Multiple sequence alignment - TraesCS5A01G076500

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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 TraesCS5A01G076500 chr5A 100.000 3476 0 0 1 3476 92198574 92195099 0.000000e+00 6420
1 TraesCS5A01G076500 chr5A 97.424 427 10 1 3051 3476 92187915 92187489 0.000000e+00 726
2 TraesCS5A01G076500 chr5D 95.429 1969 74 12 1 1962 97054184 97052225 0.000000e+00 3123
3 TraesCS5A01G076500 chr5D 92.018 1115 65 10 1957 3051 97050371 97049261 0.000000e+00 1544
4 TraesCS5A01G076500 chr1A 97.674 430 10 0 3047 3476 277707420 277706991 0.000000e+00 739
5 TraesCS5A01G076500 chr1A 97.183 426 12 0 3051 3476 289439675 289439250 0.000000e+00 721
6 TraesCS5A01G076500 chr1A 96.948 426 13 0 3051 3476 289377033 289377458 0.000000e+00 715
7 TraesCS5A01G076500 chr7A 97.892 427 8 1 3051 3476 441106626 441107052 0.000000e+00 737
8 TraesCS5A01G076500 chr2A 97.887 426 9 0 3051 3476 600242721 600243146 0.000000e+00 737
9 TraesCS5A01G076500 chr3A 97.658 427 9 1 3051 3476 346980453 346980027 0.000000e+00 732
10 TraesCS5A01G076500 chr4A 97.190 427 11 1 3051 3476 151192687 151192261 0.000000e+00 721
11 TraesCS5A01G076500 chr4A 97.190 427 11 1 3051 3476 151201305 151200879 0.000000e+00 721
12 TraesCS5A01G076500 chr5B 87.873 536 41 12 2537 3051 103323479 103322947 2.970000e-170 608
13 TraesCS5A01G076500 chr5B 87.327 434 35 11 488 918 103323907 103323491 2.430000e-131 479
14 TraesCS5A01G076500 chr5B 95.238 84 4 0 316 399 103324379 103324296 2.180000e-27 134
15 TraesCS5A01G076500 chr7B 74.715 1230 278 27 1246 2457 3342285 3341071 5.140000e-143 518
16 TraesCS5A01G076500 chr2D 74.228 1230 290 21 1243 2457 601263790 601262573 1.120000e-134 490
17 TraesCS5A01G076500 chr2D 74.140 959 238 10 1506 2457 601255007 601254052 4.210000e-104 388
18 TraesCS5A01G076500 chr2B 74.041 1225 301 15 1243 2457 731482259 731481042 5.220000e-133 484
19 TraesCS5A01G076500 chr7D 73.966 1233 289 24 1252 2468 60705306 60704090 1.460000e-128 470


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 TraesCS5A01G076500 chr5A 92195099 92198574 3475 True 6420.0 6420 100.0000 1 3476 1 chr5A.!!$R2 3475
1 TraesCS5A01G076500 chr5D 97049261 97054184 4923 True 2333.5 3123 93.7235 1 3051 2 chr5D.!!$R1 3050
2 TraesCS5A01G076500 chr5B 103322947 103324379 1432 True 407.0 608 90.1460 316 3051 3 chr5B.!!$R1 2735
3 TraesCS5A01G076500 chr7B 3341071 3342285 1214 True 518.0 518 74.7150 1246 2457 1 chr7B.!!$R1 1211
4 TraesCS5A01G076500 chr2D 601262573 601263790 1217 True 490.0 490 74.2280 1243 2457 1 chr2D.!!$R2 1214
5 TraesCS5A01G076500 chr2D 601254052 601255007 955 True 388.0 388 74.1400 1506 2457 1 chr2D.!!$R1 951
6 TraesCS5A01G076500 chr2B 731481042 731482259 1217 True 484.0 484 74.0410 1243 2457 1 chr2B.!!$R1 1214
