Multiple sequence alignment - TraesCS1D01G188200

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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 TraesCS1D01G188200 chr1D 100.000 3656 0 0 1 3656 260587411 260591066 0.000000e+00 6752.0
1 TraesCS1D01G188200 chr1D 98.000 350 5 1 3309 3656 28904438 28904089 1.120000e-169 606.0
2 TraesCS1D01G188200 chr1A 94.045 3325 147 24 1 3294 339916726 339913422 0.000000e+00 4996.0
3 TraesCS1D01G188200 chr1B 93.424 2874 163 16 115 2975 352336492 352333632 0.000000e+00 4237.0
4 TraesCS1D01G188200 chr1B 89.680 281 16 6 3038 3308 352333436 352333159 2.700000e-91 346.0
5 TraesCS1D01G188200 chr1B 94.690 113 3 1 1 113 352336787 352336678 4.850000e-39 172.0
6 TraesCS1D01G188200 chr1B 77.119 118 24 2 135 252 439839847 439839961 8.470000e-07 65.8
7 TraesCS1D01G188200 chr2D 76.074 1304 260 41 1194 2477 509229523 509230794 1.850000e-177 632.0
8 TraesCS1D01G188200 chr2D 97.429 350 7 1 3309 3656 338315232 338315581 2.430000e-166 595.0
9 TraesCS1D01G188200 chr2D 97.429 350 7 1 3309 3656 605549237 605548888 2.430000e-166 595.0
10 TraesCS1D01G188200 chr2D 96.571 350 10 1 3309 3656 239387839 239387490 2.450000e-161 579.0
11 TraesCS1D01G188200 chr2A 75.846 1300 270 34 1194 2477 653000361 653001632 4.010000e-174 621.0
12 TraesCS1D01G188200 chr7D 98.281 349 4 1 3310 3656 473831865 473831517 8.680000e-171 610.0
13 TraesCS1D01G188200 chr7D 97.443 352 7 1 3307 3656 606462016 606462367 1.880000e-167 599.0
14 TraesCS1D01G188200 chr7D 97.167 353 7 2 3306 3656 594375147 594375498 8.740000e-166 593.0
15 TraesCS1D01G188200 chr2B 75.692 1300 272 34 1194 2477 598560961 598562232 8.680000e-171 610.0
16 TraesCS1D01G188200 chr3D 97.421 349 7 1 3310 3656 476536365 476536713 8.740000e-166 593.0
17 TraesCS1D01G188200 chrUn 97.151 351 8 1 3308 3656 386421406 386421756 3.140000e-165 592.0
18 TraesCS1D01G188200 chrUn 79.476 229 33 10 138 357 87833049 87832826 2.270000e-32 150.0
19 TraesCS1D01G188200 chrUn 89.091 55 6 0 136 190 57991709 57991655 6.550000e-08 69.4
20 TraesCS1D01G188200 chrUn 90.385 52 5 0 136 187 300824526 300824577 6.550000e-08 69.4
21 TraesCS1D01G188200 chr6A 74.437 1377 280 58 1167 2513 476000185 476001519 8.990000e-146 527.0
22 TraesCS1D01G188200 chr6D 74.109 1375 288 54 1167 2513 336366515 336367849 4.210000e-139 505.0
23 TraesCS1D01G188200 chr6D 77.914 163 35 1 136 298 25022811 25022650 2.320000e-17 100.0
24 TraesCS1D01G188200 chr6B 73.910 1376 287 57 1168 2513 484100889 484099556 1.530000e-133 486.0
25 TraesCS1D01G188200 chr6B 77.500 160 35 1 139 298 40669302 40669144 1.080000e-15 95.3
26 TraesCS1D01G188200 chr3A 75.655 267 51 9 172 426 633846850 633846586 1.780000e-23 121.0
27 TraesCS1D01G188200 chr4D 80.583 103 19 1 137 239 8928819 8928718 1.090000e-10 78.7
28 TraesCS1D01G188200 chr7A 87.500 64 6 2 136 199 696848615 696848676 5.060000e-09 73.1
29 TraesCS1D01G188200 chr5B 86.538 52 5 2 1868 1918 684228716 684228766 5.100000e-04 56.5


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 TraesCS1D01G188200 chr1D 260587411 260591066 3655 False 6752 6752 100.000 1 3656 1 chr1D.!!$F1 3655
1 TraesCS1D01G188200 chr1A 339913422 339916726 3304 True 4996 4996 94.045 1 3294 1 chr1A.!!$R1 3293
2 TraesCS1D01G188200 chr1B 352333159 352336787 3628 True 1585 4237 92.598 1 3308 3 chr1B.!!$R1 3307
3 TraesCS1D01G188200 chr2D 509229523 509230794 1271 False 632 632 76.074 1194 2477 1 chr2D.!!$F2 1283
4 TraesCS1D01G188200 chr2A 653000361 653001632 1271 False 621 621 75.846 1194 2477 1 chr2A.!!$F1 1283
5 TraesCS1D01G188200 chr2B 598560961 598562232 1271 False 610 610 75.692 1194 2477 1 chr2B.!!$F1 1283
6 TraesCS1D01G188200 chr6A 476000185 476001519 1334 False 527 527 74.437 1167 2513 1 chr6A.!!$F1 1346
7 TraesCS1D01G188200 chr6D 336366515 336367849 1334 False 505 505 74.109 1167 2513 1 chr6D.!!$F1 1346
8 TraesCS1D01G188200 chr6B 484099556 484100889 1333 True 486 486 73.910 1168 2513 1 chr6B.!!$R2 1345

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
353 549 0.033796 ATGCTCAAGGTGGGATGTGG 60.034 55.000 0.0 0.00 0.0 4.17 F
879 1084 0.036858 TCAATTGCATCGACCGGTCA 60.037 50.000 32.8 20.42 0.0 4.02 F
936 1141 0.250727 TTTGAGCCTCCCCTGTTTCG 60.251 55.000 0.0 0.00 0.0 3.46 F
1998 2204 2.565841 GTGCTTATCCAGACCACATCC 58.434 52.381 0.0 0.00 0.0 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1968 2174 0.555769 GGATAAGCACCCCCATGGAA 59.444 55.000 15.22 0.0 38.00 3.53 R
1998 2204 1.067821 GACGGGAAGATGTAGAGCAGG 59.932 57.143 0.00 0.0 0.00 4.85 R
2064 2270 1.521457 GGCATCTGGACGATTCGCA 60.521 57.895 5.86 0.0 0.00 5.10 R
3585 3951 0.169672 CAGACGGCAAAGGCTTGATG 59.830 55.000 0.00 0.0 40.87 3.07 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
77 78 1.914764 CCCATTTTGCAGCACCCCT 60.915 57.895 0.00 0.00 0.00 4.79
78 79 1.593265 CCATTTTGCAGCACCCCTC 59.407 57.895 0.00 0.00 0.00 4.30
