 52.381 0.00 0.00 39.50 3.77
1680 1733 4.730613 GCTTTATTTGCCAGGTATGTGTCG 60.731 45.833 0.00 0.00 0.00 4.35
1865 1923 7.315066 TGATGTATTACTGCCCTGATGAATA 57.685 36.000 0.00 0.00 0.00 1.75
1873 1931 8.815565 TTACTGCCCTGATGAATAAAACATAA 57.184 30.769 0.00 0.00 0.00 1.90
2024 2082 6.508030 ACTACAGATCAGAGAGTCTATGGA 57.492 41.667 14.59 2.87 0.00 3.41
2332 2390 6.803154 AGAAACGGAAATGGAAGTAAGAAG 57.197 37.500 0.00 0.00 0.00 2.85
2352 2410 4.568152 AGCATGTGAACTTGTTTGTACC 57.432 40.909 0.00 0.00 0.00 3.34
2353 2411 3.003275 AGCATGTGAACTTGTTTGTACCG 59.997 43.478 0.00 0.00 0.00 4.02
2354 2412 3.242936 GCATGTGAACTTGTTTGTACCGT 60.243 43.478 0.00 0.00 0.00 4.83
2355 2413 4.278858 CATGTGAACTTGTTTGTACCGTG 58.721 43.478 0.00 0.00 0.00 4.94
2356 2414 2.096174 TGTGAACTTGTTTGTACCGTGC 59.904 45.455 0.00 0.00 0.00 5.34
2357 2415 2.096174 GTGAACTTGTTTGTACCGTGCA 59.904 45.455 0.00 0.00 0.00 4.57
2358 2416 2.353269 TGAACTTGTTTGTACCGTGCAG 59.647 45.455 0.00 0.00 0.00 4.41
2359 2417 2.319136 ACTTGTTTGTACCGTGCAGA 57.681 45.000 0.00 0.00 0.00 4.26
2360 2418 1.937899 ACTTGTTTGTACCGTGCAGAC 59.062 47.619 3.67 3.67 0.00 3.51
2361 2419 2.210116 CTTGTTTGTACCGTGCAGACT 58.790 47.619 10.82 0.00 0.00 3.24
2362 2420 3.181473 ACTTGTTTGTACCGTGCAGACTA 60.181 43.478 10.82 3.69 0.00 2.59
2363 2421 3.455990 TGTTTGTACCGTGCAGACTAA 57.544 42.857 10.82 0.00 0.00 2.24
2364 2422 3.386486 TGTTTGTACCGTGCAGACTAAG 58.614 45.455 10.82 0.00 0.00 2.18
2365 2423 3.181473 TGTTTGTACCGTGCAGACTAAGT 60.181 43.478 10.82 0.00 0.00 2.24
2366 2424 3.738830 TTGTACCGTGCAGACTAAGTT 57.261 42.857 0.00 0.00 0.00 2.66
2367 2425 4.852134 TTGTACCGTGCAGACTAAGTTA 57.148 40.909 0.00 0.00 0.00 2.24
2368 2426 4.430137 TGTACCGTGCAGACTAAGTTAG 57.570 45.455 8.41 8.41 0.00 2.34
2369 2427 3.192001 TGTACCGTGCAGACTAAGTTAGG 59.808 47.826 14.36 0.00 0.00 2.69
2370 2428 1.549170 ACCGTGCAGACTAAGTTAGGG 59.451 52.381 14.36 6.26 0.00 3.53
2371 2429 1.549170 CCGTGCAGACTAAGTTAGGGT 59.451 52.381 14.36 0.00 0.00 4.34
2372 2430 2.756760 CCGTGCAGACTAAGTTAGGGTA 59.243 50.000 14.36 0.75 0.00 3.69
2373 2431 3.428589 CCGTGCAGACTAAGTTAGGGTAC 60.429 52.174 14.36 10.94 0.00 3.34
2374 2432 3.442977 CGTGCAGACTAAGTTAGGGTACT 59.557 47.826 14.36 5.38 0.00 2.73
2375 2433 4.674623 CGTGCAGACTAAGTTAGGGTACTG 60.675 50.000 14.36 15.82 0.00 2.74
2376 2434 4.220163 GTGCAGACTAAGTTAGGGTACTGT 59.780 45.833 14.36 0.00 0.00 3.55
2377 2435 4.836736 TGCAGACTAAGTTAGGGTACTGTT 59.163 41.667 14.36 0.00 0.00 3.16
2378 2436 5.306160 TGCAGACTAAGTTAGGGTACTGTTT 59.694 40.000 14.36 0.00 0.00 2.83
2379 2437 5.868258 GCAGACTAAGTTAGGGTACTGTTTC 59.132 44.000 14.36 0.00 0.00 2.78
2380 2438 6.396450 CAGACTAAGTTAGGGTACTGTTTCC 58.604 44.000 14.36 0.00 0.00 3.13
2381 2439 5.483231 AGACTAAGTTAGGGTACTGTTTCCC 59.517 44.000 14.36 11.25 43.71 3.97
2389 2447 4.628963 GGGTACTGTTTCCCTAACTTCA 57.371 45.455 11.75 0.00 40.48 3.02
2390 2448 5.175388 GGGTACTGTTTCCCTAACTTCAT 57.825 43.478 11.75 0.00 40.48 2.57
2391 2449 6.303903 GGGTACTGTTTCCCTAACTTCATA 57.696 41.667 11.75 0.00 40.48 2.15
2392 2450 6.346896 GGGTACTGTTTCCCTAACTTCATAG 58.653 44.000 11.75 0.00 40.48 2.23
2393 2451 6.346896 GGTACTGTTTCCCTAACTTCATAGG 58.653 44.000 0.00 0.00 41.86 2.57
2394 2452 6.155737 GGTACTGTTTCCCTAACTTCATAGGA 59.844 42.308 1.95 0.00 44.46 2.94
2395 2453 6.301169 ACTGTTTCCCTAACTTCATAGGAG 57.699 41.667 1.95 0.00 44.46 3.69
2396 2454 5.099042 TGTTTCCCTAACTTCATAGGAGC 57.901 43.478 1.95 0.00 44.46 4.70
2397 2455 4.120589 GTTTCCCTAACTTCATAGGAGCG 58.879 47.826 1.95 0.00 44.46 5.03
2398 2456 3.308035 TCCCTAACTTCATAGGAGCGA 57.692 47.619 1.95 0.00 44.46 4.93
2399 2457 3.638860 TCCCTAACTTCATAGGAGCGAA 58.361 45.455 1.95 0.00 44.46 4.70
2400 2458 3.637229 TCCCTAACTTCATAGGAGCGAAG 59.363 47.826 1.95 0.00 44.46 3.79
2407 2465 4.865776 CTTCATAGGAGCGAAGTTAGAGG 58.134 47.826 0.00 0.00 35.06 3.69
2408 2466 4.166246 TCATAGGAGCGAAGTTAGAGGA 57.834 45.455 0.00 0.00 0.00 3.71
