Multiple sequence alignment - TraesCS5D01G203200

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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 TraesCS5D01G203200 chr5D 100.000 3447 0 0 1 3447 308343523 308346969 0.000000e+00 6366.0
1 TraesCS5D01G203200 chr5D 89.538 1147 107 7 1290 2434 308626055 308627190 0.000000e+00 1441.0
2 TraesCS5D01G203200 chr5A 95.008 2484 77 19 629 3095 389637699 389635246 0.000000e+00 3856.0
3 TraesCS5D01G203200 chr5A 86.219 1415 146 31 1054 2434 389167264 389165865 0.000000e+00 1487.0
4 TraesCS5D01G203200 chr5A 95.161 62 2 1 3288 3348 255617654 255617593 2.830000e-16 97.1
5 TraesCS5D01G203200 chr5B 94.056 2574 79 27 750 3278 353043262 353045806 0.000000e+00 3838.0
6 TraesCS5D01G203200 chr5B 89.189 1147 111 7 1290 2434 353920333 353921468 0.000000e+00 1419.0
7 TraesCS5D01G203200 chr7D 89.922 516 50 2 1 515 384810935 384811449 0.000000e+00 664.0
8 TraesCS5D01G203200 chr2A 89.709 515 49 2 2 515 465350478 465350989 0.000000e+00 654.0
9 TraesCS5D01G203200 chrUn 87.329 513 64 1 4 515 315787400 315786888 1.380000e-163 586.0
10 TraesCS5D01G203200 chrUn 93.333 165 10 1 3284 3447 91458175 91458339 3.440000e-60 243.0
11 TraesCS5D01G203200 chr3D 89.474 285 29 1 1 285 532116863 532116580 3.270000e-95 359.0
12 TraesCS5D01G203200 chr3D 94.118 204 12 0 312 515 532116582 532116379 9.290000e-81 311.0
13 TraesCS5D01G203200 chr3D 95.092 163 6 2 3287 3447 199098821 199098983 4.410000e-64 255.0
14 TraesCS5D01G203200 chr3A 91.156 147 11 2 3289 3434 19338331 19338476 7.550000e-47 198.0
15 TraesCS5D01G203200 chr4A 87.975 158 12 3 3294 3445 621403996 621404152 2.730000e-41 180.0
16 TraesCS5D01G203200 chr2D 96.296 108 4 0 3340 3447 47646804 47646911 9.830000e-41 178.0
17 TraesCS5D01G203200 chr1B 84.921 126 19 0 1 126 162087820 162087695 1.000000e-25 128.0
18 TraesCS5D01G203200 chr7A 95.455 66 2 1 3284 3348 576103153 576103218 1.690000e-18 104.0
19 TraesCS5D01G203200 chr4D 93.750 64 3 1 3287 3349 294679544 294679607 1.020000e-15 95.3
20 TraesCS5D01G203200 chr3B 93.651 63 2 2 3289 3349 702972348 702972410 3.660000e-15 93.5
21 TraesCS5D01G203200 chr7B 93.548 62 3 1 3289 3349 339084413 339084474 1.320000e-14 91.6


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 TraesCS5D01G203200 chr5D 308343523 308346969 3446 False 6366 6366 100.000 1 3447 1 chr5D.!!$F1 3446
1 TraesCS5D01G203200 chr5D 308626055 308627190 1135 False 1441 1441 89.538 1290 2434 1 chr5D.!!$F2 1144
2 TraesCS5D01G203200 chr5A 389635246 389637699 2453 True 3856 3856 95.008 629 3095 1 chr5A.!!$R3 2466
3 TraesCS5D01G203200 chr5A 389165865 389167264 1399 True 1487 1487 86.219 1054 2434 1 chr5A.!!$R2 1380
4 TraesCS5D01G203200 chr5B 353043262 353045806 2544 False 3838 3838 94.056 750 3278 1 chr5B.!!$F1 2528
5 TraesCS5D01G203200 chr5B 353920333 353921468 1135 False 1419 1419 89.189 1290 2434 1 chr5B.!!$F2 1144
6 TraesCS5D01G203200 chr7D 384810935 384811449 514 False 664 664 89.922 1 515 1 chr7D.!!$F1 514
7 TraesCS5D01G203200 chr2A 465350478 465350989 511 False 654 654 89.709 2 515 1 chr2A.!!$F1 513
8 TraesCS5D01G203200 chrUn 315786888 315787400 512 True 586 586 87.329 4 515 1 chrUn.!!$R1 511

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
670 672 0.107654 GATTGTAAGCGCAGACCCCT 60.108 55.0 11.47 0.0 0.0 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2665 2781 0.907704 AATCGCTACACCTCCCCACA 60.908 55.0 0.0 0.0 0.0 4.17 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
137 138 1.821332 GCCAGCATCTACCACCTGC 60.821 63.158 0.00 0.00 36.15 4.85
187 188 3.616721 AGCAGAACCGGCGTCAGT 61.617 61.111 6.01 0.00 36.08 3.41
219 220 4.364318 CCAGGAGGATCTGGTCGT 57.636 61.111 2.93 0.00 46.89 4.34
222 223 0.748367 CAGGAGGATCTGGTCGTCGA 60.748 60.000 4.70 0.00 41.53 4.20
223 224 0.748729 AGGAGGATCTGGTCGTCGAC 60.749 60.000 17.16 17.16 41.53 4.20
224 225 1.352404 GAGGATCTGGTCGTCGACG 59.648 63.158 31.30 31.30 41.45 5.12
227 228 2.045634 ATCTGGTCGTCGACGGGA 60.046 61.111 35.05 25.85 40.29 5.14