7 TraesCS5A01G076500 chr7D 60704090 60705306 1216 True 470.0 470 73.9660 1252 2468 1 chr7D.!!$R1 1216

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
593 918 1.030488 CCCGCTCGACAGAGTCCTAA 61.030 60.0 0.0 0.0 46.03 2.69 F
1176 1504 0.107703 TGCGTGATCTCCAACCCATC 60.108 55.0 0.0 0.0 0.00 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1998 4190 0.537143 TCATGTTGGCCTTGAGCGTT 60.537 50.0 3.32 0.0 45.17 4.84 R
3048 5275 0.177141 CCTTTCCCAGAACGCCGATA 59.823 55.0 0.00 0.0 0.00 2.92 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
62 63 1.290955 CGTCTTAGGCACGGGTTCA 59.709 57.895 0.00 0.00 33.46 3.18
79 80 2.040278 AGTAGAGCCCTGCCTGCT 59.960 61.111 0.00 0.00 43.03 4.24
128 129 2.091541 ACGTTTGCCCTAATCCATGTG 58.908 47.619 0.00 0.00 0.00 3.21
137 138 4.649218 GCCCTAATCCATGTGGTTTTATGT 59.351 41.667 0.00 0.00 36.34 2.29
254 255 7.864108 AAAAGCTTGAAAATACTTTGCCTTT 57.136 28.000 0.00 0.00 33.87 3.11
258 259 6.041523 AGCTTGAAAATACTTTGCCTTTGGTA 59.958 34.615 0.00 0.00 0.00 3.25
270 271 3.008157 TGCCTTTGGTAATAGAACGGACA 59.992 43.478 0.00 0.00 0.00 4.02
291 292 2.324860 TGAGACATGCACTTACGTTCG 58.675 47.619 0.00 0.00 0.00 3.95
295 296 3.057736 AGACATGCACTTACGTTCGTAGT 60.058 43.478 0.00 4.09 0.00 2.73
314 315 5.623673 CGTAGTTGTACAATTCAAAACAGGC 59.376 40.000 12.26 0.00 0.00 4.85
354 355 7.330700 GCTGAGATCCTTGCAGTAACTAATATC 59.669 40.741 0.00 0.00 32.39 1.63
376 377 9.874205 ATATCAATGTATGAAACCAACCAAAAG 57.126 29.630 0.00 0.00 42.54 2.27
448 771 9.807649 AGAAATTAGCATAAAACCATCACAATC 57.192 29.630 0.00 0.00 0.00 2.67
518 841 3.494223 CCATCAGCCCACACGTATCATTA 60.494 47.826 0.00 0.00 0.00 1.90
593 918 1.030488 CCCGCTCGACAGAGTCCTAA 61.030 60.000 0.00 0.00 46.03 2.69
814 1142 8.579850 ACTATTGGAAAGCATGTTTGATCTAA 57.420 30.769 0.00 0.00 0.00 2.10
876 1204 5.831702 ATAAGCTTCTGAATGCAAGGAAG 57.168 39.130 0.00 13.34 38.42 3.46
910 1238 2.876581 AGTTCCCAATGAAACTGTCCC 58.123 47.619 1.20 0.00 33.94 4.46
911 1239 1.539827 GTTCCCAATGAAACTGTCCCG 59.460 52.381 0.00 0.00 33.94 5.14
963 1291 2.711547 GGCCCTCACTACTCCCATTATT 59.288 50.000 0.00 0.00 0.00 1.40
1011 1339 7.811236 GCATAATCCAACATTATGACCTCATTG 59.189 37.037 15.47 0.00 41.89 2.82
1123 1451 1.298859 CCTCCTACAAGCCGCACAAC 61.299 60.000 0.00 0.00 0.00 3.32
1169 1497 1.191489 TCCCAACTGCGTGATCTCCA 61.191 55.000 0.00 0.00 0.00 3.86
1176 1504 0.107703 TGCGTGATCTCCAACCCATC 60.108 55.000 0.00 0.00 0.00 3.51
1218 1546 1.609635 TTCCGACCGCCATGCTTAGA 61.610 55.000 0.00 0.00 0.00 2.10
1373 1705 7.152645 GGCGAATCTACCACTAAATTCATAGA 58.847 38.462 0.00 0.00 0.00 1.98
1407 1739 1.028868 GCTCTGGCATGGGTGAAGAC 61.029 60.000 0.00 0.00 38.54 3.01
1529 1861 4.166011 GGCCAAGACGTGCATCGC 62.166 66.667 0.00 0.00 44.19 4.58
1614 1947 1.737816 CCGGATCGTCAACGGGTAT 59.262 57.895 0.00 0.00 43.69 2.73