2409 2467 4.138290 TCATAGGAGCGAAGTTAGAGGAG 58.862 47.826 0.00 0.00 0.00 3.69
2410 2468 1.107945 AGGAGCGAAGTTAGAGGAGC 58.892 55.000 0.00 0.00 0.00 4.70
2411 2469 0.103390 GGAGCGAAGTTAGAGGAGCC 59.897 60.000 0.00 0.00 0.00 4.70
2412 2470 0.818296 GAGCGAAGTTAGAGGAGCCA 59.182 55.000 0.00 0.00 0.00 4.75
2413 2471 0.820871 AGCGAAGTTAGAGGAGCCAG 59.179 55.000 0.00 0.00 0.00 4.85
2414 2472 0.533032 GCGAAGTTAGAGGAGCCAGT 59.467 55.000 0.00 0.00 0.00 4.00
2415 2473 1.066787 GCGAAGTTAGAGGAGCCAGTT 60.067 52.381 0.00 0.00 0.00 3.16
2416 2474 2.882324 CGAAGTTAGAGGAGCCAGTTC 58.118 52.381 0.00 0.00 0.00 3.01
2417 2475 2.417515 CGAAGTTAGAGGAGCCAGTTCC 60.418 54.545 0.00 0.00 37.52 3.62
2418 2476 2.327325 AGTTAGAGGAGCCAGTTCCA 57.673 50.000 3.23 0.00 39.84 3.53
2432 2490 4.451096 GCCAGTTCCACGTAATACATATGG 59.549 45.833 7.80 0.35 0.00 2.74
2450 2508 7.536625 ACATATGGACCTTATAGACTGTAGGT 58.463 38.462 7.80 0.00 43.48 3.08
2463 2521 2.950781 CTGTAGGTCAGGATAGGCTGA 58.049 52.381 0.00 0.00 40.23 4.26
2493 2551 8.092521 ACAAATCACAGCATGCTTATAGATAC 57.907 34.615 19.98 0.00 42.53 2.24
2494 2552 7.935755 ACAAATCACAGCATGCTTATAGATACT 59.064 33.333 19.98 7.18 42.53 2.12
2495 2553 8.441608 CAAATCACAGCATGCTTATAGATACTC 58.558 37.037 19.98 0.00 42.53 2.59
2496 2554 6.030548 TCACAGCATGCTTATAGATACTCC 57.969 41.667 19.98 0.00 42.53 3.85
2497 2555 5.047021 TCACAGCATGCTTATAGATACTCCC 60.047 44.000 19.98 0.00 42.53 4.30
2498 2556 5.046735 CACAGCATGCTTATAGATACTCCCT 60.047 44.000 19.98 0.00 42.53 4.20
2499 2557 5.186797 ACAGCATGCTTATAGATACTCCCTC 59.813 44.000 19.98 0.00 42.53 4.30
2500 2558 4.714308 AGCATGCTTATAGATACTCCCTCC 59.286 45.833 16.30 0.00 0.00 4.30
2501 2559 4.440802 GCATGCTTATAGATACTCCCTCCG 60.441 50.000 11.37 0.00 0.00 4.63
2502 2560 4.383931 TGCTTATAGATACTCCCTCCGT 57.616 45.455 0.00 0.00 0.00 4.69
2503 2561 4.333690 TGCTTATAGATACTCCCTCCGTC 58.666 47.826 0.00 0.00 0.00 4.79
2504 2562 3.695556 GCTTATAGATACTCCCTCCGTCC 59.304 52.174 0.00 0.00 0.00 4.79
2505 2563 2.903375 ATAGATACTCCCTCCGTCCC 57.097 55.000 0.00 0.00 0.00 4.46
2506 2564 1.526315 TAGATACTCCCTCCGTCCCA 58.474 55.000 0.00 0.00 0.00 4.37
2507 2565 0.635009 AGATACTCCCTCCGTCCCAA 59.365 55.000 0.00 0.00 0.00 4.12
2508 2566 1.007963 AGATACTCCCTCCGTCCCAAA 59.992 52.381 0.00 0.00 0.00 3.28
2509 2567 1.835531 GATACTCCCTCCGTCCCAAAA 59.164 52.381 0.00 0.00 0.00 2.44
2510 2568 1.961133 TACTCCCTCCGTCCCAAAAT 58.039 50.000 0.00 0.00 0.00 1.82
2511 2569 1.961133 ACTCCCTCCGTCCCAAAATA 58.039 50.000 0.00 0.00 0.00 1.40
2512 2570 2.271777 ACTCCCTCCGTCCCAAAATAA 58.728 47.619 0.00 0.00 0.00 1.40
2513 2571 2.238898 ACTCCCTCCGTCCCAAAATAAG 59.761 50.000 0.00 0.00 0.00 1.73
2514 2572 2.238898 CTCCCTCCGTCCCAAAATAAGT 59.761 50.000 0.00 0.00 0.00 2.24
2515 2573 2.026636 TCCCTCCGTCCCAAAATAAGTG 60.027 50.000 0.00 0.00 0.00 3.16
2516 2574 2.290705 CCCTCCGTCCCAAAATAAGTGT 60.291 50.000 0.00 0.00 0.00 3.55
2517 2575 3.007635 CCTCCGTCCCAAAATAAGTGTC 58.992 50.000 0.00 0.00 0.00 3.67
2518 2576 3.307480 CCTCCGTCCCAAAATAAGTGTCT 60.307 47.826 0.00 0.00 0.00 3.41
2519 2577 3.933332 CTCCGTCCCAAAATAAGTGTCTC 59.067 47.826 0.00 0.00 0.00 3.36
2520 2578 3.325425 TCCGTCCCAAAATAAGTGTCTCA 59.675 43.478 0.00 0.00 0.00 3.27
2521 2579 4.069304 CCGTCCCAAAATAAGTGTCTCAA 58.931 43.478 0.00 0.00 0.00 3.02
2522 2580 4.154195 CCGTCCCAAAATAAGTGTCTCAAG 59.846 45.833 0.00 0.00 0.00 3.02
2523 2581 4.378459 CGTCCCAAAATAAGTGTCTCAAGC 60.378 45.833 0.00 0.00 0.00 4.01
2524 2582 4.762251 GTCCCAAAATAAGTGTCTCAAGCT 59.238 41.667 0.00 0.00 0.00 3.74
2525 2583 5.241728 GTCCCAAAATAAGTGTCTCAAGCTT 59.758 40.000 0.00 0.00 0.00 3.74
2526 2584 6.430000 GTCCCAAAATAAGTGTCTCAAGCTTA 59.570 38.462 0.00 0.00 0.00 3.09
2527 2585 6.655003 TCCCAAAATAAGTGTCTCAAGCTTAG 59.345 38.462 0.00 0.00 0.00 2.18
2528 2586 6.431234 CCCAAAATAAGTGTCTCAAGCTTAGT 59.569 38.462 0.00 0.00 0.00 2.24