233 234 4.790962 TCGTCGACGGGAGGGAGG 62.791 72.222 35.05 6.54 40.29 4.30
254 255 2.925170 CCGATCCCTAGGCCCAGG 60.925 72.222 10.81 10.81 35.26 4.45
255 256 2.122813 CGATCCCTAGGCCCAGGT 60.123 66.667 16.71 0.00 33.44 4.00
272 273 2.510012 TCGGCTTGAGCTGCATCG 60.510 61.111 6.94 0.02 46.62 3.84
273 274 2.816958 CGGCTTGAGCTGCATCGT 60.817 61.111 1.02 0.00 40.93 3.73
322 323 2.045536 GCTGGAGGCAACAGGAGG 60.046 66.667 9.92 0.00 41.35 4.30
323 324 2.596851 GCTGGAGGCAACAGGAGGA 61.597 63.158 9.92 0.00 41.35 3.71
329 330 1.817099 GGCAACAGGAGGAGCATCG 60.817 63.158 0.00 0.00 34.37 3.84
331 332 0.391661 GCAACAGGAGGAGCATCGAA 60.392 55.000 0.00 0.00 34.37 3.71
349 350 4.329545 GAGTGGGAGCGTGGGCAA 62.330 66.667 0.00 0.00 43.41 4.52
365 366 1.227380 CAAGGGGCGGAGATCTTCG 60.227 63.158 19.55 19.55 0.00 3.79
370 371 2.354072 GCGGAGATCTTCGGCTCG 60.354 66.667 24.54 9.67 45.69 5.03
374 375 1.590259 GAGATCTTCGGCTCGTGGC 60.590 63.158 0.00 0.20 40.90 5.01
404 405 3.123620 GTGCGGCAGGAGCAGAAG 61.124 66.667 1.18 0.00 46.10 2.85
413 414 2.328099 GGAGCAGAAGGTTGTGGCG 61.328 63.158 0.00 0.00 0.00 5.69
414 415 1.301716 GAGCAGAAGGTTGTGGCGA 60.302 57.895 0.00 0.00 0.00 5.54
415 416 0.674895 GAGCAGAAGGTTGTGGCGAT 60.675 55.000 0.00 0.00 0.00 4.58
522 524 2.662596 CAGGGCGTGCAAGGAGTA 59.337 61.111 0.79 0.00 0.00 2.59
523 525 1.741770 CAGGGCGTGCAAGGAGTAC 60.742 63.158 0.79 0.00 0.00 2.73
524 526 1.913762 AGGGCGTGCAAGGAGTACT 60.914 57.895 0.00 0.00 0.00 2.73
525 527 0.613853 AGGGCGTGCAAGGAGTACTA 60.614 55.000 0.79 0.00 0.00 1.82
526 528 0.248289 GGGCGTGCAAGGAGTACTAA 59.752 55.000 0.79 0.00 0.00 2.24
527 529 1.338389 GGGCGTGCAAGGAGTACTAAA 60.338 52.381 0.79 0.00 0.00 1.85
528 530 2.419667 GGCGTGCAAGGAGTACTAAAA 58.580 47.619 0.79 0.00 0.00 1.52
529 531 3.007635 GGCGTGCAAGGAGTACTAAAAT 58.992 45.455 0.79 0.00 0.00 1.82
530 532 3.439129 GGCGTGCAAGGAGTACTAAAATT 59.561 43.478 0.79 0.00 0.00 1.82
531 533 4.632688 GGCGTGCAAGGAGTACTAAAATTA 59.367 41.667 0.79 0.00 0.00 1.40
532 534 5.122711 GGCGTGCAAGGAGTACTAAAATTAA 59.877 40.000 0.79 0.00 0.00 1.40
533 535 6.348704 GGCGTGCAAGGAGTACTAAAATTAAA 60.349 38.462 0.79 0.00 0.00 1.52
534 536 6.741358 GCGTGCAAGGAGTACTAAAATTAAAG 59.259 38.462 0.79 0.00 0.00 1.85
535 537 7.572539 GCGTGCAAGGAGTACTAAAATTAAAGT 60.573 37.037 0.79 0.00 0.00 2.66
536 538 7.955864 CGTGCAAGGAGTACTAAAATTAAAGTC 59.044 37.037 0.00 0.00 0.00 3.01
537 539 8.780249 GTGCAAGGAGTACTAAAATTAAAGTCA 58.220 33.333 0.00 0.00 0.00 3.41
538 540 9.344772 TGCAAGGAGTACTAAAATTAAAGTCAA 57.655 29.630 0.00 0.00 0.00 3.18
548 550 9.962759 ACTAAAATTAAAGTCAATTACGCTACG 57.037 29.630 0.00 0.00 0.00 3.51
549 551 9.962759 CTAAAATTAAAGTCAATTACGCTACGT 57.037 29.630 0.00 0.00 44.35 3.57
567 569 9.962759 ACGCTACGTAATTGACTTTAATTTTAG 57.037 29.630 0.00 0.00 38.73 1.85
568 570 9.962759 CGCTACGTAATTGACTTTAATTTTAGT 57.037 29.630 0.00 0.00 32.79 2.24
578 580 9.720769 TTGACTTTAATTTTAGTACTCCCTCTG 57.279 33.333 0.00 0.00 0.00 3.35
579 581 9.096823 TGACTTTAATTTTAGTACTCCCTCTGA 57.903 33.333 0.00 0.00 0.00 3.27
580 582 9.939802 GACTTTAATTTTAGTACTCCCTCTGAA 57.060 33.333 0.00 0.00 0.00 3.02
650 652 1.860676 TCTTCACTGCGTGGTTGTAC 58.139 50.000 8.46 0.00 33.87 2.90
669 671 1.429148 CGATTGTAAGCGCAGACCCC 61.429 60.000 11.47 0.00 0.00 4.95
670 672 0.107654 GATTGTAAGCGCAGACCCCT 60.108 55.000 11.47 0.00 0.00 4.79
671 673 1.138266 GATTGTAAGCGCAGACCCCTA 59.862 52.381 11.47 0.00 0.00 3.53
672 674 0.978151 TTGTAAGCGCAGACCCCTAA 59.022 50.000 11.47 0.00 0.00 2.69
673 675 1.200519 TGTAAGCGCAGACCCCTAAT 58.799 50.000 11.47 0.00 0.00 1.73
674 676 2.390696 TGTAAGCGCAGACCCCTAATA 58.609 47.619 11.47 0.00 0.00 0.98
675 677 2.101917 TGTAAGCGCAGACCCCTAATAC 59.898 50.000 11.47 0.00 0.00 1.89
676 678 1.200519 AAGCGCAGACCCCTAATACA 58.799 50.000 11.47 0.00 0.00 2.29
683 685 3.136626 GCAGACCCCTAATACAATGACCT 59.863 47.826 0.00 0.00 0.00 3.85
686 688 4.412528 AGACCCCTAATACAATGACCTTCC 59.587 45.833 0.00 0.00 0.00 3.46
830 839 3.795623 TGAAGACGTTATACTCCTGCC 57.204 47.619 0.00 0.00 0.00 4.85