106 107 4.060038 TCAAGAGCCCGACATAGAAATC 57.940 45.455 0.00 0.00 0.00 2.17
113 114 3.065371 GCCCGACATAGAAATCCAAACTG 59.935 47.826 0.00 0.00 0.00 3.16
134 319 3.667087 GCAATGAGCCACGAACCA 58.333 55.556 0.00 0.00 37.23 3.67
163 348 6.184789 TGGTTAGGTTTCTTATGATGGAACC 58.815 40.000 0.00 0.00 34.51 3.62
190 375 4.446371 CATCAGGGTTCAAGTCCTACATC 58.554 47.826 0.00 0.00 0.00 3.06
198 383 3.877559 TCAAGTCCTACATCTGGCATTG 58.122 45.455 0.00 0.00 0.00 2.82
199 384 3.519107 TCAAGTCCTACATCTGGCATTGA 59.481 43.478 4.76 0.00 31.28 2.57
201 386 5.366477 TCAAGTCCTACATCTGGCATTGATA 59.634 40.000 4.76 0.00 29.88 2.15
208 393 5.573380 ACATCTGGCATTGATACTGGTAT 57.427 39.130 4.76 0.00 0.00 2.73
216 401 6.096705 TGGCATTGATACTGGTATTTTTCTGG 59.903 38.462 0.00 0.00 0.00 3.86
220 405 9.956720 CATTGATACTGGTATTTTTCTGGATTC 57.043 33.333 0.00 0.00 0.00 2.52
243 428 1.640428 TCAGTCATTTCGGCGATGTC 58.360 50.000 11.76 4.93 0.00 3.06
253 438 1.080093 GGCGATGTCCGTTCAGTGA 60.080 57.895 0.00 0.00 41.15 3.41
258 443 1.819288 GATGTCCGTTCAGTGAGAGGA 59.181 52.381 12.86 12.86 0.00 3.71
260 445 1.249407 GTCCGTTCAGTGAGAGGAGT 58.751 55.000 16.15 0.00 0.00 3.85
278 463 1.952296 AGTCGTTCCTGTTGACTACGT 59.048 47.619 0.00 0.00 40.98 3.57
286 477 0.241749 TGTTGACTACGTAGGCACCG 59.758 55.000 30.59 2.92 42.01 4.94
306 499 3.684788 CCGGTGGTGACTTCAATCTTAAG 59.315 47.826 0.00 0.00 0.00 1.85
311 504 6.092807 GGTGGTGACTTCAATCTTAAGATGTC 59.907 42.308 18.61 19.15 38.61 3.06
313 506 5.220491 GGTGACTTCAATCTTAAGATGTCGC 60.220 44.000 24.98 24.98 43.20 5.19
314 507 5.348724 GTGACTTCAATCTTAAGATGTCGCA 59.651 40.000 26.54 16.15 43.31 5.10
316 509 5.482908 ACTTCAATCTTAAGATGTCGCACT 58.517 37.500 18.61 0.00 34.49 4.40
324 517 1.468985 AGATGTCGCACTAGCTCAGT 58.531 50.000 0.00 0.00 39.10 3.41
333 526 3.058570 CGCACTAGCTCAGTATCTCGAAT 60.059 47.826 0.00 0.00 39.10 3.34
334 527 4.152580 CGCACTAGCTCAGTATCTCGAATA 59.847 45.833 0.00 0.00 39.10 1.75
341 534 5.242615 AGCTCAGTATCTCGAATATGCTCAA 59.757 40.000 0.00 0.00 0.00 3.02
342 535 5.572511 GCTCAGTATCTCGAATATGCTCAAG 59.427 44.000 0.00 0.00 0.00 3.02
343 536 6.018589 TCAGTATCTCGAATATGCTCAAGG 57.981 41.667 0.00 0.00 0.00 3.61
346 542 3.459232 TCTCGAATATGCTCAAGGTGG 57.541 47.619 0.00 0.00 0.00 4.61
353 549 0.033796 ATGCTCAAGGTGGGATGTGG 60.034 55.000 0.00 0.00 0.00 4.17
354 550 1.133181 TGCTCAAGGTGGGATGTGGA 61.133 55.000 0.00 0.00 0.00 4.02
371 568 5.482163 TGTGGATGTGTTCATAGAGTGAA 57.518 39.130 0.00 0.00 44.36 3.18
405 602 3.564235 TTGTGAGCATCTGCAATTGTC 57.436 42.857 7.40 0.07 45.16 3.18
413 610 3.191162 GCATCTGCAATTGTCCTGTGTTA 59.809 43.478 7.40 0.00 41.59 2.41
442 639 1.607148 GACCCAAAGACTTTCAACCCG 59.393 52.381 0.00 0.00 0.00 5.28
459 656 1.860950 CCCGCAGACACGATAAATCTG 59.139 52.381 0.00 0.00 42.33 2.90
474 671 8.774586 ACGATAAATCTGATAATTAGGCAACAC 58.225 33.333 0.00 0.00 41.41 3.32
512 709 7.721399 AGGAGGTGCATATAATTAAAAGGACTG 59.279 37.037 0.00 0.00 0.00 3.51
516 713 9.555727 GGTGCATATAATTAAAAGGACTGAGTA 57.444 33.333 0.00 0.00 0.00 2.59
698 903 0.742990 CACTGCTCCGGCCGAATTAA 60.743 55.000 30.73 7.05 37.74 1.40
841 1046 4.276431 GCTCCGCTCTAAAGTCACTATAGT 59.724 45.833 0.00 0.00 0.00 2.12
879 1084 0.036858 TCAATTGCATCGACCGGTCA 60.037 50.000 32.80 20.42 0.00 4.02
889 1094 3.380479 TCGACCGGTCATATCCATTTC 57.620 47.619 32.80 3.31 0.00 2.17
905 1110 9.759473 ATATCCATTTCCCTATAAATTCAGTGG 57.241 33.333 0.00 0.00 0.00 4.00
910 1115 4.792068 TCCCTATAAATTCAGTGGCCTTG 58.208 43.478 3.32 2.41 0.00 3.61
936 1141 0.250727 TTTGAGCCTCCCCTGTTTCG 60.251 55.000 0.00 0.00 0.00 3.46
1054 1260 4.440127 GCCGGTGCAATGCCAAGG 62.440 66.667 1.90 4.12 37.47 3.61
1257 1463 3.726607 GATGATCTCGATGCTGTTCCTT 58.273 45.455 0.00 0.00 0.00 3.36
1836 2042 5.105997 GCTGTCATACAAGCTTTTCAAGGAT 60.106 40.000 0.00 0.00 0.00 3.24
1998 2204 2.565841 GTGCTTATCCAGACCACATCC 58.434 52.381 0.00 0.00 0.00 3.51
2480 2686 4.760047 GCGCACGGACTGGGACAT 62.760 66.667 0.30 0.00 38.20 3.06
2633 2839 0.959372 AGCTTGCTCATCACTGTGGC 60.959 55.000 8.11 3.92 0.00 5.01
2635 2841 0.520404 CTTGCTCATCACTGTGGCAC 59.480 55.000 11.55 11.55 34.16 5.01
2859 3065 6.929606 GTCTTAATTAGGTGTGTTGAGTGACT 59.070 38.462 0.00 0.00 0.00 3.41
3138 3478 4.163441 TGGTGAACTTTGAGGAACATGA 57.837 40.909 0.00 0.00 0.00 3.07
3141 3481 5.163561 TGGTGAACTTTGAGGAACATGAAAC 60.164 40.000 0.00 0.00 0.00 2.78
3183 3523 3.988379 TTGTCGTAGAAAGGTACGTGT 57.012 42.857 0.00 0.00 44.94 4.49
3184 3524 3.272439 TGTCGTAGAAAGGTACGTGTG 57.728 47.619 0.00 0.00 44.94 3.82
3288 3654 4.332819 ACGATTAGCATCCTTAGTTTGTGC 59.667 41.667 0.00 0.00 36.11 4.57
3294 3660 3.753272 GCATCCTTAGTTTGTGCTCTTGA 59.247 43.478 0.00 0.00 33.25 3.02
3295 3661 4.378874 GCATCCTTAGTTTGTGCTCTTGAC 60.379 45.833 0.00 0.00 33.25 3.18
3308 3674 4.635765 GTGCTCTTGACAGGTAATGCATTA 59.364 41.667 15.21 15.21 0.00 1.90
3309 3675 4.635765 TGCTCTTGACAGGTAATGCATTAC 59.364 41.667 32.54 32.54 41.38 1.89
3310 3676 4.635765 GCTCTTGACAGGTAATGCATTACA 59.364 41.667 37.49 22.00 43.33 2.41