2529 2587 7.606456 CCCAAAATAAGTGTCTCAAGCTTAGTA 59.394 37.037 0.00 0.00 0.00 1.82
2530 2588 8.443937 CCAAAATAAGTGTCTCAAGCTTAGTAC 58.556 37.037 0.00 0.00 0.00 2.73
2531 2589 8.988934 CAAAATAAGTGTCTCAAGCTTAGTACA 58.011 33.333 0.00 0.36 0.00 2.90
2532 2590 9.555727 AAAATAAGTGTCTCAAGCTTAGTACAA 57.444 29.630 0.00 0.00 0.00 2.41
2533 2591 8.535690 AATAAGTGTCTCAAGCTTAGTACAAC 57.464 34.615 0.00 0.00 0.00 3.32
2534 2592 5.793030 AGTGTCTCAAGCTTAGTACAACT 57.207 39.130 0.00 0.00 0.00 3.16
2535 2593 6.163135 AGTGTCTCAAGCTTAGTACAACTT 57.837 37.500 0.00 0.00 0.00 2.66
2536 2594 6.583562 AGTGTCTCAAGCTTAGTACAACTTT 58.416 36.000 0.00 0.00 0.00 2.66
2537 2595 7.723324 AGTGTCTCAAGCTTAGTACAACTTTA 58.277 34.615 0.00 0.00 0.00 1.85
2538 2596 8.368668 AGTGTCTCAAGCTTAGTACAACTTTAT 58.631 33.333 0.00 0.00 0.00 1.40
2539 2597 9.635520 GTGTCTCAAGCTTAGTACAACTTTATA 57.364 33.333 0.00 0.00 0.00 0.98
2540 2598 9.635520 TGTCTCAAGCTTAGTACAACTTTATAC 57.364 33.333 0.00 0.00 0.00 1.47
2541 2599 9.857957 GTCTCAAGCTTAGTACAACTTTATACT 57.142 33.333 0.00 0.00 35.76 2.12
2565 2623 9.310716 ACTAAAGTTAGTACAAAGTTGAGACAC 57.689 33.333 1.81 0.00 41.92 3.67
2566 2624 9.530633 CTAAAGTTAGTACAAAGTTGAGACACT 57.469 33.333 0.00 0.00 0.00 3.55
2567 2625 8.788325 AAAGTTAGTACAAAGTTGAGACACTT 57.212 30.769 0.00 0.98 38.74 3.16
2568 2626 9.880157 AAAGTTAGTACAAAGTTGAGACACTTA 57.120 29.630 0.00 0.00 35.87 2.24
2574 2632 8.621286 AGTACAAAGTTGAGACACTTATTTTGG 58.379 33.333 0.00 0.00 35.87 3.28
2575 2633 6.805713 ACAAAGTTGAGACACTTATTTTGGG 58.194 36.000 0.00 0.00 35.87 4.12
2576 2634 6.605594 ACAAAGTTGAGACACTTATTTTGGGA 59.394 34.615 0.00 0.00 35.87 4.37
2577 2635 6.635030 AAGTTGAGACACTTATTTTGGGAC 57.365 37.500 0.00 0.00 35.10 4.46
2578 2636 5.690865 AGTTGAGACACTTATTTTGGGACA 58.309 37.500 0.00 0.00 0.00 4.02
2579 2637 5.765182 AGTTGAGACACTTATTTTGGGACAG 59.235 40.000 0.00 0.00 42.39 3.51
2580 2638 5.560722 TGAGACACTTATTTTGGGACAGA 57.439 39.130 0.00 0.00 42.39 3.41
2581 2639 5.551233 TGAGACACTTATTTTGGGACAGAG 58.449 41.667 0.00 0.00 42.39 3.35
2582 2640 4.911390 AGACACTTATTTTGGGACAGAGG 58.089 43.478 0.00 0.00 42.39 3.69
2583 2641 4.010349 GACACTTATTTTGGGACAGAGGG 58.990 47.826 0.00 0.00 42.39 4.30
2584 2642 3.655777 ACACTTATTTTGGGACAGAGGGA 59.344 43.478 0.00 0.00 42.39 4.20
2585 2643 4.263506 ACACTTATTTTGGGACAGAGGGAG 60.264 45.833 0.00 0.00 42.39 4.30
2586 2644 3.916989 ACTTATTTTGGGACAGAGGGAGT 59.083 43.478 0.00 0.00 42.39 3.85
2587 2645 5.045869 CACTTATTTTGGGACAGAGGGAGTA 60.046 44.000 0.00 0.00 42.39 2.59
2631 2689 3.456277 CTGGACTCCTAATGGCTTAAGGT 59.544 47.826 4.29 0.00 0.00 3.50
2670 2728 9.109393 GATACACATGAAAACTCTGGCTAATTA 57.891 33.333 0.00 0.00 0.00 1.40
2704 2762 4.833380 AGATATACCTGAATGTGTACGGCT 59.167 41.667 0.00 0.00 0.00 5.52
2790 2947 3.196685 CCTCCTAACCTTCCTGTCTTCAG 59.803 52.174 0.00 0.00 41.01 3.02
3046 3203 2.099756 GCAGGCTCCAATTGGTATGAAC 59.900 50.000 23.76 9.70 36.34 3.18
3107 3265 8.803201 ATAGTGTACACTGAATATCATCAACG 57.197 34.615 33.77 0.00 42.52 4.10
3387 3545 6.522946 AGGTAAGAGATGACACATGATCATG 58.477 40.000 29.95 29.95 44.15 3.07
3569 3732 3.485463 AGGCTTAACACAACAGTGCTA 57.515 42.857 0.00 0.00 36.74 3.49
3639 3802 5.063880 ACAATCTTTACCAGGTGAGTTCAC 58.936 41.667 0.76 3.67 45.72 3.18
3735 3898 3.365820 GCATTTGGCAGAAAATGAACTCG 59.634 43.478 17.86 0.00 46.13 4.18
3765 3928 3.192844 GGTTCTCTACTGACACGATGGAA 59.807 47.826 0.00 0.00 0.00 3.53
3771 3934 2.893637 ACTGACACGATGGAAGTATGC 58.106 47.619 0.00 0.00 0.00 3.14
3953 4116 2.560105 ACAGTACTACGGAACAGGGTTC 59.440 50.000 0.00 0.54 0.00 3.62
4021 4184 4.691860 AATCATGTTGCTACAAGTCAGC 57.308 40.909 4.79 0.00 37.91 4.26
4101 4264 1.181786 GATATGGAGGGGCTCGAGAG 58.818 60.000 18.75 0.00 0.00 3.20
4172 4335 7.395190 TCACAGATAAAATGCTTACATGCTT 57.605 32.000 0.00 0.00 36.36 3.91
4300 4463 4.000331 AGCTTAGCAGTACCATATGCAG 58.000 45.455 7.07 0.00 45.01 4.41
4569 4737 5.440610 GGGATCATGACCAGAACATAACTT 58.559 41.667 13.95 0.00 0.00 2.66