837 846 2.287427 CGTTATACTCCTGCCGGTACAG 60.287 54.545 1.90 2.13 37.42 2.74
845 854 1.399714 CTGCCGGTACAGGATCTACA 58.600 55.000 16.97 2.78 33.85 2.74
846 855 1.754803 CTGCCGGTACAGGATCTACAA 59.245 52.381 16.97 0.00 33.85 2.41
847 856 2.167693 CTGCCGGTACAGGATCTACAAA 59.832 50.000 16.97 0.00 33.85 2.83
853 862 4.641094 CGGTACAGGATCTACAAACTCTCT 59.359 45.833 0.00 0.00 0.00 3.10
862 881 5.326200 TCTACAAACTCTCTTTCCGATCC 57.674 43.478 0.00 0.00 0.00 3.36
863 882 5.017490 TCTACAAACTCTCTTTCCGATCCT 58.983 41.667 0.00 0.00 0.00 3.24
865 884 5.074584 ACAAACTCTCTTTCCGATCCTAC 57.925 43.478 0.00 0.00 0.00 3.18
889 910 3.589735 TCCACTAACCTCTCTCTCACTCT 59.410 47.826 0.00 0.00 0.00 3.24
890 911 4.043561 TCCACTAACCTCTCTCTCACTCTT 59.956 45.833 0.00 0.00 0.00 2.85
1051 1075 4.047059 CCTGGCGCCACAAGCTTG 62.047 66.667 29.03 24.84 40.39 4.01
1052 1076 4.047059 CTGGCGCCACAAGCTTGG 62.047 66.667 29.03 15.63 40.39 3.61
1729 1797 3.065306 TCGCCGTTCCTGGTGAAT 58.935 55.556 0.00 0.00 45.19 2.57
1879 1988 1.341913 TGCACCCGGCCATGTACTAT 61.342 55.000 2.24 0.00 43.89 2.12
1906 2015 4.856801 GCGGTGATCGGGTGCCAT 62.857 66.667 0.00 0.00 39.69 4.40
2297 2406 1.447140 TACATGAACGCGTCCCTGC 60.447 57.895 14.44 0.19 0.00 4.85
2480 2589 0.107116 AACCGTAGTTTGGCACCACA 60.107 50.000 0.00 0.00 29.61 4.17
2583 2692 3.233578 CGAAAACATCGGTTTGTCCATG 58.766 45.455 0.00 0.00 46.20 3.66
2622 2738 4.002506 TGGTGAGTGCATCGGCGT 62.003 61.111 6.85 0.00 45.35 5.68
2682 2798 0.907704 ATTGTGGGGAGGTGTAGCGA 60.908 55.000 0.00 0.00 0.00 4.93
2885 3015 1.559065 CCCACACGGTACCCAAGGAT 61.559 60.000 6.25 0.00 0.00 3.24
2892 3022 1.278127 CGGTACCCAAGGATCACAACT 59.722 52.381 6.25 0.00 0.00 3.16
2918 3048 4.615452 CGACAGTGTTCAAGGAGTACTACC 60.615 50.000 0.00 2.33 0.00 3.18
3125 3262 4.188462 TGTCGTATGATGCCCTTGTTAAG 58.812 43.478 0.00 0.00 0.00 1.85
3200 3337 2.998670 CAGTCACGAAGATCTGTGCAAT 59.001 45.455 8.06 0.00 36.06 3.56
3201 3338 3.434641 CAGTCACGAAGATCTGTGCAATT 59.565 43.478 8.06 0.00 36.06 2.32
3202 3339 3.434641 AGTCACGAAGATCTGTGCAATTG 59.565 43.478 8.06 0.00 36.06 2.32
3249 3386 0.236711 CACGTGAGAGGCAAGCTTTG 59.763 55.000 10.90 0.00 0.00 2.77
3256 3393 5.294306 CGTGAGAGGCAAGCTTTGAAATATA 59.706 40.000 0.00 0.00 0.00 0.86
3260 3397 7.093322 AGAGGCAAGCTTTGAAATATAACAG 57.907 36.000 0.00 0.00 0.00 3.16
3262 3399 4.805719 GGCAAGCTTTGAAATATAACAGCC 59.194 41.667 0.00 0.00 0.00 4.85
3263 3400 4.805719 GCAAGCTTTGAAATATAACAGCCC 59.194 41.667 0.00 0.00 0.00 5.19
3278 3415 2.972713 ACAGCCCTTTCAGACTTAGACA 59.027 45.455 0.00 0.00 0.00 3.41
3279 3416 3.391296 ACAGCCCTTTCAGACTTAGACAA 59.609 43.478 0.00 0.00 0.00 3.18
3280 3417 4.042187 ACAGCCCTTTCAGACTTAGACAAT 59.958 41.667 0.00 0.00 0.00 2.71
3281 3418 5.006386 CAGCCCTTTCAGACTTAGACAATT 58.994 41.667 0.00 0.00 0.00 2.32
3282 3419 6.173339 CAGCCCTTTCAGACTTAGACAATTA 58.827 40.000 0.00 0.00 0.00 1.40
3283 3420 6.825721 CAGCCCTTTCAGACTTAGACAATTAT 59.174 38.462 0.00 0.00 0.00 1.28
3284 3421 7.987458 CAGCCCTTTCAGACTTAGACAATTATA 59.013 37.037 0.00 0.00 0.00 0.98
3285 3422 7.988028 AGCCCTTTCAGACTTAGACAATTATAC 59.012 37.037 0.00 0.00 0.00 1.47
3286 3423 7.769044 GCCCTTTCAGACTTAGACAATTATACA 59.231 37.037 0.00 0.00 0.00 2.29
3287 3424 9.838339 CCCTTTCAGACTTAGACAATTATACAT 57.162 33.333 0.00 0.00 0.00 2.29
3314 3451 8.486942 TCTCTATTATTAAAGGGGATCGAACA 57.513 34.615 0.00 0.00 0.00 3.18
3315 3452 9.101325 TCTCTATTATTAAAGGGGATCGAACAT 57.899 33.333 0.00 0.00 0.00 2.71
3316 3453 9.372369 CTCTATTATTAAAGGGGATCGAACATC 57.628 37.037 0.00 0.00 0.00 3.06
3317 3454 8.033038 TCTATTATTAAAGGGGATCGAACATCG 58.967 37.037 0.00 0.00 42.10 3.84
3318 3455 3.899052 TTAAAGGGGATCGAACATCGT 57.101 42.857 0.00 0.00 41.35 3.73
3319 3456 2.024176 AAAGGGGATCGAACATCGTG 57.976 50.000 0.00 0.00 41.35 4.35
3320 3457 1.191535 AAGGGGATCGAACATCGTGA 58.808 50.000 0.00 0.00 41.35 4.35
3321 3458 1.414158 AGGGGATCGAACATCGTGAT 58.586 50.000 0.00 0.00 41.35 3.06
3322 3459 1.069204 AGGGGATCGAACATCGTGATG 59.931 52.381 8.27 8.27 41.35 3.07
3323 3460 1.502231 GGGATCGAACATCGTGATGG 58.498 55.000 13.95 0.00 42.91 3.51