3311 3677 5.447818 GCTCTTGACAGGTAATGCATTACAC 60.448 44.000 37.49 28.97 43.33 2.90
3312 3678 5.804639 TCTTGACAGGTAATGCATTACACT 58.195 37.500 37.49 30.22 43.33 3.55
3313 3679 6.941857 TCTTGACAGGTAATGCATTACACTA 58.058 36.000 37.49 24.09 43.33 2.74
3314 3680 6.816640 TCTTGACAGGTAATGCATTACACTAC 59.183 38.462 37.49 27.62 43.33 2.73
3315 3681 6.043854 TGACAGGTAATGCATTACACTACA 57.956 37.500 37.49 29.18 43.33 2.74
3316 3682 6.106003 TGACAGGTAATGCATTACACTACAG 58.894 40.000 37.49 24.22 43.33 2.74
3317 3683 5.428253 ACAGGTAATGCATTACACTACAGG 58.572 41.667 37.49 24.61 43.33 4.00
3318 3684 5.188948 ACAGGTAATGCATTACACTACAGGA 59.811 40.000 37.49 9.17 43.33 3.86
3319 3685 6.112734 CAGGTAATGCATTACACTACAGGAA 58.887 40.000 37.49 8.69 43.33 3.36
3320 3686 6.767902 CAGGTAATGCATTACACTACAGGAAT 59.232 38.462 37.49 15.02 43.33 3.01
3321 3687 6.992715 AGGTAATGCATTACACTACAGGAATC 59.007 38.462 37.49 21.93 43.33 2.52
3322 3688 6.765989 GGTAATGCATTACACTACAGGAATCA 59.234 38.462 37.49 7.49 43.33 2.57
3323 3689 6.932356 AATGCATTACACTACAGGAATCAG 57.068 37.500 11.02 0.00 0.00 2.90
3324 3690 4.191544 TGCATTACACTACAGGAATCAGC 58.808 43.478 0.00 0.00 0.00 4.26
3325 3691 4.080919 TGCATTACACTACAGGAATCAGCT 60.081 41.667 0.00 0.00 0.00 4.24
3326 3692 5.128663 TGCATTACACTACAGGAATCAGCTA 59.871 40.000 0.00 0.00 0.00 3.32
3327 3693 5.463724 GCATTACACTACAGGAATCAGCTAC 59.536 44.000 0.00 0.00 0.00 3.58
3328 3694 6.684111 GCATTACACTACAGGAATCAGCTACT 60.684 42.308 0.00 0.00 0.00 2.57
3329 3695 6.852420 TTACACTACAGGAATCAGCTACTT 57.148 37.500 0.00 0.00 0.00 2.24
3330 3696 5.746990 ACACTACAGGAATCAGCTACTTT 57.253 39.130 0.00 0.00 0.00 2.66
3331 3697 5.482908 ACACTACAGGAATCAGCTACTTTG 58.517 41.667 0.00 0.00 0.00 2.77
3332 3698 4.331168 CACTACAGGAATCAGCTACTTTGC 59.669 45.833 0.00 0.00 0.00 3.68
3333 3699 2.716217 ACAGGAATCAGCTACTTTGCC 58.284 47.619 0.00 0.00 0.00 4.52
3334 3700 1.667724 CAGGAATCAGCTACTTTGCCG 59.332 52.381 0.00 0.00 0.00 5.69
3335 3701 1.279271 AGGAATCAGCTACTTTGCCGT 59.721 47.619 0.00 0.00 0.00 5.68
3336 3702 1.666189 GGAATCAGCTACTTTGCCGTC 59.334 52.381 0.00 0.00 0.00 4.79
3337 3703 2.622436 GAATCAGCTACTTTGCCGTCT 58.378 47.619 0.00 0.00 0.00 4.18
3338 3704 2.015736 ATCAGCTACTTTGCCGTCTG 57.984 50.000 0.00 0.00 0.00 3.51
3339 3705 0.670546 TCAGCTACTTTGCCGTCTGC 60.671 55.000 0.00 0.00 41.77 4.26
3340 3706 1.376037 AGCTACTTTGCCGTCTGCC 60.376 57.895 0.00 0.00 40.16 4.85
3341 3707 1.671054 GCTACTTTGCCGTCTGCCA 60.671 57.895 0.00 0.00 40.16 4.92
3342 3708 1.912371 GCTACTTTGCCGTCTGCCAC 61.912 60.000 0.00 0.00 40.16 5.01
3361 3727 2.256461 GCAGACGGCAAAGGCAAG 59.744 61.111 0.00 0.00 43.71 4.01
3362 3728 2.956987 CAGACGGCAAAGGCAAGG 59.043 61.111 0.00 0.00 43.71 3.61
3363 3729 2.282462 AGACGGCAAAGGCAAGGG 60.282 61.111 0.00 0.00 43.71 3.95
3364 3730 2.597510 GACGGCAAAGGCAAGGGT 60.598 61.111 0.00 0.00 43.71 4.34
3365 3731 2.912025 ACGGCAAAGGCAAGGGTG 60.912 61.111 0.00 0.00 43.71 4.61
3366 3732 3.683937 CGGCAAAGGCAAGGGTGG 61.684 66.667 0.00 0.00 43.71 4.61
3396 3762 4.090057 GCCTTTGCCGTCTGTCGC 62.090 66.667 0.00 0.00 38.35 5.19
3397 3763 3.777925 CCTTTGCCGTCTGTCGCG 61.778 66.667 0.00 0.00 38.35 5.87
3409 3775 4.084888 GTCGCGGACGGCAAAAGG 62.085 66.667 6.13 0.00 45.32 3.11
3412 3778 4.103103 GCGGACGGCAAAAGGCTC 62.103 66.667 0.00 0.00 44.01 4.70
3413 3779 3.431725 CGGACGGCAAAAGGCTCC 61.432 66.667 0.00 0.00 44.01 4.70
3415 3781 3.431725 GACGGCAAAAGGCTCCGG 61.432 66.667 15.66 0.00 46.78 5.14
3418 3784 3.302344 GGCAAAAGGCTCCGGCAA 61.302 61.111 0.00 0.00 44.01 4.52
3419 3785 2.733945 GCAAAAGGCTCCGGCAAA 59.266 55.556 0.00 0.00 40.87 3.68
3420 3786 1.373371 GCAAAAGGCTCCGGCAAAG 60.373 57.895 0.00 0.00 40.87 2.77
3421 3787 2.041153 CAAAAGGCTCCGGCAAAGT 58.959 52.632 0.00 0.00 40.87 2.66
3422 3788 1.243902 CAAAAGGCTCCGGCAAAGTA 58.756 50.000 0.00 0.00 40.87 2.24
3423 3789 1.200020 CAAAAGGCTCCGGCAAAGTAG 59.800 52.381 0.00 0.00 40.87 2.57
3424 3790 0.322546 AAAGGCTCCGGCAAAGTAGG 60.323 55.000 0.00 0.00 40.87 3.18
3425 3791 2.821679 AAGGCTCCGGCAAAGTAGGC 62.822 60.000 0.00 0.00 40.87 3.93
3426 3792 2.269241 GCTCCGGCAAAGTAGGCT 59.731 61.111 0.00 0.00 38.54 4.58
3427 3793 1.520666 GCTCCGGCAAAGTAGGCTA 59.479 57.895 0.00 0.00 38.54 3.93
3428 3794 0.810426 GCTCCGGCAAAGTAGGCTAC 60.810 60.000 16.93 16.93 38.54 3.58
3429 3795 0.527817 CTCCGGCAAAGTAGGCTACG 60.528 60.000 18.41 6.37 0.00 3.51
3430 3796 1.520787 CCGGCAAAGTAGGCTACGG 60.521 63.158 18.41 11.37 0.00 4.02
3431 3797 1.217244 CGGCAAAGTAGGCTACGGT 59.783 57.895 18.41 8.42 0.00 4.83
3432 3798 0.457035 CGGCAAAGTAGGCTACGGTA 59.543 55.000 18.41 0.00 0.00 4.02
3433 3799 1.135024 CGGCAAAGTAGGCTACGGTAA 60.135 52.381 18.41 0.00 0.00 2.85
3434 3800 2.674747 CGGCAAAGTAGGCTACGGTAAA 60.675 50.000 18.41 0.00 0.00 2.01
3435 3801 2.934553 GGCAAAGTAGGCTACGGTAAAG 59.065 50.000 18.41 8.26 0.00 1.85