4573 4744 8.778358 GGATCATGACCAGAACATAACTTTATC 58.222 37.037 0.00 0.00 0.00 1.75
4611 4782 6.500684 AGCAAACCACTACATTGTGATAAG 57.499 37.500 0.00 0.00 40.12 1.73
4810 5003 4.130118 ACTAAGTCGATGAATCAATGCCC 58.870 43.478 0.00 0.00 0.00 5.36
4949 5142 5.988287 TGGAAATTTTCAGTTCCTTTGCTT 58.012 33.333 11.09 0.00 45.84 3.91
4976 5169 7.902087 CCCCCTTAAAAATGAACAGTAATTGA 58.098 34.615 0.00 0.00 0.00 2.57
4978 5171 8.585018 CCCCTTAAAAATGAACAGTAATTGACT 58.415 33.333 0.00 0.00 39.82 3.41
5008 5210 6.938596 TCAGTGATCAAGTCTGTTGAAATCAT 59.061 34.615 10.60 0.00 31.55 2.45
5050 5252 1.071814 GTGTGAAGGCCCCGTTACA 59.928 57.895 0.00 0.00 0.00 2.41
5055 5257 0.323957 GAAGGCCCCGTTACAACTCT 59.676 55.000 0.00 0.00 0.00 3.24
5276 5481 7.872483 GGAAGTTTGATTAAGGATGCTCAAAAA 59.128 33.333 1.75 0.00 38.81 1.94
5305 5518 3.689347 TGTGGAAAGAGCAATGCATAGT 58.311 40.909 8.35 0.00 0.00 2.12
5370 5583 2.069273 CAAACAGGAATCGAGCGACTT 58.931 47.619 0.00 0.00 0.00 3.01
5404 5617 2.460669 AGAAAATGCCACCCAGGAATC 58.539 47.619 0.00 0.00 32.86 2.52
5429 5642 4.282703 GTGGGAGACTTGGAGTTACAGTTA 59.717 45.833 0.00 0.00 0.00 2.24
5434 5647 7.416551 GGGAGACTTGGAGTTACAGTTATAGAC 60.417 44.444 0.00 0.00 0.00 2.59
5509 5736 2.383338 AGATCAAATGTTTGGGGAGGGT 59.617 45.455 5.71 0.00 38.66 4.34
5527 5754 1.473434 GGTAGACCTCCGCTGAATTGG 60.473 57.143 0.00 0.00 0.00 3.16
5533 5760 1.156736 CTCCGCTGAATTGGTCGTTT 58.843 50.000 0.00 0.00 0.00 3.60
5722 6032 9.865152 TTAGATGATAATGATCCAAAATGGTCA 57.135 29.630 0.00 0.95 39.03 4.02
5768 6080 7.012894 ACGAGTGAAAACTGGAATTTCATGTTA 59.987 33.333 5.15 0.00 45.50 2.41
5779 6091 6.014755 TGGAATTTCATGTTATGGCAACTGAA 60.015 34.615 0.00 0.00 37.61 3.02
5782 6094 9.241317 GAATTTCATGTTATGGCAACTGAATAG 57.759 33.333 0.00 0.00 37.61 1.73
5801 6115 5.993106 ATAGCTACTTCATTTTTCTCGGC 57.007 39.130 0.00 0.00 0.00 5.54
5851 6165 9.941664 CAAATTGGAAGTCATTAGATATCACAC 57.058 33.333 5.32 0.00 0.00 3.82
5977 6291 6.381801 AGATCATTCAACGACCAAATTTGAC 58.618 36.000 19.86 11.62 0.00 3.18
6047 6361 5.009911 TCAACTCACCAAATTCATGAACTGG 59.990 40.000 26.30 26.30 34.47 4.00
6076 6390 0.733729 GCCTGAAAGCTCAGCTCATG 59.266 55.000 0.00 0.00 46.76 3.07
6137 6451 4.499023 CACAATCCGTTCGCCGCG 62.499 66.667 6.39 6.39 34.38 6.46
6152 6466 4.500116 GCGGCGACTCCAGGACTC 62.500 72.222 12.98 0.00 34.01 3.36
6156 6470 2.640302 GCGACTCCAGGACTCAGCA 61.640 63.158 0.00 0.00 0.00 4.41
6191 6505 1.737236 CAATGCGATCCGAAGTTCCAA 59.263 47.619 0.00 0.00 0.00 3.53
6195 6509 0.108138 CGATCCGAAGTTCCAAGCCT 60.108 55.000 0.00 0.00 0.00 4.58
6196 6510 1.373570 GATCCGAAGTTCCAAGCCTG 58.626 55.000 0.00 0.00 0.00 4.85
6199 6513 1.600636 CGAAGTTCCAAGCCTGCCA 60.601 57.895 0.00 0.00 0.00 4.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.367450 CTGTTACAGCTCTTAGCATCCTC 58.633 47.826 0.00 0.00 45.56 3.71
50 52 5.840715 TGCTTTTATTTTGTGATGCTGTCA 58.159 33.333 0.00 0.00 0.00 3.58
98 100 4.889832 AATATTCTTCTCTTTGGCTGCG 57.110 40.909 0.00 0.00 0.00 5.18
118 120 9.170890 ACACTATGAGAATAGGGGATTCAATAA 57.829 33.333 0.44 0.00 45.69 1.40
120 122 7.639062 ACACTATGAGAATAGGGGATTCAAT 57.361 36.000 0.44 0.00 45.69 2.57
121 123 8.561536 TTACACTATGAGAATAGGGGATTCAA 57.438 34.615 0.44 0.00 45.69 2.69
122 124 8.429641 GTTTACACTATGAGAATAGGGGATTCA 58.570 37.037 0.44 0.00 45.69 2.57
123 125 8.652290 AGTTTACACTATGAGAATAGGGGATTC 58.348 37.037 0.44 0.00 43.89 2.52
164 166 8.445493 GGCTCATTGGAAAATTAAAATCTTGTG 58.555 33.333 0.00 0.00 0.00 3.33
165 167 7.607607 GGGCTCATTGGAAAATTAAAATCTTGT 59.392 33.333 0.00 0.00 0.00 3.16
186 188 4.785453 CGCAAGGGTCCTGGGCTC 62.785 72.222 0.00 0.00 0.00 4.70
305 308 0.179026 TCGGATCGGAGGGAGTACTG 60.179 60.000 0.00 0.00 0.00 2.74
317 320 6.144854 ACATTGCATCATTTAATTCGGATCG 58.855 36.000 0.00 0.00 0.00 3.69
352 380 4.393062 CCCTCCGATCCGAATTAATTGATG 59.607 45.833 5.17 0.00 0.00 3.07
353 381 4.286032 TCCCTCCGATCCGAATTAATTGAT 59.714 41.667 5.17 3.10 0.00 2.57