1625 1958 4.569023 CGGGTATGCGCTGCGAGA 62.569 66.667 28.07 11.69 0.00 4.04
1626 1959 2.962253 GGGTATGCGCTGCGAGAC 60.962 66.667 28.07 18.25 0.00 3.36
1821 2154 1.770294 ACATTTTGTTCCGTGTGGGT 58.230 45.000 0.00 0.00 37.00 4.51
1853 2186 3.920446 TGCTGTTATCGACTTGTAAGCA 58.080 40.909 5.53 5.53 0.00 3.91
1923 2256 3.488090 GACGCTGCTTACCGGTGC 61.488 66.667 19.93 14.32 33.51 5.01
2223 4418 4.424626 GTCTATCAGACGAGCATGTTGAA 58.575 43.478 0.00 0.00 35.28 2.69
2300 4495 1.207089 CCAGTTGGCCTACATCGAAGA 59.793 52.381 19.71 0.00 45.75 2.87
2304 4499 4.747108 CAGTTGGCCTACATCGAAGATAAG 59.253 45.833 19.71 0.00 45.12 1.73
2413 4608 0.569204 ATCCCCCAATGCCAATGGAT 59.431 50.000 2.05 0.00 40.56 3.41
2465 4660 2.716217 GGATGTCTCCAAAGAAGGTGG 58.284 52.381 0.00 0.00 41.64 4.61
2466 4661 2.040412 GGATGTCTCCAAAGAAGGTGGT 59.960 50.000 0.00 0.00 41.64 4.16
2467 4662 3.498661 GGATGTCTCCAAAGAAGGTGGTT 60.499 47.826 0.00 0.00 41.64 3.67
2468 4663 3.208747 TGTCTCCAAAGAAGGTGGTTC 57.791 47.619 0.00 0.00 37.43 3.62
2491 4686 3.288809 CTTAGCAAAGCTTTCACCCAC 57.711 47.619 9.23 0.00 40.44 4.61
2492 4687 2.356665 TAGCAAAGCTTTCACCCACA 57.643 45.000 9.23 0.00 40.44 4.17
2493 4688 1.484038 AGCAAAGCTTTCACCCACAA 58.516 45.000 9.23 0.00 33.89 3.33
2495 4690 1.838913 CAAAGCTTTCACCCACAACG 58.161 50.000 9.23 0.00 0.00 4.10
2512 4713 3.942748 ACAACGTGGACAAACTACAACAT 59.057 39.130 0.00 0.00 0.00 2.71
2523 4724 7.333528 ACAAACTACAACATGTGAAATCACT 57.666 32.000 14.15 0.00 46.55 3.41
2533 4734 9.559958 CAACATGTGAAATCACTATTCTTAACC 57.440 33.333 14.15 0.00 46.55 2.85
2557 4758 7.180408 ACCTAAGAATAAAACTAGCTGAGTGGA 59.820 37.037 0.00 0.00 38.87 4.02
2638 4841 7.650890 ACGTTTTTATGGAATTCCTAAACGTT 58.349 30.769 34.94 27.28 45.59 3.99
2646 4849 3.636282 ATTCCTAAACGTTGTTGCCAC 57.364 42.857 0.00 0.00 0.00 5.01
2648 4851 2.577700 TCCTAAACGTTGTTGCCACAT 58.422 42.857 0.00 0.00 31.06 3.21
2649 4852 3.741249 TCCTAAACGTTGTTGCCACATA 58.259 40.909 0.00 0.00 31.06 2.29
2651 4854 4.155099 TCCTAAACGTTGTTGCCACATATG 59.845 41.667 0.00 0.00 31.06 1.78
2652 4855 2.346099 AACGTTGTTGCCACATATGC 57.654 45.000 0.00 0.00 31.06 3.14
2712 4916 3.014604 ACTACACGACTTGAGTGAAGC 57.985 47.619 3.20 0.00 41.83 3.86
2764 4976 4.577693 TGCCATATGAGCATTTTCTCAGTC 59.422 41.667 12.98 0.00 45.22 3.51
2771 4983 5.550290 TGAGCATTTTCTCAGTCATGTGTA 58.450 37.500 0.00 0.00 38.11 2.90
2842 5055 3.198872 AGAAGAATAAGCAAGCTACCGC 58.801 45.455 0.00 0.00 0.00 5.68
2865 5078 7.011950 CCGCTCATGGTATTTCTGTTAAATGTA 59.988 37.037 0.00 0.00 0.00 2.29
2929 5142 6.315393 GGAACCGCTTCTTTTATCAATGTCTA 59.685 38.462 0.00 0.00 0.00 2.59
2943 5156 7.741027 ATCAATGTCTAATGTATCTGCTTGG 57.259 36.000 0.00 0.00 0.00 3.61
2960 5187 3.066760 GCTTGGCATCCAGTACAATTACC 59.933 47.826 0.00 0.00 33.81 2.85