3436 3802 3.368739 GGCAAAGTAGGCTACGGTAAAGA 60.369 47.826 18.41 0.00 0.00 2.52
3437 3803 3.864003 GCAAAGTAGGCTACGGTAAAGAG 59.136 47.826 18.41 5.93 0.00 2.85
3438 3804 3.797451 AAGTAGGCTACGGTAAAGAGC 57.203 47.619 18.41 0.00 35.39 4.09
3439 3805 3.015675 AGTAGGCTACGGTAAAGAGCT 57.984 47.619 18.41 0.00 36.43 4.09
3440 3806 3.363627 AGTAGGCTACGGTAAAGAGCTT 58.636 45.455 18.41 0.00 36.43 3.74
3441 3807 2.963548 AGGCTACGGTAAAGAGCTTC 57.036 50.000 0.00 0.00 36.43 3.86
3442 3808 2.458620 AGGCTACGGTAAAGAGCTTCT 58.541 47.619 0.00 0.00 36.43 2.85
3443 3809 2.832733 AGGCTACGGTAAAGAGCTTCTT 59.167 45.455 0.00 0.00 38.59 2.52
3445 3811 3.371285 GGCTACGGTAAAGAGCTTCTTTG 59.629 47.826 16.59 6.98 45.45 2.77
3446 3812 3.181519 GCTACGGTAAAGAGCTTCTTTGC 60.182 47.826 16.59 15.29 45.45 3.68
3450 3816 3.457198 GTAAAGAGCTTCTTTGCCGTC 57.543 47.619 16.59 4.17 45.45 4.79
3451 3817 2.262423 AAAGAGCTTCTTTGCCGTCT 57.738 45.000 9.46 0.00 44.34 4.18
3452 3818 1.517242 AAGAGCTTCTTTGCCGTCTG 58.483 50.000 0.00 0.00 31.57 3.51
3453 3819 0.952984 AGAGCTTCTTTGCCGTCTGC 60.953 55.000 0.00 0.00 41.77 4.26
3454 3820 0.952984 GAGCTTCTTTGCCGTCTGCT 60.953 55.000 0.00 0.00 42.00 4.24
3455 3821 0.536006 AGCTTCTTTGCCGTCTGCTT 60.536 50.000 0.00 0.00 42.00 3.91
3456 3822 0.312102 GCTTCTTTGCCGTCTGCTTT 59.688 50.000 0.00 0.00 42.00 3.51
3457 3823 1.664302 GCTTCTTTGCCGTCTGCTTTC 60.664 52.381 0.00 0.00 42.00 2.62
3458 3824 1.876156 CTTCTTTGCCGTCTGCTTTCT 59.124 47.619 0.00 0.00 42.00 2.52
3459 3825 1.229428 TCTTTGCCGTCTGCTTTCTG 58.771 50.000 0.00 0.00 42.00 3.02
3460 3826 1.202639 TCTTTGCCGTCTGCTTTCTGA 60.203 47.619 0.00 0.00 42.00 3.27
3461 3827 1.603802 CTTTGCCGTCTGCTTTCTGAA 59.396 47.619 0.00 0.00 42.00 3.02
3462 3828 1.229428 TTGCCGTCTGCTTTCTGAAG 58.771 50.000 0.00 0.00 42.00 3.02
3470 3836 3.169198 CTTTCTGAAGCGGACGGC 58.831 61.111 0.00 0.00 44.05 5.68
3526 3892 3.142796 CCGACGGCAATAAATTCGC 57.857 52.632 0.00 0.00 0.00 4.70
3527 3893 0.655733 CCGACGGCAATAAATTCGCT 59.344 50.000 0.00 0.00 0.00 4.93
3528 3894 1.594518 CCGACGGCAATAAATTCGCTG 60.595 52.381 0.00 0.00 38.04 5.18
3530 3896 2.475519 CGACGGCAATAAATTCGCTGTT 60.476 45.455 10.71 0.49 45.04 3.16
3531 3897 3.242155 CGACGGCAATAAATTCGCTGTTA 60.242 43.478 10.71 0.00 45.04 2.41
3532 3898 4.271687 GACGGCAATAAATTCGCTGTTAG 58.728 43.478 10.71 0.00 45.04 2.34
3533 3899 3.687698 ACGGCAATAAATTCGCTGTTAGT 59.312 39.130 0.00 0.00 42.51 2.24
3534 3900 4.201783 ACGGCAATAAATTCGCTGTTAGTC 60.202 41.667 0.00 0.00 42.51 2.59
3535 3901 4.598062 GGCAATAAATTCGCTGTTAGTCC 58.402 43.478 0.00 0.00 0.00 3.85
3536 3902 4.271687 GCAATAAATTCGCTGTTAGTCCG 58.728 43.478 0.00 0.00 0.00 4.79
3537 3903 4.201783 GCAATAAATTCGCTGTTAGTCCGT 60.202 41.667 0.00 0.00 0.00 4.69
3538 3904 5.672819 GCAATAAATTCGCTGTTAGTCCGTT 60.673 40.000 0.00 0.00 0.00 4.44
3539 3905 6.455913 GCAATAAATTCGCTGTTAGTCCGTTA 60.456 38.462 0.00 0.00 0.00 3.18
3540 3906 6.823678 ATAAATTCGCTGTTAGTCCGTTAG 57.176 37.500 0.00 0.00 0.00 2.34
3541 3907 2.642139 TTCGCTGTTAGTCCGTTAGG 57.358 50.000 0.00 0.00 39.46 2.69
3542 3908 0.171903 TCGCTGTTAGTCCGTTAGGC 59.828 55.000 0.00 0.00 37.47 3.93
3543 3909 1.138047 CGCTGTTAGTCCGTTAGGCG 61.138 60.000 0.00 0.00 40.95 5.52
3544 3910 0.108945 GCTGTTAGTCCGTTAGGCGT 60.109 55.000 0.00 0.00 39.32 5.68
3545 3911 1.905449 CTGTTAGTCCGTTAGGCGTC 58.095 55.000 0.00 0.00 39.32 5.19
3546 3912 1.471684 CTGTTAGTCCGTTAGGCGTCT 59.528 52.381 0.00 0.00 39.32 4.18
3547 3913 2.679837 CTGTTAGTCCGTTAGGCGTCTA 59.320 50.000 0.00 0.00 39.32 2.59
3548 3914 3.081061 TGTTAGTCCGTTAGGCGTCTAA 58.919 45.455 5.12 5.12 39.32 2.10
3558 3924 2.434359 GCGTCTAACGGCAGCCTT 60.434 61.111 10.54 5.63 42.82 4.35
3559 3925 2.033194 GCGTCTAACGGCAGCCTTT 61.033 57.895 10.54 9.43 42.82 3.11
3560 3926 1.787847 CGTCTAACGGCAGCCTTTG 59.212 57.895 13.47 6.16 38.08 2.77
3598 3964 2.334838 CAAAGAGCATCAAGCCTTTGC 58.665 47.619 13.78 0.00 45.49 3.68
3599 3965 2.929592 CAAAGAGCATCAAGCCTTTGCC 60.930 50.000 13.78 0.00 45.49 4.52
3601 3967 2.964978 GCATCAAGCCTTTGCCGT 59.035 55.556 0.00 0.00 38.69 5.68
3602 3968 1.153958 GCATCAAGCCTTTGCCGTC 60.154 57.895 0.00 0.00 38.69 4.79
3603 3969 1.589716 GCATCAAGCCTTTGCCGTCT 61.590 55.000 0.00 0.00 38.69 4.18
3604 3970 0.169672 CATCAAGCCTTTGCCGTCTG 59.830 55.000 0.00 0.00 38.69 3.51
3605 3971 1.589716 ATCAAGCCTTTGCCGTCTGC 61.590 55.000 0.00 0.00 38.69 4.26
3606 3972 2.985847 AAGCCTTTGCCGTCTGCC 60.986 61.111 0.00 0.00 40.16 4.85
3607 3973 3.790416 AAGCCTTTGCCGTCTGCCA 62.790 57.895 0.00 0.00 40.16 4.92
3608 3974 4.043200 GCCTTTGCCGTCTGCCAC 62.043 66.667 0.00 0.00 40.16 5.01
3609 3975 2.281761 CCTTTGCCGTCTGCCACT 60.282 61.111 0.00 0.00 40.16 4.00
3610 3976 2.620112 CCTTTGCCGTCTGCCACTG 61.620 63.158 0.00 0.00 40.16 3.66
3611 3977 1.893808 CTTTGCCGTCTGCCACTGT 60.894 57.895 0.00 0.00 40.16 3.55
3612 3978 0.602638 CTTTGCCGTCTGCCACTGTA 60.603 55.000 0.00 0.00 40.16 2.74
3613 3979 0.602638 TTTGCCGTCTGCCACTGTAG 60.603 55.000 0.00 0.00 40.16 2.74