364 392 0.896019 ATGCTACTCCCTCCGATCCG 60.896 60.000 0.00 0.00 0.00 4.18
426 454 7.277174 AGTGAAGTGAAATTTTAGTCCCAAG 57.723 36.000 0.00 0.00 0.00 3.61
427 455 7.996644 AGTAGTGAAGTGAAATTTTAGTCCCAA 59.003 33.333 0.00 0.00 0.00 4.12
429 457 7.981102 AGTAGTGAAGTGAAATTTTAGTCCC 57.019 36.000 0.00 0.00 0.00 4.46
438 466 6.127026 GGGACTCCATAGTAGTGAAGTGAAAT 60.127 42.308 0.00 0.00 35.56 2.17
565 601 7.279615 TCTTTTCAGATTTCACAGACAGGTTA 58.720 34.615 0.00 0.00 0.00 2.85
568 604 6.624352 TTCTTTTCAGATTTCACAGACAGG 57.376 37.500 0.00 0.00 0.00 4.00
598 634 2.942804 TGATGTTTGCAGTCCTTTGGA 58.057 42.857 0.00 0.00 0.00 3.53
618 654 2.572104 GTGTGGTCAGGGTTTAGGAGAT 59.428 50.000 0.00 0.00 0.00 2.75
641 677 7.560626 TGTAACTGTTTTGGTTTACCATTACCT 59.439 33.333 13.91 3.73 46.97 3.08
652 688 2.741145 TGGGCTGTAACTGTTTTGGTT 58.259 42.857 0.00 0.00 0.00 3.67
706 742 4.965119 AAACAAACAAGTGGTCTGAGTC 57.035 40.909 0.00 0.00 0.00 3.36
913 952 9.943163 GATTATTGAAGAGGATTTTAGTCTTGC 57.057 33.333 0.00 0.00 30.55 4.01
968 1008 1.138266 TGAAGCAGGGCGTATCTTACC 59.862 52.381 0.00 0.00 0.00 2.85
1370 1413 7.615757 TCCACTAGAAGATAAGACTTGTGATCA 59.384 37.037 0.00 0.00 38.75 2.92
1441 1484 6.021596 GTGCTTTACCATTAAGAATGACACG 58.978 40.000 0.70 0.00 41.46 4.49
1713 1766 6.424683 GGGCGATTTACCTTAGTAATTTTCG 58.575 40.000 0.00 0.00 38.26 3.46
1873 1931 2.149578 GCTCAGTCAAACATGCAGAGT 58.850 47.619 0.00 0.00 0.00 3.24
1960 2018 1.486310 CAGGTTCTTGATGGATCGGGA 59.514 52.381 0.00 0.00 0.00 5.14
2024 2082 8.077991 CCAATAAATTGCTGTCACATATCGAAT 58.922 33.333 0.00 0.00 36.48 3.34
2332 2390 3.242936 ACGGTACAAACAAGTTCACATGC 60.243 43.478 0.00 0.00 0.00 4.06
2352 2410 3.442977 AGTACCCTAACTTAGTCTGCACG 59.557 47.826 0.00 0.00 0.00 5.34
2353 2411 4.220163 ACAGTACCCTAACTTAGTCTGCAC 59.780 45.833 0.00 0.00 0.00 4.57
2354 2412 4.413760 ACAGTACCCTAACTTAGTCTGCA 58.586 43.478 0.00 0.00 0.00 4.41
2355 2413 5.402997 AACAGTACCCTAACTTAGTCTGC 57.597 43.478 0.00 0.00 0.00 4.26
2356 2414 6.396450 GGAAACAGTACCCTAACTTAGTCTG 58.604 44.000 0.00 0.00 0.00 3.51
2357 2415 5.483231 GGGAAACAGTACCCTAACTTAGTCT 59.517 44.000 8.14 0.00 42.56 3.24
2358 2416 5.728471 GGGAAACAGTACCCTAACTTAGTC 58.272 45.833 8.14 0.00 42.56 2.59
2359 2417 5.752036 GGGAAACAGTACCCTAACTTAGT 57.248 43.478 8.14 0.00 42.56 2.24
2368 2426 4.628963 TGAAGTTAGGGAAACAGTACCC 57.371 45.455 7.47 7.47 45.88 3.69
2369 2427 6.155737 TCCTATGAAGTTAGGGAAACAGTACC 59.844 42.308 0.00 0.00 40.83 3.34
2370 2428 7.179076 TCCTATGAAGTTAGGGAAACAGTAC 57.821 40.000 0.00 0.00 40.83 2.73
2371 2429 6.127140 GCTCCTATGAAGTTAGGGAAACAGTA 60.127 42.308 0.00 0.00 40.83 2.74
2372 2430 5.338463 GCTCCTATGAAGTTAGGGAAACAGT 60.338 44.000 0.00 0.00 40.83 3.55
2373 2431 5.119694 GCTCCTATGAAGTTAGGGAAACAG 58.880 45.833 0.00 0.00 40.83 3.16
2374 2432 4.382685 CGCTCCTATGAAGTTAGGGAAACA 60.383 45.833 0.00 0.00 40.83 2.83
2375 2433 4.120589 CGCTCCTATGAAGTTAGGGAAAC 58.879 47.826 0.00 0.00 39.45 2.78
2376 2434 4.028131 TCGCTCCTATGAAGTTAGGGAAA 58.972 43.478 0.00 0.00 39.45 3.13
2377 2435 3.638860 TCGCTCCTATGAAGTTAGGGAA 58.361 45.455 0.00 0.00 39.45 3.97
2378 2436 3.308035 TCGCTCCTATGAAGTTAGGGA 57.692 47.619 0.00 0.00 39.45 4.20
2379 2437 3.983741 CTTCGCTCCTATGAAGTTAGGG 58.016 50.000 0.00 0.00 39.45 3.53
2385 2443 4.580995 TCCTCTAACTTCGCTCCTATGAAG 59.419 45.833 0.71 0.71 45.53 3.02
2386 2444 4.533815 TCCTCTAACTTCGCTCCTATGAA 58.466 43.478 0.00 0.00 0.00 2.57
2387 2445 4.138290 CTCCTCTAACTTCGCTCCTATGA 58.862 47.826 0.00 0.00 0.00 2.15
2388 2446 3.305064 GCTCCTCTAACTTCGCTCCTATG 60.305 52.174 0.00 0.00 0.00 2.23
2389 2447 2.888414 GCTCCTCTAACTTCGCTCCTAT 59.112 50.000 0.00 0.00 0.00 2.57
2390 2448 2.299521 GCTCCTCTAACTTCGCTCCTA 58.700 52.381 0.00 0.00 0.00 2.94
2391 2449 1.107945 GCTCCTCTAACTTCGCTCCT 58.892 55.000 0.00 0.00 0.00 3.69
2392 2450 0.103390 GGCTCCTCTAACTTCGCTCC 59.897 60.000 0.00 0.00 0.00 4.70