3324 3461 1.202533 GGGATCGAACATCGTGATGGT 60.203 52.381 13.95 7.48 42.34 3.55
3325 3462 2.550978 GGATCGAACATCGTGATGGTT 58.449 47.619 13.95 6.18 39.18 3.67
3326 3463 2.540101 GGATCGAACATCGTGATGGTTC 59.460 50.000 13.95 12.60 39.18 3.62
3327 3464 1.624487 TCGAACATCGTGATGGTTCG 58.376 50.000 24.87 24.87 44.18 3.95
3328 3465 1.200484 TCGAACATCGTGATGGTTCGA 59.800 47.619 27.01 27.01 46.18 3.71
3329 3466 1.320555 CGAACATCGTGATGGTTCGAC 59.679 52.381 25.72 7.58 44.77 4.20
3330 3467 1.659098 GAACATCGTGATGGTTCGACC 59.341 52.381 13.95 0.00 39.18 4.79
3331 3468 0.895530 ACATCGTGATGGTTCGACCT 59.104 50.000 13.95 0.00 42.91 3.85
3332 3469 1.275291 ACATCGTGATGGTTCGACCTT 59.725 47.619 13.95 0.06 42.91 3.50
3333 3470 1.927174 CATCGTGATGGTTCGACCTTC 59.073 52.381 1.81 10.83 41.38 3.46
3334 3471 0.245539 TCGTGATGGTTCGACCTTCC 59.754 55.000 13.52 3.79 40.58 3.46
3335 3472 0.739813 CGTGATGGTTCGACCTTCCC 60.740 60.000 13.52 5.47 40.58 3.97
3336 3473 0.613777 GTGATGGTTCGACCTTCCCT 59.386 55.000 13.52 0.00 40.58 4.20
3337 3474 0.902531 TGATGGTTCGACCTTCCCTC 59.097 55.000 13.52 5.84 40.58 4.30
3338 3475 0.179108 GATGGTTCGACCTTCCCTCG 60.179 60.000 5.77 0.00 39.58 4.63
3339 3476 0.903454 ATGGTTCGACCTTCCCTCGT 60.903 55.000 5.77 0.00 39.58 4.18
3340 3477 1.080025 GGTTCGACCTTCCCTCGTG 60.080 63.158 0.00 0.00 34.73 4.35
3341 3478 1.080025 GTTCGACCTTCCCTCGTGG 60.080 63.158 0.00 0.00 32.77 4.94
3342 3479 1.532316 TTCGACCTTCCCTCGTGGT 60.532 57.895 2.33 0.00 36.70 4.16
3343 3480 1.117142 TTCGACCTTCCCTCGTGGTT 61.117 55.000 2.33 0.00 33.74 3.67
3344 3481 1.080025 CGACCTTCCCTCGTGGTTC 60.080 63.158 2.33 0.00 33.74 3.62
3345 3482 1.080025 GACCTTCCCTCGTGGTTCG 60.080 63.158 2.33 0.00 41.41 3.95
3346 3483 1.530013 GACCTTCCCTCGTGGTTCGA 61.530 60.000 2.33 0.00 46.83 3.71
3347 3484 1.080025 CCTTCCCTCGTGGTTCGAC 60.080 63.158 2.33 0.00 44.01 4.20
3348 3485 1.080025 CTTCCCTCGTGGTTCGACC 60.080 63.158 2.33 0.00 44.01 4.79
3349 3486 1.532316 TTCCCTCGTGGTTCGACCT 60.532 57.895 2.33 0.00 44.01 3.85
3350 3487 1.530013 TTCCCTCGTGGTTCGACCTC 61.530 60.000 2.33 1.96 44.01 3.85
3351 3488 1.977544 CCCTCGTGGTTCGACCTCT 60.978 63.158 2.33 0.00 44.01 3.69
3352 3489 1.507174 CCTCGTGGTTCGACCTCTC 59.493 63.158 0.00 0.00 44.01 3.20
3353 3490 1.507174 CTCGTGGTTCGACCTCTCC 59.493 63.158 5.77 0.00 44.01 3.71
3354 3491 1.228337 TCGTGGTTCGACCTCTCCA 60.228 57.895 5.77 0.00 44.01 3.86
3355 3492 1.213013 CGTGGTTCGACCTCTCCAG 59.787 63.158 5.77 0.00 42.86 3.86
3356 3493 1.079750 GTGGTTCGACCTCTCCAGC 60.080 63.158 5.77 0.00 39.58 4.85
3357 3494 2.283529 TGGTTCGACCTCTCCAGCC 61.284 63.158 5.77 0.00 39.58 4.85
3358 3495 1.985116 GGTTCGACCTCTCCAGCCT 60.985 63.158 0.00 0.00 34.73 4.58
3359 3496 1.513622 GTTCGACCTCTCCAGCCTC 59.486 63.158 0.00 0.00 0.00 4.70
3360 3497 2.046864 TTCGACCTCTCCAGCCTCG 61.047 63.158 0.00 0.00 0.00 4.63
3361 3498 2.752238 CGACCTCTCCAGCCTCGT 60.752 66.667 0.00 0.00 0.00 4.18
3362 3499 1.451567 CGACCTCTCCAGCCTCGTA 60.452 63.158 0.00 0.00 0.00 3.43
3363 3500 1.716826 CGACCTCTCCAGCCTCGTAC 61.717 65.000 0.00 0.00 0.00 3.67
3364 3501 1.716826 GACCTCTCCAGCCTCGTACG 61.717 65.000 9.53 9.53 0.00 3.67
3365 3502 1.749638 CCTCTCCAGCCTCGTACGT 60.750 63.158 16.05 0.00 0.00 3.57
3366 3503 0.463295 CCTCTCCAGCCTCGTACGTA 60.463 60.000 16.05 0.00 0.00 3.57
3367 3504 1.376543 CTCTCCAGCCTCGTACGTAA 58.623 55.000 16.05 0.00 0.00 3.18
3368 3505 1.063764 CTCTCCAGCCTCGTACGTAAC 59.936 57.143 16.05 5.64 0.00 2.50
3369 3506 1.093159 CTCCAGCCTCGTACGTAACT 58.907 55.000 16.05 7.95 0.00 2.24
3370 3507 1.471684 CTCCAGCCTCGTACGTAACTT 59.528 52.381 16.05 0.00 0.00 2.66
3371 3508 1.200716 TCCAGCCTCGTACGTAACTTG 59.799 52.381 16.05 8.56 0.00 3.16
3372 3509 1.068055 CCAGCCTCGTACGTAACTTGT 60.068 52.381 16.05 0.00 0.00 3.16
3373 3510 1.983605 CAGCCTCGTACGTAACTTGTG 59.016 52.381 16.05 1.65 0.00 3.33
3374 3511 0.712222 GCCTCGTACGTAACTTGTGC 59.288 55.000 16.05 4.07 0.00 4.57
3375 3512 1.343506 CCTCGTACGTAACTTGTGCC 58.656 55.000 16.05 0.00 0.00 5.01