3614 3980 2.125512 GCCGTCTGCCACTGTAGG 60.126 66.667 0.00 0.00 0.00 3.18
3624 3990 1.523758 CCACTGTAGGCAAACTGACC 58.476 55.000 4.36 0.00 0.00 4.02
3625 3991 1.202758 CCACTGTAGGCAAACTGACCA 60.203 52.381 4.36 0.00 0.00 4.02
3626 3992 2.571212 CACTGTAGGCAAACTGACCAA 58.429 47.619 4.36 0.00 0.00 3.67
3627 3993 2.948979 CACTGTAGGCAAACTGACCAAA 59.051 45.455 4.36 0.00 0.00 3.28
3628 3994 3.569701 CACTGTAGGCAAACTGACCAAAT 59.430 43.478 4.36 0.00 0.00 2.32
3629 3995 3.569701 ACTGTAGGCAAACTGACCAAATG 59.430 43.478 4.36 0.00 0.00 2.32
3630 3996 2.890311 TGTAGGCAAACTGACCAAATGG 59.110 45.455 0.00 0.00 42.17 3.16
3631 3997 1.341080 AGGCAAACTGACCAAATGGG 58.659 50.000 4.17 0.00 44.81 4.00
3640 4006 3.291611 CCAAATGGGTCAGCTGCC 58.708 61.111 9.47 13.62 0.00 4.85
3641 4007 1.607178 CCAAATGGGTCAGCTGCCA 60.607 57.895 23.05 19.23 0.00 4.92
3642 4008 1.601419 CCAAATGGGTCAGCTGCCAG 61.601 60.000 23.05 9.40 0.00 4.85
3643 4009 1.304713 AAATGGGTCAGCTGCCAGG 60.305 57.895 23.05 0.00 0.00 4.45
3644 4010 1.792757 AAATGGGTCAGCTGCCAGGA 61.793 55.000 23.05 10.75 0.00 3.86
3645 4011 1.792757 AATGGGTCAGCTGCCAGGAA 61.793 55.000 23.05 10.09 0.00 3.36
3646 4012 2.045536 GGGTCAGCTGCCAGGAAG 60.046 66.667 23.05 0.00 0.00 3.46
3647 4013 2.749441 GGTCAGCTGCCAGGAAGC 60.749 66.667 12.34 12.34 41.15 3.86
3648 4014 2.033141 GTCAGCTGCCAGGAAGCA 59.967 61.111 22.82 0.00 43.37 3.91
3649 4015 2.033141 TCAGCTGCCAGGAAGCAC 59.967 61.111 22.82 0.00 43.37 4.40
3650 4016 2.281970 CAGCTGCCAGGAAGCACA 60.282 61.111 22.82 0.00 43.37 4.57
3651 4017 2.033757 AGCTGCCAGGAAGCACAG 59.966 61.111 22.82 4.37 43.37 3.66
3652 4018 3.060615 GCTGCCAGGAAGCACAGG 61.061 66.667 15.66 0.00 40.52 4.00
3653 4019 2.433446 CTGCCAGGAAGCACAGGT 59.567 61.111 0.00 0.00 38.00 4.00
3654 4020 1.970114 CTGCCAGGAAGCACAGGTG 60.970 63.158 0.00 0.00 38.00 4.00
3655 4021 2.674380 GCCAGGAAGCACAGGTGG 60.674 66.667 1.10 0.00 0.00 4.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 9.129532 GGAGTCAATGGATGATTCTTCTTAATT 57.870 33.333 0.00 0.00 42.68 1.40
77 78 0.541998 TCGGGCTCTTGAAGACAGGA 60.542 55.000 0.00 0.00 32.94 3.86
78 79 0.390472 GTCGGGCTCTTGAAGACAGG 60.390 60.000 0.00 0.00 32.94 4.00
106 107 2.036217 TGGCTCATTGCTTTCAGTTTGG 59.964 45.455 0.00 0.00 42.39 3.28
113 114 1.401539 GGTTCGTGGCTCATTGCTTTC 60.402 52.381 0.00 0.00 42.39 2.62
133 318 7.012704 CCATCATAAGAAACCTAACCATCTGTG 59.987 40.741 0.00 0.00 0.00 3.66
134 319 7.056635 CCATCATAAGAAACCTAACCATCTGT 58.943 38.462 0.00 0.00 0.00 3.41
149 334 4.879295 ATGGGTTGGTTCCATCATAAGA 57.121 40.909 0.00 0.00 40.74 2.10
178 363 3.877559 TCAATGCCAGATGTAGGACTTG 58.122 45.455 0.00 0.00 0.00 3.16
190 375 7.198390 CAGAAAAATACCAGTATCAATGCCAG 58.802 38.462 0.00 0.00 0.00 4.85
201 386 8.421249 TGAAATGAATCCAGAAAAATACCAGT 57.579 30.769 0.00 0.00 0.00 4.00
208 393 9.480053 GAAATGACTGAAATGAATCCAGAAAAA 57.520 29.630 0.00 0.00 0.00 1.94
216 401 4.031028 CGCCGAAATGACTGAAATGAATC 58.969 43.478 0.00 0.00 0.00 2.52
220 405 3.181507 ACATCGCCGAAATGACTGAAATG 60.182 43.478 0.00 0.00 0.00 2.32
243 428 0.169230 CGACTCCTCTCACTGAACGG 59.831 60.000 0.00 0.00 0.00 4.44
258 443 1.952296 ACGTAGTCAACAGGAACGACT 59.048 47.619 0.00 0.00 42.49 4.18
260 445 2.485426 CCTACGTAGTCAACAGGAACGA 59.515 50.000 20.73 0.00 43.93 3.85
266 451 1.731424 CGGTGCCTACGTAGTCAACAG 60.731 57.143 20.49 10.11 43.93 3.16
267 452 0.241749 CGGTGCCTACGTAGTCAACA 59.758 55.000 20.49 10.76 43.93 3.33
270 455 1.303561 ACCGGTGCCTACGTAGTCA 60.304 57.895 20.73 12.25 43.93 3.41
286 477 5.940470 ACATCTTAAGATTGAAGTCACCACC 59.060 40.000 15.49 0.00 31.21 4.61
297 488 5.046529 AGCTAGTGCGACATCTTAAGATTG 58.953 41.667 15.49 12.90 45.42 2.67
298 489 5.163509 TGAGCTAGTGCGACATCTTAAGATT 60.164 40.000 15.49 7.44 45.42 2.40
299 490 4.339530 TGAGCTAGTGCGACATCTTAAGAT 59.660 41.667 12.37 12.37 45.42 2.40
300 491 3.694566 TGAGCTAGTGCGACATCTTAAGA 59.305 43.478 7.82 7.82 45.42 2.10
306 499 3.252215 AGATACTGAGCTAGTGCGACATC 59.748 47.826 0.00 0.00 45.42 3.06
311 504 1.867865 TCGAGATACTGAGCTAGTGCG 59.132 52.381 0.00 0.00 45.42 5.34
313 506 6.027131 GCATATTCGAGATACTGAGCTAGTG 58.973 44.000 0.00 0.00 40.65 2.74
314 507 5.943416 AGCATATTCGAGATACTGAGCTAGT 59.057 40.000 0.00 0.00 43.56 2.57
316 509 5.940470 TGAGCATATTCGAGATACTGAGCTA 59.060 40.000 0.00 0.00 0.00 3.32
324 517 4.021104 CCCACCTTGAGCATATTCGAGATA 60.021 45.833 0.00 0.00 31.34 1.98
333 526 1.212688 CCACATCCCACCTTGAGCATA 59.787 52.381 0.00 0.00 0.00 3.14
334 527 0.033796 CCACATCCCACCTTGAGCAT 60.034 55.000 0.00 0.00 0.00 3.79
341 534 1.004745 GAACACATCCACATCCCACCT 59.995 52.381 0.00 0.00 0.00 4.00
342 535 1.271871 TGAACACATCCACATCCCACC 60.272 52.381 0.00 0.00 0.00 4.61
343 536 2.198827 TGAACACATCCACATCCCAC 57.801 50.000 0.00 0.00 0.00 4.61
346 542 4.813161 CACTCTATGAACACATCCACATCC 59.187 45.833 0.00 0.00 0.00 3.51
371 568 3.938334 TGCTCACAAACACGCACATATAT 59.062 39.130 0.00 0.00 0.00 0.86