2393 2451 0.818296 TGGCTCCTCTAACTTCGCTC 59.182 55.000 0.00 0.00 0.00 5.03
2394 2452 0.820871 CTGGCTCCTCTAACTTCGCT 59.179 55.000 0.00 0.00 0.00 4.93
2395 2453 0.533032 ACTGGCTCCTCTAACTTCGC 59.467 55.000 0.00 0.00 0.00 4.70
2396 2454 2.417515 GGAACTGGCTCCTCTAACTTCG 60.418 54.545 0.00 0.00 32.21 3.79
2397 2455 2.567615 TGGAACTGGCTCCTCTAACTTC 59.432 50.000 0.57 0.00 36.35 3.01
2398 2456 2.303311 GTGGAACTGGCTCCTCTAACTT 59.697 50.000 0.57 0.00 36.35 2.66
2399 2457 1.903183 GTGGAACTGGCTCCTCTAACT 59.097 52.381 0.57 0.00 36.35 2.24
2400 2458 1.404315 CGTGGAACTGGCTCCTCTAAC 60.404 57.143 0.57 0.00 36.35 2.34
2401 2459 0.895530 CGTGGAACTGGCTCCTCTAA 59.104 55.000 0.57 0.00 36.35 2.10
2402 2460 0.251653 ACGTGGAACTGGCTCCTCTA 60.252 55.000 0.00 0.00 36.35 2.43
2403 2461 0.251653 TACGTGGAACTGGCTCCTCT 60.252 55.000 0.00 0.00 36.35 3.69
2404 2462 0.606604 TTACGTGGAACTGGCTCCTC 59.393 55.000 0.00 0.00 36.35 3.71
2405 2463 1.276622 ATTACGTGGAACTGGCTCCT 58.723 50.000 0.00 0.00 36.35 3.69
2406 2464 2.093869 TGTATTACGTGGAACTGGCTCC 60.094 50.000 0.00 0.00 35.88 4.70
2407 2465 3.241067 TGTATTACGTGGAACTGGCTC 57.759 47.619 0.00 0.00 31.75 4.70
2408 2466 3.906720 ATGTATTACGTGGAACTGGCT 57.093 42.857 0.00 0.00 31.75 4.75
2409 2467 4.451096 CCATATGTATTACGTGGAACTGGC 59.549 45.833 0.00 0.00 31.59 4.85
2410 2468 5.694910 GTCCATATGTATTACGTGGAACTGG 59.305 44.000 13.64 0.00 40.38 4.00
2411 2469 5.694910 GGTCCATATGTATTACGTGGAACTG 59.305 44.000 17.03 2.58 42.14 3.16
2412 2470 5.850614 GGTCCATATGTATTACGTGGAACT 58.149 41.667 17.03 0.00 42.14 3.01
2413 2471 5.850614 AGGTCCATATGTATTACGTGGAAC 58.149 41.667 16.77 16.77 44.98 3.62
2414 2472 6.488769 AAGGTCCATATGTATTACGTGGAA 57.511 37.500 13.64 0.00 40.38 3.53
2415 2473 7.786046 ATAAGGTCCATATGTATTACGTGGA 57.214 36.000 0.00 9.88 36.66 4.02
2416 2474 8.963725 TCTATAAGGTCCATATGTATTACGTGG 58.036 37.037 0.00 3.21 0.00 4.94
2417 2475 9.784680 GTCTATAAGGTCCATATGTATTACGTG 57.215 37.037 0.00 0.00 0.00 4.49
2418 2476 9.750783 AGTCTATAAGGTCCATATGTATTACGT 57.249 33.333 1.24 0.00 0.00 3.57
2493 2551 2.238898 ACTTATTTTGGGACGGAGGGAG 59.761 50.000 0.00 0.00 0.00 4.30
2494 2552 2.026636 CACTTATTTTGGGACGGAGGGA 60.027 50.000 0.00 0.00 0.00 4.20
2495 2553 2.290705 ACACTTATTTTGGGACGGAGGG 60.291 50.000 0.00 0.00 0.00 4.30
2496 2554 3.007635 GACACTTATTTTGGGACGGAGG 58.992 50.000 0.00 0.00 0.00 4.30
2497 2555 3.933332 GAGACACTTATTTTGGGACGGAG 59.067 47.826 0.00 0.00 0.00 4.63
2498 2556 3.325425 TGAGACACTTATTTTGGGACGGA 59.675 43.478 0.00 0.00 0.00 4.69
2499 2557 3.670625 TGAGACACTTATTTTGGGACGG 58.329 45.455 0.00 0.00 0.00 4.79
2500 2558 4.378459 GCTTGAGACACTTATTTTGGGACG 60.378 45.833 0.00 0.00 0.00 4.79
2501 2559 4.762251 AGCTTGAGACACTTATTTTGGGAC 59.238 41.667 0.00 0.00 0.00 4.46
2502 2560 4.985538 AGCTTGAGACACTTATTTTGGGA 58.014 39.130 0.00 0.00 0.00 4.37
2503 2561 5.712152 AAGCTTGAGACACTTATTTTGGG 57.288 39.130 0.00 0.00 0.00 4.12
2504 2562 7.440523 ACTAAGCTTGAGACACTTATTTTGG 57.559 36.000 9.86 0.00 0.00 3.28
2505 2563 8.988934 TGTACTAAGCTTGAGACACTTATTTTG 58.011 33.333 9.86 0.00 0.00 2.44
2506 2564 9.555727 TTGTACTAAGCTTGAGACACTTATTTT 57.444 29.630 9.86 0.00 0.00 1.82
2507 2565 8.989980 GTTGTACTAAGCTTGAGACACTTATTT 58.010 33.333 9.86 0.00 0.00 1.40
2508 2566 8.368668 AGTTGTACTAAGCTTGAGACACTTATT 58.631 33.333 9.86 0.00 0.00 1.40
2509 2567 7.897864 AGTTGTACTAAGCTTGAGACACTTAT 58.102 34.615 9.86 0.00 0.00 1.73
2510 2568 7.286215 AGTTGTACTAAGCTTGAGACACTTA 57.714 36.000 9.86 0.00 0.00 2.24
2511 2569 6.163135 AGTTGTACTAAGCTTGAGACACTT 57.837 37.500 9.86 0.00 0.00 3.16
2512 2570 5.793030 AGTTGTACTAAGCTTGAGACACT 57.207 39.130 9.86 7.29 0.00 3.55
2513 2571 6.846325 AAAGTTGTACTAAGCTTGAGACAC 57.154 37.500 9.86 7.18 0.00 3.67
2514 2572 9.635520 GTATAAAGTTGTACTAAGCTTGAGACA 57.364 33.333 9.86 7.12 0.00 3.41
2515 2573 9.857957 AGTATAAAGTTGTACTAAGCTTGAGAC 57.142 33.333 9.86 4.39 34.01 3.36