3376 3513 1.068055 CCTCGTACGTAACTTGTGCCT 60.068 52.381 16.05 0.00 0.00 4.75
3377 3514 1.983605 CTCGTACGTAACTTGTGCCTG 59.016 52.381 16.05 0.00 0.00 4.85
3378 3515 1.337703 TCGTACGTAACTTGTGCCTGT 59.662 47.619 16.05 0.00 0.00 4.00
3379 3516 1.454276 CGTACGTAACTTGTGCCTGTG 59.546 52.381 7.22 0.00 0.00 3.66
3380 3517 2.746269 GTACGTAACTTGTGCCTGTGA 58.254 47.619 0.00 0.00 0.00 3.58
3381 3518 2.319136 ACGTAACTTGTGCCTGTGAA 57.681 45.000 0.00 0.00 0.00 3.18
3382 3519 2.210116 ACGTAACTTGTGCCTGTGAAG 58.790 47.619 0.00 0.00 0.00 3.02
3383 3520 2.159014 ACGTAACTTGTGCCTGTGAAGA 60.159 45.455 0.00 0.00 0.00 2.87
3384 3521 2.869801 CGTAACTTGTGCCTGTGAAGAA 59.130 45.455 0.00 0.00 0.00 2.52
3385 3522 3.311322 CGTAACTTGTGCCTGTGAAGAAA 59.689 43.478 0.00 0.00 0.00 2.52
3386 3523 4.201871 CGTAACTTGTGCCTGTGAAGAAAA 60.202 41.667 0.00 0.00 0.00 2.29
3387 3524 4.799564 AACTTGTGCCTGTGAAGAAAAA 57.200 36.364 0.00 0.00 0.00 1.94
3404 3541 3.502123 AAAAATCGGACCTCCTCACAA 57.498 42.857 0.00 0.00 0.00 3.33
3405 3542 2.474410 AAATCGGACCTCCTCACAAC 57.526 50.000 0.00 0.00 0.00 3.32
3406 3543 0.613777 AATCGGACCTCCTCACAACC 59.386 55.000 0.00 0.00 0.00 3.77
3407 3544 1.265454 ATCGGACCTCCTCACAACCC 61.265 60.000 0.00 0.00 0.00 4.11
3408 3545 2.214216 CGGACCTCCTCACAACCCA 61.214 63.158 0.00 0.00 0.00 4.51
3409 3546 1.553690 CGGACCTCCTCACAACCCAT 61.554 60.000 0.00 0.00 0.00 4.00
3410 3547 0.253327 GGACCTCCTCACAACCCATC 59.747 60.000 0.00 0.00 0.00 3.51
3411 3548 0.253327 GACCTCCTCACAACCCATCC 59.747 60.000 0.00 0.00 0.00 3.51
3412 3549 1.221840 CCTCCTCACAACCCATCCG 59.778 63.158 0.00 0.00 0.00 4.18
3413 3550 1.553690 CCTCCTCACAACCCATCCGT 61.554 60.000 0.00 0.00 0.00 4.69
3414 3551 0.391661 CTCCTCACAACCCATCCGTG 60.392 60.000 0.00 0.00 0.00 4.94
3415 3552 2.040544 CCTCACAACCCATCCGTGC 61.041 63.158 0.00 0.00 0.00 5.34
3416 3553 1.302431 CTCACAACCCATCCGTGCA 60.302 57.895 0.00 0.00 0.00 4.57
3417 3554 1.577328 CTCACAACCCATCCGTGCAC 61.577 60.000 6.82 6.82 0.00 4.57
3418 3555 2.668212 ACAACCCATCCGTGCACG 60.668 61.111 31.77 31.77 39.44 5.34
3419 3556 2.358125 CAACCCATCCGTGCACGA 60.358 61.111 39.10 24.83 43.02 4.35
3420 3557 1.745115 CAACCCATCCGTGCACGAT 60.745 57.895 39.10 25.85 43.02 3.73
3421 3558 0.461163 CAACCCATCCGTGCACGATA 60.461 55.000 39.10 26.36 43.02 2.92
3422 3559 0.179084 AACCCATCCGTGCACGATAG 60.179 55.000 39.10 25.48 43.02 2.08
3423 3560 1.040893 ACCCATCCGTGCACGATAGA 61.041 55.000 39.10 27.33 43.02 1.98
3424 3561 0.104120 CCCATCCGTGCACGATAGAA 59.896 55.000 39.10 18.88 43.02 2.10
3425 3562 1.472552 CCCATCCGTGCACGATAGAAA 60.473 52.381 39.10 17.15 43.02 2.52
3426 3563 2.276201 CCATCCGTGCACGATAGAAAA 58.724 47.619 39.10 15.46 43.02 2.29
3427 3564 2.675844 CCATCCGTGCACGATAGAAAAA 59.324 45.455 39.10 14.11 43.02 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
167 168 3.112709 GACGCCGGTTCTGCTGTC 61.113 66.667 1.90 0.00 0.00 3.51
170 171 3.616721 ACTGACGCCGGTTCTGCT 61.617 61.111 1.90 0.00 0.00 4.24
204 205 0.748729 GTCGACGACCAGATCCTCCT 60.749 60.000 17.25 0.00 0.00 3.69
224 225 4.173701 ATCGGTCCCCTCCCTCCC 62.174 72.222 0.00 0.00 0.00 4.30
239 240 2.210711 CGACCTGGGCCTAGGGATC 61.211 68.421 35.91 24.59 42.35 3.36
254 255 2.806856 CGATGCAGCTCAAGCCGAC 61.807 63.158 0.00 0.00 43.38 4.79
255 256 2.510012 CGATGCAGCTCAAGCCGA 60.510 61.111 0.00 0.00 43.38 5.54
260 261 2.815211 GCCGACGATGCAGCTCAA 60.815 61.111 0.00 0.00 0.00 3.02
294 295 1.917495 CCTCCAGCATCATCACCCA 59.083 57.895 0.00 0.00 0.00 4.51
295 296 1.527844 GCCTCCAGCATCATCACCC 60.528 63.158 0.00 0.00 42.97 4.61
320 321 0.324738 TCCCACTCTTCGATGCTCCT 60.325 55.000 0.00 0.00 0.00 3.69
322 323 0.529555 GCTCCCACTCTTCGATGCTC 60.530 60.000 0.00 0.00 0.00 4.26
323 324 1.519719 GCTCCCACTCTTCGATGCT 59.480 57.895 0.00 0.00 0.00 3.79
329 330 2.266055 CCCACGCTCCCACTCTTC 59.734 66.667 0.00 0.00 0.00 2.87
349 350 2.840102 CCGAAGATCTCCGCCCCT 60.840 66.667 0.00 0.00 0.00 4.79
404 405 2.870372 GCTCACATCGCCACAACC 59.130 61.111 0.00 0.00 0.00 3.77
413 414 2.202987 CTGCTCCCCGCTCACATC 60.203 66.667 0.00 0.00 40.11 3.06