421 618 2.748465 CGGGTTGAAAGTCTTTGGGTCT 60.748 50.000 1.60 0.00 0.00 3.85
423 620 1.687563 CGGGTTGAAAGTCTTTGGGT 58.312 50.000 1.60 0.00 0.00 4.51
435 632 0.604073 TTATCGTGTCTGCGGGTTGA 59.396 50.000 0.00 0.00 0.00 3.18
442 639 8.651588 CCTAATTATCAGATTTATCGTGTCTGC 58.348 37.037 0.00 0.00 39.30 4.26
486 683 7.721399 CAGTCCTTTTAATTATATGCACCTCCT 59.279 37.037 0.00 0.00 0.00 3.69
487 684 7.719633 TCAGTCCTTTTAATTATATGCACCTCC 59.280 37.037 0.00 0.00 0.00 4.30
488 685 8.677148 TCAGTCCTTTTAATTATATGCACCTC 57.323 34.615 0.00 0.00 0.00 3.85
489 686 8.275040 ACTCAGTCCTTTTAATTATATGCACCT 58.725 33.333 0.00 0.00 0.00 4.00
496 693 9.555727 GCATGGTACTCAGTCCTTTTAATTATA 57.444 33.333 0.00 0.00 0.00 0.98
512 709 0.181114 TGAGCCCATGCATGGTACTC 59.819 55.000 36.51 36.51 46.65 2.59
516 713 1.117150 GATTTGAGCCCATGCATGGT 58.883 50.000 37.30 24.41 46.65 3.55
698 903 3.133767 TATTGCGCGGCTCGTAGCT 62.134 57.895 8.83 0.00 41.99 3.32
841 1046 5.749596 TTGAGAAACGAGATCAAAGCAAA 57.250 34.783 0.00 0.00 30.33 3.68
879 1084 9.759473 CCACTGAATTTATAGGGAAATGGATAT 57.241 33.333 0.00 0.00 0.00 1.63
889 1094 3.319122 GCAAGGCCACTGAATTTATAGGG 59.681 47.826 5.01 0.00 0.00 3.53
905 1110 1.315981 GGCTCAAACCCTAGCAAGGC 61.316 60.000 0.00 0.00 42.14 4.35
910 1115 1.224870 GGGAGGCTCAAACCCTAGC 59.775 63.158 17.69 0.00 40.39 3.42
1530 1736 3.126831 GCAGAATAGAATGTAGCGCTGT 58.873 45.455 22.90 2.57 0.00 4.40
1836 2042 4.634703 ACCCACGCGGCAACATCA 62.635 61.111 12.47 0.00 33.26 3.07
1968 2174 0.555769 GGATAAGCACCCCCATGGAA 59.444 55.000 15.22 0.00 38.00 3.53
1998 2204 1.067821 GACGGGAAGATGTAGAGCAGG 59.932 57.143 0.00 0.00 0.00 4.85
2064 2270 1.521457 GGCATCTGGACGATTCGCA 60.521 57.895 5.86 0.00 0.00 5.10
2558 2764 2.502080 ACTCGCTCGCGTCTTTCG 60.502 61.111 5.77 3.97 40.74 3.46
2596 2802 3.745803 GGAGTCCTCGTCGCCGTT 61.746 66.667 0.41 0.00 35.01 4.44
2988 3195 6.642131 TGAATTGAAAACAGTGCTAATTCTGC 59.358 34.615 0.00 0.00 36.20 4.26
3117 3457 4.163441 TCATGTTCCTCAAAGTTCACCA 57.837 40.909 0.00 0.00 0.00 4.17
3118 3458 5.067805 AGTTTCATGTTCCTCAAAGTTCACC 59.932 40.000 0.00 0.00 0.00 4.02
3183 3523 4.520111 GCATGCCAGTTATGATGTATTCCA 59.480 41.667 6.36 0.00 0.00 3.53
3184 3524 4.520111 TGCATGCCAGTTATGATGTATTCC 59.480 41.667 16.68 0.00 0.00 3.01
3266 3632 4.572389 AGCACAAACTAAGGATGCTAATCG 59.428 41.667 0.00 0.00 44.59 3.34
3288 3654 5.877012 AGTGTAATGCATTACCTGTCAAGAG 59.123 40.000 35.25 0.00 41.41 2.85
3294 3660 5.188948 TCCTGTAGTGTAATGCATTACCTGT 59.811 40.000 35.25 24.99 41.41 4.00
3295 3661 5.670485 TCCTGTAGTGTAATGCATTACCTG 58.330 41.667 35.25 24.98 41.41 4.00
3308 3674 5.482908 CAAAGTAGCTGATTCCTGTAGTGT 58.517 41.667 0.00 0.00 0.00 3.55
3309 3675 4.331168 GCAAAGTAGCTGATTCCTGTAGTG 59.669 45.833 0.00 0.00 0.00 2.74
3310 3676 4.508662 GCAAAGTAGCTGATTCCTGTAGT 58.491 43.478 0.00 0.00 0.00 2.73
3311 3677 3.873952 GGCAAAGTAGCTGATTCCTGTAG 59.126 47.826 0.00 0.00 34.17 2.74
3312 3678 3.678806 CGGCAAAGTAGCTGATTCCTGTA 60.679 47.826 0.00 0.00 43.63 2.74
3313 3679 2.716217 GGCAAAGTAGCTGATTCCTGT 58.284 47.619 0.00 0.00 34.17 4.00
3314 3680 1.667724 CGGCAAAGTAGCTGATTCCTG 59.332 52.381 0.00 0.00 43.63 3.86
3315 3681 1.279271 ACGGCAAAGTAGCTGATTCCT 59.721 47.619 0.00 0.00 43.63 3.36
3316 3682 1.666189 GACGGCAAAGTAGCTGATTCC 59.334 52.381 0.00 0.00 43.63 3.01
3317 3683 2.349886 CAGACGGCAAAGTAGCTGATTC 59.650 50.000 0.00 0.00 43.63 2.52
3318 3684 2.350522 CAGACGGCAAAGTAGCTGATT 58.649 47.619 0.00 0.00 43.63 2.57
3319 3685 2.009042 GCAGACGGCAAAGTAGCTGAT 61.009 52.381 0.00 0.00 43.63 2.90
3320 3686 0.670546 GCAGACGGCAAAGTAGCTGA 60.671 55.000 0.00 0.00 43.63 4.26
3321 3687 1.790387 GCAGACGGCAAAGTAGCTG 59.210 57.895 0.00 0.00 46.31 4.24
3322 3688 2.111999 TGGCAGACGGCAAAGTAGCT 62.112 55.000 0.00 0.00 46.20 3.32
3323 3689 1.671054 TGGCAGACGGCAAAGTAGC 60.671 57.895 0.00 0.00 46.20 3.58
3324 3690 4.693532 TGGCAGACGGCAAAGTAG 57.306 55.556 0.00 0.00 46.20 2.57
3339 3705 3.726517 CTTTGCCGTCTGCCGTGG 61.727 66.667 0.00 0.00 40.16 4.94
3340 3706 3.726517 CCTTTGCCGTCTGCCGTG 61.727 66.667 0.00 0.00 40.16 4.94
3343 3709 3.273080 CTTGCCTTTGCCGTCTGCC 62.273 63.158 0.00 0.00 40.16 4.85
3344 3710 2.256461 CTTGCCTTTGCCGTCTGC 59.744 61.111 0.00 0.00 41.77 4.26
3345 3711 2.629656 CCCTTGCCTTTGCCGTCTG 61.630 63.158 0.00 0.00 36.33 3.51
3346 3712 2.282462 CCCTTGCCTTTGCCGTCT 60.282 61.111 0.00 0.00 36.33 4.18
3347 3713 2.597510 ACCCTTGCCTTTGCCGTC 60.598 61.111 0.00 0.00 36.33 4.79
3348 3714 2.912025 CACCCTTGCCTTTGCCGT 60.912 61.111 0.00 0.00 36.33 5.68
3349 3715 3.683937 CCACCCTTGCCTTTGCCG 61.684 66.667 0.00 0.00 36.33 5.69
3350 3716 4.007644 GCCACCCTTGCCTTTGCC 62.008 66.667 0.00 0.00 36.33 4.52
3351 3717 4.362476 CGCCACCCTTGCCTTTGC 62.362 66.667 0.00 0.00 38.26 3.68
3352 3718 3.683937 CCGCCACCCTTGCCTTTG 61.684 66.667 0.00 0.00 0.00 2.77
3353 3719 3.897122 TCCGCCACCCTTGCCTTT 61.897 61.111 0.00 0.00 0.00 3.11