2539 2597 9.310716 GTGTCTCAACTTTGTACTAACTTTAGT 57.689 33.333 6.85 6.85 45.39 2.24
2540 2598 9.530633 AGTGTCTCAACTTTGTACTAACTTTAG 57.469 33.333 0.00 0.00 36.82 1.85
2541 2599 9.880157 AAGTGTCTCAACTTTGTACTAACTTTA 57.120 29.630 0.00 0.00 37.05 1.85
2542 2600 8.788325 AAGTGTCTCAACTTTGTACTAACTTT 57.212 30.769 0.00 0.00 37.05 2.66
2548 2606 8.621286 CCAAAATAAGTGTCTCAACTTTGTACT 58.379 33.333 0.00 0.00 40.77 2.73
2549 2607 7.860872 CCCAAAATAAGTGTCTCAACTTTGTAC 59.139 37.037 0.00 0.00 40.77 2.90
2550 2608 7.776030 TCCCAAAATAAGTGTCTCAACTTTGTA 59.224 33.333 0.00 0.00 40.77 2.41
2551 2609 6.605594 TCCCAAAATAAGTGTCTCAACTTTGT 59.394 34.615 0.00 0.00 40.77 2.83
2552 2610 6.918022 GTCCCAAAATAAGTGTCTCAACTTTG 59.082 38.462 0.00 0.00 40.77 2.77
2553 2611 6.605594 TGTCCCAAAATAAGTGTCTCAACTTT 59.394 34.615 0.00 0.00 40.77 2.66
2554 2612 6.126409 TGTCCCAAAATAAGTGTCTCAACTT 58.874 36.000 0.00 0.00 42.89 2.66
2555 2613 5.690865 TGTCCCAAAATAAGTGTCTCAACT 58.309 37.500 0.00 0.00 0.00 3.16
2556 2614 5.763204 TCTGTCCCAAAATAAGTGTCTCAAC 59.237 40.000 0.00 0.00 0.00 3.18
2557 2615 5.935945 TCTGTCCCAAAATAAGTGTCTCAA 58.064 37.500 0.00 0.00 0.00 3.02
2558 2616 5.513094 CCTCTGTCCCAAAATAAGTGTCTCA 60.513 44.000 0.00 0.00 0.00 3.27
2559 2617 4.938226 CCTCTGTCCCAAAATAAGTGTCTC 59.062 45.833 0.00 0.00 0.00 3.36
2560 2618 4.263506 CCCTCTGTCCCAAAATAAGTGTCT 60.264 45.833 0.00 0.00 0.00 3.41
2561 2619 4.010349 CCCTCTGTCCCAAAATAAGTGTC 58.990 47.826 0.00 0.00 0.00 3.67
2562 2620 3.655777 TCCCTCTGTCCCAAAATAAGTGT 59.344 43.478 0.00 0.00 0.00 3.55
2563 2621 4.263506 ACTCCCTCTGTCCCAAAATAAGTG 60.264 45.833 0.00 0.00 0.00 3.16
2564 2622 3.916989 ACTCCCTCTGTCCCAAAATAAGT 59.083 43.478 0.00 0.00 0.00 2.24
2565 2623 4.576330 ACTCCCTCTGTCCCAAAATAAG 57.424 45.455 0.00 0.00 0.00 1.73
2566 2624 5.491078 ACATACTCCCTCTGTCCCAAAATAA 59.509 40.000 0.00 0.00 0.00 1.40
2567 2625 5.036916 ACATACTCCCTCTGTCCCAAAATA 58.963 41.667 0.00 0.00 0.00 1.40
2568 2626 3.852578 ACATACTCCCTCTGTCCCAAAAT 59.147 43.478 0.00 0.00 0.00 1.82
2569 2627 3.256704 ACATACTCCCTCTGTCCCAAAA 58.743 45.455 0.00 0.00 0.00 2.44
2570 2628 2.838202 GACATACTCCCTCTGTCCCAAA 59.162 50.000 0.00 0.00 34.55 3.28
2571 2629 2.225522 TGACATACTCCCTCTGTCCCAA 60.226 50.000 0.00 0.00 38.79 4.12
2572 2630 1.361197 TGACATACTCCCTCTGTCCCA 59.639 52.381 0.00 0.00 38.79 4.37
2573 2631 1.757699 GTGACATACTCCCTCTGTCCC 59.242 57.143 0.00 0.00 38.79 4.46
2574 2632 2.741145 AGTGACATACTCCCTCTGTCC 58.259 52.381 0.00 0.00 38.79 4.02
2575 2633 3.316868 GCTAGTGACATACTCCCTCTGTC 59.683 52.174 0.00 0.00 40.89 3.51
2576 2634 3.292460 GCTAGTGACATACTCCCTCTGT 58.708 50.000 0.00 0.00 40.89 3.41
2577 2635 3.291584 TGCTAGTGACATACTCCCTCTG 58.708 50.000 0.00 0.00 40.89 3.35
2578 2636 3.671740 TGCTAGTGACATACTCCCTCT 57.328 47.619 0.00 0.00 40.89 3.69
2579 2637 3.639094 ACATGCTAGTGACATACTCCCTC 59.361 47.826 0.00 0.00 40.89 4.30
2580 2638 3.639094 GACATGCTAGTGACATACTCCCT 59.361 47.826 0.00 0.00 40.89 4.20
2581 2639 3.243907 GGACATGCTAGTGACATACTCCC 60.244 52.174 0.00 0.00 40.89 4.30
2582 2640 3.639094 AGGACATGCTAGTGACATACTCC 59.361 47.826 0.00 0.00 40.89 3.85
2583 2641 4.500545 CCAGGACATGCTAGTGACATACTC 60.501 50.000 0.00 0.00 40.89 2.59
2584 2642 3.386078 CCAGGACATGCTAGTGACATACT 59.614 47.826 0.00 0.00 43.56 2.12
2585 2643 3.722147 CCAGGACATGCTAGTGACATAC 58.278 50.000 0.00 0.00 0.00 2.39
2586 2644 2.103094 GCCAGGACATGCTAGTGACATA 59.897 50.000 0.00 0.00 0.00 2.29
2587 2645 1.134280 GCCAGGACATGCTAGTGACAT 60.134 52.381 0.00 0.00 0.00 3.06
2631 2689 5.744666 CATGTGTATCTGAACATGCATGA 57.255 39.130 32.75 10.72 45.05 3.07
2670 2728 9.578576 ACATTCAGGTATATCTACATGCATTTT 57.421 29.630 0.00 0.00 39.04 1.82
2790 2947 2.029110 GGATGGTATCTCTCTGCAGAGC 60.029 54.545 34.48 21.43 45.46 4.09
3005 3162 5.221224 CCTGCAAGTAAAAGAAACACCATGA 60.221 40.000 0.00 0.00 0.00 3.07
3006 3163 4.984161 CCTGCAAGTAAAAGAAACACCATG 59.016 41.667 0.00 0.00 0.00 3.66