414 415 3.790437 CCTGCTCCCCGCTCACAT 61.790 66.667 0.00 0.00 40.11 3.21
446 447 0.250727 TGGCTAACACCAACCTGCTC 60.251 55.000 0.00 0.00 36.55 4.26
500 502 4.047059 CTTGCACGCCCTGCCTTG 62.047 66.667 0.00 0.00 46.51 3.61
505 507 1.741770 GTACTCCTTGCACGCCCTG 60.742 63.158 0.00 0.00 0.00 4.45
506 508 0.613853 TAGTACTCCTTGCACGCCCT 60.614 55.000 0.00 0.00 0.00 5.19
522 524 9.962759 CGTAGCGTAATTGACTTTAATTTTAGT 57.037 29.630 0.00 0.00 32.79 2.24
523 525 9.962759 ACGTAGCGTAATTGACTTTAATTTTAG 57.037 29.630 0.00 0.00 38.73 1.85
541 543 9.962759 CTAAAATTAAAGTCAATTACGTAGCGT 57.037 29.630 0.00 0.00 44.35 5.07
542 544 9.962759 ACTAAAATTAAAGTCAATTACGTAGCG 57.037 29.630 0.00 0.00 0.00 4.26
552 554 9.720769 CAGAGGGAGTACTAAAATTAAAGTCAA 57.279 33.333 0.00 0.00 0.00 3.18
553 555 9.096823 TCAGAGGGAGTACTAAAATTAAAGTCA 57.903 33.333 0.00 0.00 0.00 3.41
554 556 9.939802 TTCAGAGGGAGTACTAAAATTAAAGTC 57.060 33.333 0.00 0.00 0.00 3.01
614 616 9.084164 GCAGTGAAGATACTCTTAAAAATCGTA 57.916 33.333 0.00 0.00 36.73 3.43
615 617 7.201444 CGCAGTGAAGATACTCTTAAAAATCGT 60.201 37.037 0.00 0.00 36.73 3.73
616 618 7.113658 CGCAGTGAAGATACTCTTAAAAATCG 58.886 38.462 0.00 0.00 36.73 3.34
617 619 7.965045 ACGCAGTGAAGATACTCTTAAAAATC 58.035 34.615 0.00 0.00 42.51 2.17
618 620 7.907214 ACGCAGTGAAGATACTCTTAAAAAT 57.093 32.000 0.00 0.00 42.51 1.82
650 652 1.429148 GGGGTCTGCGCTTACAATCG 61.429 60.000 9.73 0.00 0.00 3.34
669 671 5.615289 CCTCCAGGAAGGTCATTGTATTAG 58.385 45.833 0.00 0.00 39.02 1.73
670 672 5.630415 CCTCCAGGAAGGTCATTGTATTA 57.370 43.478 0.00 0.00 39.02 0.98
671 673 4.510167 CCTCCAGGAAGGTCATTGTATT 57.490 45.455 0.00 0.00 39.02 1.89
683 685 9.594936 TCAAAATAAAATAGAAACCTCCAGGAA 57.405 29.630 0.00 0.00 38.94 3.36
705 707 4.782019 AGCGCCACTGAATTTAATCAAA 57.218 36.364 2.29 0.00 0.00 2.69
830 839 4.641094 AGAGAGTTTGTAGATCCTGTACCG 59.359 45.833 0.00 0.00 0.00 4.02
837 846 5.326200 TCGGAAAGAGAGTTTGTAGATCC 57.674 43.478 0.00 0.00 0.00 3.36
838 847 5.980715 GGATCGGAAAGAGAGTTTGTAGATC 59.019 44.000 0.00 0.00 0.00 2.75
839 848 5.659079 AGGATCGGAAAGAGAGTTTGTAGAT 59.341 40.000 0.00 0.00 0.00 1.98
840 849 5.017490 AGGATCGGAAAGAGAGTTTGTAGA 58.983 41.667 0.00 0.00 0.00 2.59
841 850 5.331876 AGGATCGGAAAGAGAGTTTGTAG 57.668 43.478 0.00 0.00 0.00 2.74
842 851 5.126707 GGTAGGATCGGAAAGAGAGTTTGTA 59.873 44.000 0.00 0.00 0.00 2.41
843 852 4.081586 GGTAGGATCGGAAAGAGAGTTTGT 60.082 45.833 0.00 0.00 0.00 2.83
844 853 4.160626 AGGTAGGATCGGAAAGAGAGTTTG 59.839 45.833 0.00 0.00 0.00 2.93
845 854 4.354662 AGGTAGGATCGGAAAGAGAGTTT 58.645 43.478 0.00 0.00 0.00 2.66
846 855 3.955551 GAGGTAGGATCGGAAAGAGAGTT 59.044 47.826 0.00 0.00 0.00 3.01
847 856 3.558033 GAGGTAGGATCGGAAAGAGAGT 58.442 50.000 0.00 0.00 0.00 3.24
853 862 2.544844 AGTGGAGGTAGGATCGGAAA 57.455 50.000 0.00 0.00 0.00 3.13
862 881 4.080243 TGAGAGAGAGGTTAGTGGAGGTAG 60.080 50.000 0.00 0.00 0.00 3.18
863 882 3.850774 TGAGAGAGAGGTTAGTGGAGGTA 59.149 47.826 0.00 0.00 0.00 3.08
865 884 3.020984 GTGAGAGAGAGGTTAGTGGAGG 58.979 54.545 0.00 0.00 0.00 4.30
890 911 5.313712 GTGACTAGTTTCCAAATGGAGGAA 58.686 41.667 0.00 0.00 46.36 3.36
1044 1068 2.328099 GGTGAGGCGTCCAAGCTTG 61.328 63.158 19.93 19.93 37.29 4.01
1051 1075 0.250513 ATCTTCTTGGTGAGGCGTCC 59.749 55.000 3.56 0.00 0.00 4.79
1052 1076 1.646189 GATCTTCTTGGTGAGGCGTC 58.354 55.000 0.00 0.00 0.00 5.19
1422 1490 3.818787 CCATGCAGTTCTGCCCGC 61.819 66.667 19.91 0.00 0.00 6.13
1550 1618 4.487412 GTCCCCGACGAACGCGAT 62.487 66.667 15.93 0.00 41.64 4.58
1729 1797 2.649034 GACGACTTCTCCGTGCCA 59.351 61.111 0.00 0.00 40.67 4.92
2583 2692 2.227388 CCAACCAAGCACAGAATCACTC 59.773 50.000 0.00 0.00 0.00 3.51
2665 2781 0.907704 AATCGCTACACCTCCCCACA 60.908 55.000 0.00 0.00 0.00 4.17
2682 2798 5.502089 TGAATGGAATGGAAAAGGCAAAT 57.498 34.783 0.00 0.00 0.00 2.32
2783 2901 1.214062 GGCTGGCTAGGATCGATCG 59.786 63.158 18.81 9.36 0.00 3.69
2885 3015 2.427812 TGAACACTGTCGGTAGTTGTGA 59.572 45.455 0.00 0.00 33.41 3.58
2892 3022 2.313317 ACTCCTTGAACACTGTCGGTA 58.687 47.619 0.00 0.00 0.00 4.02