3354 3720 4.660938 GTCCGCCACCCTTGCCTT 62.661 66.667 0.00 0.00 0.00 4.35
3379 3745 4.090057 GCGACAGACGGCAAAGGC 62.090 66.667 0.00 0.00 42.83 4.35
3380 3746 3.777925 CGCGACAGACGGCAAAGG 61.778 66.667 0.00 0.00 42.83 3.11
3381 3747 3.777925 CCGCGACAGACGGCAAAG 61.778 66.667 8.23 0.00 44.90 2.77
3389 3755 3.793775 TTTTGCCGTCCGCGACAGA 62.794 57.895 8.23 0.00 42.08 3.41
3390 3756 3.295228 CTTTTGCCGTCCGCGACAG 62.295 63.158 8.23 0.00 42.08 3.51
3391 3757 3.342627 CTTTTGCCGTCCGCGACA 61.343 61.111 8.23 0.00 42.08 4.35
3392 3758 4.084888 CCTTTTGCCGTCCGCGAC 62.085 66.667 8.23 2.72 42.08 5.19
3395 3761 4.103103 GAGCCTTTTGCCGTCCGC 62.103 66.667 0.00 0.00 42.71 5.54
3396 3762 3.431725 GGAGCCTTTTGCCGTCCG 61.432 66.667 0.00 0.00 42.71 4.79
3397 3763 3.431725 CGGAGCCTTTTGCCGTCC 61.432 66.667 0.00 0.00 42.71 4.79
3398 3764 3.431725 CCGGAGCCTTTTGCCGTC 61.432 66.667 0.00 0.00 43.35 4.79
3401 3767 2.770132 CTTTGCCGGAGCCTTTTGCC 62.770 60.000 5.05 0.00 42.71 4.52
3402 3768 1.373371 CTTTGCCGGAGCCTTTTGC 60.373 57.895 5.05 0.00 38.69 3.68
3403 3769 1.200020 CTACTTTGCCGGAGCCTTTTG 59.800 52.381 5.05 0.00 38.69 2.44
3404 3770 1.534729 CTACTTTGCCGGAGCCTTTT 58.465 50.000 5.05 0.00 38.69 2.27
3405 3771 0.322546 CCTACTTTGCCGGAGCCTTT 60.323 55.000 5.05 0.00 38.69 3.11
3406 3772 1.299976 CCTACTTTGCCGGAGCCTT 59.700 57.895 5.05 0.00 38.69 4.35
3407 3773 2.990479 CCTACTTTGCCGGAGCCT 59.010 61.111 5.05 0.00 38.69 4.58
3408 3774 1.968050 TAGCCTACTTTGCCGGAGCC 61.968 60.000 5.05 0.00 38.69 4.70
3409 3775 0.810426 GTAGCCTACTTTGCCGGAGC 60.810 60.000 5.05 0.00 40.48 4.70
3410 3776 0.527817 CGTAGCCTACTTTGCCGGAG 60.528 60.000 5.05 0.00 0.00 4.63
3411 3777 1.514087 CGTAGCCTACTTTGCCGGA 59.486 57.895 5.05 0.00 0.00 5.14
3412 3778 1.520787 CCGTAGCCTACTTTGCCGG 60.521 63.158 0.00 0.00 0.00 6.13
3413 3779 0.457035 TACCGTAGCCTACTTTGCCG 59.543 55.000 0.00 0.00 0.00 5.69
3414 3780 2.678471 TTACCGTAGCCTACTTTGCC 57.322 50.000 0.00 0.00 0.00 4.52
3415 3781 3.853475 TCTTTACCGTAGCCTACTTTGC 58.147 45.455 0.00 0.00 0.00 3.68
3416 3782 3.864003 GCTCTTTACCGTAGCCTACTTTG 59.136 47.826 0.00 0.00 0.00 2.77
3417 3783 3.768215 AGCTCTTTACCGTAGCCTACTTT 59.232 43.478 0.00 0.00 36.92 2.66
3418 3784 3.363627 AGCTCTTTACCGTAGCCTACTT 58.636 45.455 0.00 0.00 36.92 2.24
3419 3785 3.015675 AGCTCTTTACCGTAGCCTACT 57.984 47.619 0.00 0.00 36.92 2.57
3420 3786 3.380954 AGAAGCTCTTTACCGTAGCCTAC 59.619 47.826 0.00 0.00 36.92 3.18
3421 3787 3.629087 AGAAGCTCTTTACCGTAGCCTA 58.371 45.455 0.00 0.00 36.92 3.93
3422 3788 2.458620 AGAAGCTCTTTACCGTAGCCT 58.541 47.619 0.00 0.00 36.92 4.58
3423 3789 2.963548 AGAAGCTCTTTACCGTAGCC 57.036 50.000 0.00 0.00 36.92 3.93
3424 3790 3.181519 GCAAAGAAGCTCTTTACCGTAGC 60.182 47.826 9.78 6.01 44.23 3.58
3425 3791 3.371285 GGCAAAGAAGCTCTTTACCGTAG 59.629 47.826 10.34 1.92 44.23 3.51
3426 3792 3.332034 GGCAAAGAAGCTCTTTACCGTA 58.668 45.455 10.34 0.00 44.23 4.02
3427 3793 2.152016 GGCAAAGAAGCTCTTTACCGT 58.848 47.619 10.34 0.00 44.23 4.83
3428 3794 2.902065 GGCAAAGAAGCTCTTTACCG 57.098 50.000 10.34 2.93 44.23 4.02
3429 3795 2.152016 ACGGCAAAGAAGCTCTTTACC 58.848 47.619 13.69 13.69 44.23 2.85
3430 3796 3.067833 AGACGGCAAAGAAGCTCTTTAC 58.932 45.455 9.78 5.86 44.23 2.01
3431 3797 3.067106 CAGACGGCAAAGAAGCTCTTTA 58.933 45.455 9.78 0.00 44.23 1.85
3432 3798 1.876156 CAGACGGCAAAGAAGCTCTTT 59.124 47.619 0.00 5.61 46.75 2.52
3433 3799 1.517242 CAGACGGCAAAGAAGCTCTT 58.483 50.000 0.00 0.00 38.59 2.85
3434 3800 0.952984 GCAGACGGCAAAGAAGCTCT 60.953 55.000 0.00 0.00 43.97 4.09
3435 3801 1.499502 GCAGACGGCAAAGAAGCTC 59.500 57.895 0.00 0.00 43.97 4.09
3436 3802 3.660621 GCAGACGGCAAAGAAGCT 58.339 55.556 0.00 0.00 43.97 3.74
3453 3819 1.227999 TTGCCGTCCGCTTCAGAAAG 61.228 55.000 0.00 0.00 38.78 2.62
3454 3820 0.816018 TTTGCCGTCCGCTTCAGAAA 60.816 50.000 0.00 0.00 38.78 2.52
3455 3821 1.227704 TTTGCCGTCCGCTTCAGAA 60.228 52.632 0.00 0.00 38.78 3.02
3456 3822 1.667830 CTTTGCCGTCCGCTTCAGA 60.668 57.895 0.00 0.00 38.78 3.27
3457 3823 2.680913 CCTTTGCCGTCCGCTTCAG 61.681 63.158 0.00 0.00 38.78 3.02
3458 3824 2.668212 CCTTTGCCGTCCGCTTCA 60.668 61.111 0.00 0.00 38.78 3.02
3459 3825 3.431725 CCCTTTGCCGTCCGCTTC 61.432 66.667 0.00 0.00 38.78 3.86
3508 3874 0.655733 AGCGAATTTATTGCCGTCGG 59.344 50.000 6.99 6.99 32.46 4.79
3509 3875 1.062002 ACAGCGAATTTATTGCCGTCG 59.938 47.619 0.00 0.00 34.89 5.12
3510 3876 2.825086 ACAGCGAATTTATTGCCGTC 57.175 45.000 0.00 0.00 0.00 4.79
3511 3877 3.687698 ACTAACAGCGAATTTATTGCCGT 59.312 39.130 0.00 0.00 0.00 5.68
3512 3878 4.271687 GACTAACAGCGAATTTATTGCCG 58.728 43.478 0.00 0.00 0.00 5.69
3513 3879 4.598062 GGACTAACAGCGAATTTATTGCC 58.402 43.478 0.00 0.00 0.00 4.52
3514 3880 4.201783 ACGGACTAACAGCGAATTTATTGC 60.202 41.667 0.00 0.00 0.00 3.56
3515 3881 5.464965 ACGGACTAACAGCGAATTTATTG 57.535 39.130 0.00 0.00 0.00 1.90
3516 3882 6.257193 CCTAACGGACTAACAGCGAATTTATT 59.743 38.462 0.00 0.00 0.00 1.40