3017 3174 3.006752 CCAATTGGAGCCTGCAAGTAAAA 59.993 43.478 20.50 0.00 37.39 1.52
3066 3223 8.645487 GTGTACACTATTTTACACTTGCTCTAC 58.355 37.037 18.92 0.00 43.18 2.59
3107 3265 8.828688 AGGCGATAACATATTACCTTCTAAAC 57.171 34.615 0.00 0.00 0.00 2.01
3313 3471 3.658757 TCCTGCCAAACAAAATAGCAC 57.341 42.857 0.00 0.00 0.00 4.40
3735 3898 5.172205 GTGTCAGTAGAGAACCTTTGATCC 58.828 45.833 0.00 0.00 0.00 3.36
3771 3934 1.184349 GTTGATCGAGCGTCTCTTCG 58.816 55.000 0.00 0.00 0.00 3.79
4021 4184 2.420022 CTGCCTTCCATTTGTCCGTAAG 59.580 50.000 0.00 0.00 0.00 2.34
4087 4250 2.520741 CCTCTCTCGAGCCCCTCC 60.521 72.222 7.81 0.00 35.90 4.30
4101 4264 3.907894 TGCCGTATGTTTTTGAACCTC 57.092 42.857 0.00 0.00 0.00 3.85
4117 4280 2.290641 GCCCTAATATTGTGTCTTGCCG 59.709 50.000 0.00 0.00 0.00 5.69
4300 4463 9.474920 CAGAGATTCTGGTAGATTTATGACTTC 57.525 37.037 0.00 0.00 40.71 3.01
4537 4705 4.471025 TCTGGTCATGATCCCGCATTATAT 59.529 41.667 2.86 0.00 0.00 0.86
4569 4737 7.812648 GTTTGCTAACCAATACTGTGTGATAA 58.187 34.615 0.00 0.00 32.49 1.75
4599 4770 9.559732 TTATGTTAGCATAGCTTATCACAATGT 57.440 29.630 0.00 0.00 40.44 2.71
4611 4782 9.046296 AGTGTGATAAAGTTATGTTAGCATAGC 57.954 33.333 5.46 5.46 38.64 2.97
4904 5097 2.554370 ACTAAAACAGGGCGCAACTA 57.446 45.000 10.83 0.00 0.00 2.24
4976 5169 4.526262 ACAGACTTGATCACTGAGCTAAGT 59.474 41.667 16.38 0.00 35.85 2.24
4978 5171 5.011023 TCAACAGACTTGATCACTGAGCTAA 59.989 40.000 16.38 0.00 35.85 3.09
5050 5252 3.330701 TGGTTTCTGGCATTAGGAGAGTT 59.669 43.478 0.00 0.00 0.00 3.01
5055 5257 1.354031 TGCTGGTTTCTGGCATTAGGA 59.646 47.619 0.00 0.00 0.00 2.94
5276 5481 5.762218 GCATTGCTCTTTCCACAGTCTATAT 59.238 40.000 0.16 0.00 0.00 0.86
5305 5518 9.083422 CCTCAAATGAGAGTCCTACTTCATATA 57.917 37.037 11.94 0.00 44.74 0.86
5370 5583 5.011840 TGGCATTTTCTTCATGATTTCACCA 59.988 36.000 0.00 0.00 0.00 4.17
5404 5617 2.632996 TGTAACTCCAAGTCTCCCACTG 59.367 50.000 0.00 0.00 34.56 3.66
5434 5647 9.335891 CACATCTTCGTATCTACATTTAGCTAG 57.664 37.037 0.00 0.00 0.00 3.42
5451 5678 5.362556 AAACTGTTTCCATCACATCTTCG 57.637 39.130 0.00 0.00 0.00 3.79
5509 5736 1.480954 GACCAATTCAGCGGAGGTCTA 59.519 52.381 14.02 0.00 44.10 2.59
5527 5754 7.845066 AAGTGATATTCTTCCCTAAAACGAC 57.155 36.000 0.00 0.00 0.00 4.34
5533 5760 6.069673 TGCCTGAAAGTGATATTCTTCCCTAA 60.070 38.462 0.00 0.00 0.00 2.69
5580 5807 8.740123 TTTTGACTAGTTATCTTGGTGAAACA 57.260 30.769 0.00 0.00 39.98 2.83
5669 5979 0.385223 CAGTCTCAAAGCGCACAAGC 60.385 55.000 11.47 0.00 37.42 4.01
5722 6032 9.878599 CACTCGTACTAATTTGTTGAAGAATTT 57.121 29.630 0.00 0.00 0.00 1.82
5768 6080 5.102953 TGAAGTAGCTATTCAGTTGCCAT 57.897 39.130 11.99 0.00 32.96 4.40
5779 6091 5.428253 TGCCGAGAAAAATGAAGTAGCTAT 58.572 37.500 0.00 0.00 0.00 2.97
5782 6094 3.684788 TCTGCCGAGAAAAATGAAGTAGC 59.315 43.478 0.00 0.00 0.00 3.58
5801 6115 9.613428 TTGAACACCCAGAGTTATTATTATCTG 57.387 33.333 0.00 0.00 39.10 2.90
5813 6127 3.593442 TCCAATTTGAACACCCAGAGT 57.407 42.857 0.00 0.00 0.00 3.24
5977 6291 3.608506 GTGTGACTTACTGTGCATAGTCG 59.391 47.826 20.26 14.27 39.83 4.18
6047 6361 4.764172 TGAGCTTTCAGGCTTCTTATCTC 58.236 43.478 0.00 0.00 43.20 2.75
6137 6451 2.888863 CTGAGTCCTGGAGTCGCC 59.111 66.667 22.99 4.65 34.98 5.54
6152 6466 3.677648 GCTGCTGGGTGGTTGCTG 61.678 66.667 0.00 0.00 0.00 4.41
6156 6470 4.892965 TTGCGCTGCTGGGTGGTT 62.893 61.111 9.73 0.00 0.00 3.67
6170 6484 0.028110 GGAACTTCGGATCGCATTGC 59.972 55.000 0.00 0.00 0.00 3.56
6182 6496 0.538287 ACTGGCAGGCTTGGAACTTC 60.538 55.000 20.34 0.00 0.00 3.01
6191 6505 2.644212 CGTGAGAGACTGGCAGGCT 61.644 63.158 26.05 26.05 35.22 4.58
6195 6509 3.695606 GGCCGTGAGAGACTGGCA 61.696 66.667 4.32 0.00 42.58 4.92
6196 6510 3.655810 CTGGCCGTGAGAGACTGGC 62.656 68.421 0.00 0.00 41.07 4.85
6199 6513 2.936912 GCACTGGCCGTGAGAGACT 61.937 63.158 25.37 0.00 46.81 3.24


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

AutoCloner maintained by Alex Coulton.