3125 3262 5.418840 ACCAACCTGAAATGGACAATCATAC 59.581 40.000 0.00 0.00 39.12 2.39
3200 3337 4.082625 CCACTATGAAAGCACATTCAGCAA 60.083 41.667 5.93 0.00 42.21 3.91
3201 3338 3.441222 CCACTATGAAAGCACATTCAGCA 59.559 43.478 5.93 0.00 42.21 4.41
3202 3339 3.733077 GCCACTATGAAAGCACATTCAGC 60.733 47.826 5.93 0.00 42.21 4.26
3249 3386 7.631717 AAGTCTGAAAGGGCTGTTATATTTC 57.368 36.000 0.00 0.00 0.00 2.17
3256 3393 3.391296 TGTCTAAGTCTGAAAGGGCTGTT 59.609 43.478 0.00 0.00 0.00 3.16
3260 3397 7.769044 TGTATAATTGTCTAAGTCTGAAAGGGC 59.231 37.037 0.00 0.00 0.00 5.19
3288 3425 9.101325 TGTTCGATCCCCTTTAATAATAGAGAT 57.899 33.333 0.00 0.00 0.00 2.75
3289 3426 8.486942 TGTTCGATCCCCTTTAATAATAGAGA 57.513 34.615 0.00 0.00 0.00 3.10
3290 3427 9.372369 GATGTTCGATCCCCTTTAATAATAGAG 57.628 37.037 0.00 0.00 0.00 2.43
3291 3428 8.033038 CGATGTTCGATCCCCTTTAATAATAGA 58.967 37.037 0.00 0.00 43.74 1.98
3292 3429 7.817962 ACGATGTTCGATCCCCTTTAATAATAG 59.182 37.037 3.62 0.00 43.74 1.73
3293 3430 7.601130 CACGATGTTCGATCCCCTTTAATAATA 59.399 37.037 3.62 0.00 43.74 0.98
3294 3431 6.426937 CACGATGTTCGATCCCCTTTAATAAT 59.573 38.462 3.62 0.00 43.74 1.28
3295 3432 5.756347 CACGATGTTCGATCCCCTTTAATAA 59.244 40.000 3.62 0.00 43.74 1.40
3296 3433 5.069383 TCACGATGTTCGATCCCCTTTAATA 59.931 40.000 3.62 0.00 43.74 0.98
3297 3434 4.127171 CACGATGTTCGATCCCCTTTAAT 58.873 43.478 3.62 0.00 43.74 1.40
3298 3435 3.196039 TCACGATGTTCGATCCCCTTTAA 59.804 43.478 3.62 0.00 43.74 1.52
3299 3436 2.761767 TCACGATGTTCGATCCCCTTTA 59.238 45.455 3.62 0.00 43.74 1.85
3300 3437 1.553248 TCACGATGTTCGATCCCCTTT 59.447 47.619 3.62 0.00 43.74 3.11
3301 3438 1.191535 TCACGATGTTCGATCCCCTT 58.808 50.000 3.62 0.00 43.74 3.95
3302 3439 1.069204 CATCACGATGTTCGATCCCCT 59.931 52.381 3.62 0.00 43.74 4.79
3303 3440 1.502231 CATCACGATGTTCGATCCCC 58.498 55.000 3.62 0.00 43.74 4.81
3304 3441 1.202533 ACCATCACGATGTTCGATCCC 60.203 52.381 3.62 0.00 43.74 3.85
3305 3442 2.225068 ACCATCACGATGTTCGATCC 57.775 50.000 3.62 0.00 43.74 3.36
3306 3443 2.216488 CGAACCATCACGATGTTCGATC 59.784 50.000 24.44 9.06 44.77 3.69
3307 3444 2.159296 TCGAACCATCACGATGTTCGAT 60.159 45.455 25.81 4.66 45.10 3.59
3308 3445 1.200484 TCGAACCATCACGATGTTCGA 59.800 47.619 25.81 25.81 46.18 3.71
3309 3446 1.320555 GTCGAACCATCACGATGTTCG 59.679 52.381 23.61 23.61 46.93 3.95
3310 3447 1.659098 GGTCGAACCATCACGATGTTC 59.341 52.381 6.30 8.58 40.50 3.18
3311 3448 1.275291 AGGTCGAACCATCACGATGTT 59.725 47.619 0.00 1.39 41.95 2.71
3312 3449 0.895530 AGGTCGAACCATCACGATGT 59.104 50.000 0.00 0.00 41.95 3.06
3313 3450 1.927174 GAAGGTCGAACCATCACGATG 59.073 52.381 0.00 0.00 41.95 3.84
3314 3451 1.134788 GGAAGGTCGAACCATCACGAT 60.135 52.381 0.00 0.00 41.95 3.73
3315 3452 0.245539 GGAAGGTCGAACCATCACGA 59.754 55.000 0.00 0.00 41.95 4.35
3316 3453 0.739813 GGGAAGGTCGAACCATCACG 60.740 60.000 0.00 0.00 41.95 4.35
3317 3454 0.613777 AGGGAAGGTCGAACCATCAC 59.386 55.000 0.00 0.00 39.57 3.06
3318 3455 0.902531 GAGGGAAGGTCGAACCATCA 59.097 55.000 0.00 0.00 41.95 3.07
3319 3456 0.179108 CGAGGGAAGGTCGAACCATC 60.179 60.000 0.00 0.00 41.95 3.51
3320 3457 0.903454 ACGAGGGAAGGTCGAACCAT 60.903 55.000 0.00 0.00 41.95 3.55
3321 3458 1.532316 ACGAGGGAAGGTCGAACCA 60.532 57.895 0.00 0.00 41.95 3.67
3322 3459 1.080025 CACGAGGGAAGGTCGAACC 60.080 63.158 0.00 0.00 39.92 3.62
3323 3460 1.080025 CCACGAGGGAAGGTCGAAC 60.080 63.158 0.00 0.00 39.92 3.95
3324 3461 1.117142 AACCACGAGGGAAGGTCGAA 61.117 55.000 3.29 0.00 39.92 3.71
3325 3462 1.530013 GAACCACGAGGGAAGGTCGA 61.530 60.000 3.29 0.00 39.92 4.20
3326 3463 1.080025 GAACCACGAGGGAAGGTCG 60.080 63.158 3.29 0.00 43.25 4.79
3327 3464 1.080025 CGAACCACGAGGGAAGGTC 60.080 63.158 3.29 0.00 45.77 3.85
3328 3465 1.532316 TCGAACCACGAGGGAAGGT 60.532 57.895 3.29 0.00 46.45 3.50
3329 3466 3.373226 TCGAACCACGAGGGAAGG 58.627 61.111 3.29 0.00 46.45 3.46
3337 3474 1.213013 CTGGAGAGGTCGAACCACG 59.787 63.158 0.00 0.00 41.95 4.94
3338 3475 1.079750 GCTGGAGAGGTCGAACCAC 60.080 63.158 0.00 0.00 41.95 4.16