3517 3883 5.751990 CCTAACGGACTAACAGCGAATTTAT 59.248 40.000 0.00 0.00 0.00 1.40
3518 3884 5.104374 CCTAACGGACTAACAGCGAATTTA 58.896 41.667 0.00 0.00 0.00 1.40
3519 3885 3.930848 CCTAACGGACTAACAGCGAATTT 59.069 43.478 0.00 0.00 0.00 1.82
3520 3886 3.518590 CCTAACGGACTAACAGCGAATT 58.481 45.455 0.00 0.00 0.00 2.17
3521 3887 2.737679 GCCTAACGGACTAACAGCGAAT 60.738 50.000 0.00 0.00 0.00 3.34
3522 3888 1.403249 GCCTAACGGACTAACAGCGAA 60.403 52.381 0.00 0.00 0.00 4.70
3523 3889 0.171903 GCCTAACGGACTAACAGCGA 59.828 55.000 0.00 0.00 0.00 4.93
3524 3890 1.138047 CGCCTAACGGACTAACAGCG 61.138 60.000 0.00 0.00 38.44 5.18
3525 3891 2.662150 CGCCTAACGGACTAACAGC 58.338 57.895 0.00 0.00 38.44 4.40
3537 3903 1.153706 GCTGCCGTTAGACGCCTAA 60.154 57.895 0.00 0.00 40.91 2.69
3538 3904 2.493030 GCTGCCGTTAGACGCCTA 59.507 61.111 0.00 0.00 40.91 3.93
3539 3905 4.452733 GGCTGCCGTTAGACGCCT 62.453 66.667 1.35 0.00 40.91 5.52
3540 3906 3.952628 AAGGCTGCCGTTAGACGCC 62.953 63.158 13.96 0.00 40.91 5.68
3541 3907 2.033194 AAAGGCTGCCGTTAGACGC 61.033 57.895 18.31 0.00 40.91 5.19
3542 3908 1.787847 CAAAGGCTGCCGTTAGACG 59.212 57.895 19.25 3.90 42.11 4.18
3543 3909 1.502190 GCAAAGGCTGCCGTTAGAC 59.498 57.895 19.25 8.69 46.13 2.59
3544 3910 3.981308 GCAAAGGCTGCCGTTAGA 58.019 55.556 19.25 0.00 46.13 2.10
3570 3936 1.300971 TGATGCTCTTTGCCGTCAGC 61.301 55.000 0.00 0.00 42.00 4.26
3571 3937 1.129998 CTTGATGCTCTTTGCCGTCAG 59.870 52.381 0.00 0.00 42.00 3.51
3572 3938 1.159285 CTTGATGCTCTTTGCCGTCA 58.841 50.000 0.00 0.00 42.00 4.35
3573 3939 0.179179 GCTTGATGCTCTTTGCCGTC 60.179 55.000 0.00 0.00 42.00 4.79
3574 3940 1.589716 GGCTTGATGCTCTTTGCCGT 61.590 55.000 0.00 0.00 42.00 5.68
3575 3941 1.138247 GGCTTGATGCTCTTTGCCG 59.862 57.895 0.00 0.00 42.00 5.69
3576 3942 0.893447 AAGGCTTGATGCTCTTTGCC 59.107 50.000 0.00 0.00 42.00 4.52
3577 3943 2.334838 CAAAGGCTTGATGCTCTTTGC 58.665 47.619 15.56 0.00 44.50 3.68
3579 3945 1.274447 GGCAAAGGCTTGATGCTCTTT 59.726 47.619 20.00 2.55 40.33 2.52
3580 3946 0.893447 GGCAAAGGCTTGATGCTCTT 59.107 50.000 20.00 0.00 42.39 2.85
3581 3947 1.310933 CGGCAAAGGCTTGATGCTCT 61.311 55.000 20.00 0.00 42.39 4.09
3582 3948 1.138247 CGGCAAAGGCTTGATGCTC 59.862 57.895 20.00 11.34 42.39 4.26
3583 3949 1.589716 GACGGCAAAGGCTTGATGCT 61.590 55.000 20.00 4.91 42.39 3.79
3584 3950 1.153958 GACGGCAAAGGCTTGATGC 60.154 57.895 14.14 14.14 40.87 3.91
3585 3951 0.169672 CAGACGGCAAAGGCTTGATG 59.830 55.000 0.00 0.00 40.87 3.07
3586 3952 1.589716 GCAGACGGCAAAGGCTTGAT 61.590 55.000 0.00 0.00 43.97 2.57
3587 3953 2.260869 GCAGACGGCAAAGGCTTGA 61.261 57.895 0.00 0.00 43.97 3.02
3588 3954 2.256461 GCAGACGGCAAAGGCTTG 59.744 61.111 0.00 0.00 43.97 4.01
3589 3955 3.790416 TGGCAGACGGCAAAGGCTT 62.790 57.895 0.00 0.00 46.20 4.35
3590 3956 4.269523 TGGCAGACGGCAAAGGCT 62.270 61.111 0.00 0.00 46.20 4.58
3597 3963 2.125512 CCTACAGTGGCAGACGGC 60.126 66.667 0.00 0.00 43.74 5.68
3605 3971 1.202758 TGGTCAGTTTGCCTACAGTGG 60.203 52.381 0.00 0.00 0.00 4.00
3606 3972 2.254546 TGGTCAGTTTGCCTACAGTG 57.745 50.000 0.00 0.00 0.00 3.66
3607 3973 3.290948 TTTGGTCAGTTTGCCTACAGT 57.709 42.857 0.00 0.00 0.00 3.55
3608 3974 3.057315 CCATTTGGTCAGTTTGCCTACAG 60.057 47.826 0.00 0.00 0.00 2.74
3609 3975 2.890311 CCATTTGGTCAGTTTGCCTACA 59.110 45.455 0.00 0.00 0.00 2.74
3610 3976 2.231235 CCCATTTGGTCAGTTTGCCTAC 59.769 50.000 0.00 0.00 0.00 3.18
3611 3977 2.524306 CCCATTTGGTCAGTTTGCCTA 58.476 47.619 0.00 0.00 0.00 3.93
3612 3978 1.341080 CCCATTTGGTCAGTTTGCCT 58.659 50.000 0.00 0.00 0.00 4.75
3613 3979 3.912899 CCCATTTGGTCAGTTTGCC 57.087 52.632 0.00 0.00 0.00 4.52
3623 3989 1.601419 CTGGCAGCTGACCCATTTGG 61.601 60.000 19.23 0.00 41.37 3.28
3624 3990 1.601419 CCTGGCAGCTGACCCATTTG 61.601 60.000 19.23 4.22 0.00 2.32
3625 3991 1.304713 CCTGGCAGCTGACCCATTT 60.305 57.895 19.23 0.00 0.00 2.32
3626 3992 1.792757 TTCCTGGCAGCTGACCCATT 61.793 55.000 19.23 0.00 0.00 3.16
3627 3993 2.207501 CTTCCTGGCAGCTGACCCAT 62.208 60.000 19.23 0.00 0.00 4.00
3628 3994 2.853542 TTCCTGGCAGCTGACCCA 60.854 61.111 19.23 14.97 0.00 4.51
3629 3995 2.045536 CTTCCTGGCAGCTGACCC 60.046 66.667 19.23 10.51 0.00 4.46
3630 3996 2.749441 GCTTCCTGGCAGCTGACC 60.749 66.667 19.23 18.04 34.15 4.02
3631 3997 2.033141 TGCTTCCTGGCAGCTGAC 59.967 61.111 20.43 17.52 38.19 3.51
3632 3998 2.033141 GTGCTTCCTGGCAGCTGA 59.967 61.111 20.43 0.00 43.25 4.26
3633 3999 2.281970 TGTGCTTCCTGGCAGCTG 60.282 61.111 18.88 10.11 43.25 4.24
3634 4000 2.033757 CTGTGCTTCCTGGCAGCT 59.966 61.111 18.88 0.00 43.25 4.24
3635 4001 3.060615 CCTGTGCTTCCTGGCAGC 61.061 66.667 11.61 11.61 43.25 5.25
3636 4002 1.970114 CACCTGTGCTTCCTGGCAG 60.970 63.158 7.75 7.75 43.25 4.85
3637 4003 2.113774 CACCTGTGCTTCCTGGCA 59.886 61.111 0.00 0.00 40.15 4.92
3638 4004 2.674380 CCACCTGTGCTTCCTGGC 60.674 66.667 0.00 0.00 0.00 4.85


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

AutoCloner maintained by Alex Coulton.