3339 3476 2.283529 GGCTGGAGAGGTCGAACCA 61.284 63.158 0.00 0.00 41.95 3.67
3340 3477 1.950973 GAGGCTGGAGAGGTCGAACC 61.951 65.000 0.00 0.00 38.99 3.62
3341 3478 1.513622 GAGGCTGGAGAGGTCGAAC 59.486 63.158 0.00 0.00 0.00 3.95
3342 3479 2.046864 CGAGGCTGGAGAGGTCGAA 61.047 63.158 0.00 0.00 32.32 3.71
3343 3480 1.907222 TACGAGGCTGGAGAGGTCGA 61.907 60.000 2.65 0.00 34.72 4.20
3344 3481 1.451567 TACGAGGCTGGAGAGGTCG 60.452 63.158 2.65 0.00 36.71 4.79
3345 3482 1.716826 CGTACGAGGCTGGAGAGGTC 61.717 65.000 10.44 0.00 0.00 3.85
3346 3483 1.749638 CGTACGAGGCTGGAGAGGT 60.750 63.158 10.44 0.00 0.00 3.85
3347 3484 0.463295 TACGTACGAGGCTGGAGAGG 60.463 60.000 24.41 0.00 0.00 3.69
3348 3485 1.063764 GTTACGTACGAGGCTGGAGAG 59.936 57.143 24.41 0.00 0.00 3.20
3349 3486 1.089920 GTTACGTACGAGGCTGGAGA 58.910 55.000 24.41 0.00 0.00 3.71
3350 3487 1.093159 AGTTACGTACGAGGCTGGAG 58.907 55.000 24.41 0.00 0.00 3.86
3351 3488 1.200716 CAAGTTACGTACGAGGCTGGA 59.799 52.381 24.41 0.00 0.00 3.86
3352 3489 1.068055 ACAAGTTACGTACGAGGCTGG 60.068 52.381 24.41 15.04 0.00 4.85
3353 3490 1.983605 CACAAGTTACGTACGAGGCTG 59.016 52.381 24.41 13.85 0.00 4.85
3354 3491 1.668047 GCACAAGTTACGTACGAGGCT 60.668 52.381 24.41 12.84 0.00 4.58
3355 3492 0.712222 GCACAAGTTACGTACGAGGC 59.288 55.000 24.41 10.70 0.00 4.70
3356 3493 1.068055 AGGCACAAGTTACGTACGAGG 60.068 52.381 24.41 6.65 0.00 4.63
3357 3494 1.983605 CAGGCACAAGTTACGTACGAG 59.016 52.381 24.41 6.65 0.00 4.18
3358 3495 1.337703 ACAGGCACAAGTTACGTACGA 59.662 47.619 24.41 2.43 0.00 3.43
3359 3496 1.454276 CACAGGCACAAGTTACGTACG 59.546 52.381 15.01 15.01 0.00 3.67
3360 3497 2.746269 TCACAGGCACAAGTTACGTAC 58.254 47.619 0.00 0.00 0.00 3.67
3361 3498 3.068448 TCTTCACAGGCACAAGTTACGTA 59.932 43.478 0.00 0.00 0.00 3.57
3362 3499 2.159014 TCTTCACAGGCACAAGTTACGT 60.159 45.455 0.00 0.00 0.00 3.57
3363 3500 2.479837 TCTTCACAGGCACAAGTTACG 58.520 47.619 0.00 0.00 0.00 3.18
3364 3501 4.893424 TTTCTTCACAGGCACAAGTTAC 57.107 40.909 0.00 0.00 0.00 2.50
3365 3502 5.906113 TTTTTCTTCACAGGCACAAGTTA 57.094 34.783 0.00 0.00 0.00 2.24
3366 3503 4.799564 TTTTTCTTCACAGGCACAAGTT 57.200 36.364 0.00 0.00 0.00 2.66
3384 3521 3.146847 GTTGTGAGGAGGTCCGATTTTT 58.853 45.455 0.00 0.00 42.08 1.94
3385 3522 2.552373 GGTTGTGAGGAGGTCCGATTTT 60.552 50.000 0.00 0.00 42.08 1.82
3386 3523 1.003233 GGTTGTGAGGAGGTCCGATTT 59.997 52.381 0.00 0.00 42.08 2.17
3387 3524 0.613777 GGTTGTGAGGAGGTCCGATT 59.386 55.000 0.00 0.00 42.08 3.34
3388 3525 1.265454 GGGTTGTGAGGAGGTCCGAT 61.265 60.000 0.00 0.00 42.08 4.18
3389 3526 1.911766 GGGTTGTGAGGAGGTCCGA 60.912 63.158 0.00 0.00 42.08 4.55
3390 3527 1.553690 ATGGGTTGTGAGGAGGTCCG 61.554 60.000 0.00 0.00 42.08 4.79
3391 3528 0.253327 GATGGGTTGTGAGGAGGTCC 59.747 60.000 0.00 0.00 0.00 4.46
3392 3529 0.253327 GGATGGGTTGTGAGGAGGTC 59.747 60.000 0.00 0.00 0.00 3.85
3393 3530 1.553690 CGGATGGGTTGTGAGGAGGT 61.554 60.000 0.00 0.00 0.00 3.85
3394 3531 1.221840 CGGATGGGTTGTGAGGAGG 59.778 63.158 0.00 0.00 0.00 4.30
3395 3532 0.391661 CACGGATGGGTTGTGAGGAG 60.392 60.000 0.00 0.00 35.66 3.69
3396 3533 1.676968 CACGGATGGGTTGTGAGGA 59.323 57.895 0.00 0.00 35.66 3.71
3397 3534 2.040544 GCACGGATGGGTTGTGAGG 61.041 63.158 0.00 0.00 35.66 3.86
3398 3535 1.302431 TGCACGGATGGGTTGTGAG 60.302 57.895 0.00 0.00 35.66 3.51
3399 3536 1.599518 GTGCACGGATGGGTTGTGA 60.600 57.895 0.00 0.00 35.66 3.58
3400 3537 2.953821 GTGCACGGATGGGTTGTG 59.046 61.111 0.00 0.00 36.70 3.33
3401 3538 2.463589 ATCGTGCACGGATGGGTTGT 62.464 55.000 36.41 10.56 40.29 3.32
3402 3539 0.461163 TATCGTGCACGGATGGGTTG 60.461 55.000 36.41 7.84 40.29 3.77
3403 3540 0.179084 CTATCGTGCACGGATGGGTT 60.179 55.000 36.41 15.94 40.29 4.11
3404 3541 1.040893 TCTATCGTGCACGGATGGGT 61.041 55.000 36.41 18.39 40.29 4.51
3405 3542 0.104120 TTCTATCGTGCACGGATGGG 59.896 55.000 36.41 21.68 40.29 4.00
3406 3543 1.934589 TTTCTATCGTGCACGGATGG 58.065 50.000 36.41 27.13 40.29 3.51


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

AutoCloner maintained by Alex Coulton.