2986 5213 7.774157 CACTAGTCCAGTCACCTTAGATTACTA 59.226 40.741 0.00 0.00 34.26 1.82
2990 5217 7.674772 AGTCCAGTCACCTTAGATTACTAAAGT 59.325 37.037 0.00 0.00 38.01 2.66
3013 5240 5.050499 GTCATCTATCATGTACAGCAAGTGC 60.050 44.000 0.33 0.00 42.49 4.40
3030 5257 4.351874 AGTGCTTGTTACCTTTCTAGCA 57.648 40.909 0.00 0.00 39.25 3.49
3048 5275 7.473735 TCTAGCATGAAATAGATCGAGGATT 57.526 36.000 0.00 0.00 0.00 3.01
3051 5278 9.462174 CTAGCATGAAATAGATCGAGGATTATC 57.538 37.037 0.00 0.00 0.00 1.75
3052 5279 6.977502 AGCATGAAATAGATCGAGGATTATCG 59.022 38.462 0.00 0.00 44.07 2.92
3053 5280 6.199908 GCATGAAATAGATCGAGGATTATCGG 59.800 42.308 0.00 0.00 42.93 4.18
3054 5281 5.651530 TGAAATAGATCGAGGATTATCGGC 58.348 41.667 0.00 0.00 42.93 5.54
3055 5282 3.972950 ATAGATCGAGGATTATCGGCG 57.027 47.619 0.00 0.00 42.93 6.46
3056 5283 1.535833 AGATCGAGGATTATCGGCGT 58.464 50.000 6.85 0.00 42.93 5.68
3057 5284 1.887198 AGATCGAGGATTATCGGCGTT 59.113 47.619 6.85 0.00 42.93 4.84
3058 5285 2.095161 AGATCGAGGATTATCGGCGTTC 60.095 50.000 6.85 0.00 42.93 3.95
3059 5286 1.315690 TCGAGGATTATCGGCGTTCT 58.684 50.000 6.85 0.00 42.93 3.01
3060 5287 1.001706 TCGAGGATTATCGGCGTTCTG 60.002 52.381 6.85 0.00 42.93 3.02
3061 5288 1.784525 GAGGATTATCGGCGTTCTGG 58.215 55.000 6.85 0.00 0.00 3.86
3062 5289 0.393077 AGGATTATCGGCGTTCTGGG 59.607 55.000 6.85 0.00 0.00 4.45
3063 5290 0.391597 GGATTATCGGCGTTCTGGGA 59.608 55.000 6.85 0.00 0.00 4.37
3064 5291 1.202604 GGATTATCGGCGTTCTGGGAA 60.203 52.381 6.85 0.00 0.00 3.97
3065 5292 2.557317 GATTATCGGCGTTCTGGGAAA 58.443 47.619 6.85 0.00 0.00 3.13
3066 5293 2.018542 TTATCGGCGTTCTGGGAAAG 57.981 50.000 6.85 0.00 0.00 2.62
3067 5294 0.177141 TATCGGCGTTCTGGGAAAGG 59.823 55.000 6.85 0.00 0.00 3.11
3068 5295 2.536997 ATCGGCGTTCTGGGAAAGGG 62.537 60.000 6.85 0.00 0.00 3.95
3069 5296 2.361230 GGCGTTCTGGGAAAGGGG 60.361 66.667 0.00 0.00 0.00 4.79
3070 5297 2.361230 GCGTTCTGGGAAAGGGGG 60.361 66.667 0.00 0.00 0.00 5.40
3071 5298 3.167414 CGTTCTGGGAAAGGGGGT 58.833 61.111 0.00 0.00 0.00 4.95
3072 5299 1.002502 CGTTCTGGGAAAGGGGGTC 60.003 63.158 0.00 0.00 0.00 4.46
3073 5300 1.383019 GTTCTGGGAAAGGGGGTCC 59.617 63.158 0.00 0.00 0.00 4.46
3084 5311 4.048470 GGGGTCCCCAGACTTGCC 62.048 72.222 23.53 0.00 44.65 4.52
3085 5312 2.936032 GGGTCCCCAGACTTGCCT 60.936 66.667 0.00 0.00 43.05 4.75
3086 5313 2.352805 GGTCCCCAGACTTGCCTG 59.647 66.667 0.00 0.00 43.05 4.85
3087 5314 2.360475 GTCCCCAGACTTGCCTGC 60.360 66.667 0.00 0.00 40.10 4.85
3088 5315 3.650950 TCCCCAGACTTGCCTGCC 61.651 66.667 0.00 0.00 32.97 4.85
3089 5316 3.655211 CCCCAGACTTGCCTGCCT 61.655 66.667 0.00 0.00 32.97 4.75
3090 5317 2.360852 CCCAGACTTGCCTGCCTG 60.361 66.667 0.00 0.00 32.97 4.85
3091 5318 3.060615 CCAGACTTGCCTGCCTGC 61.061 66.667 0.00 0.00 32.97 4.85
3092 5319 3.429141 CAGACTTGCCTGCCTGCG 61.429 66.667 0.00 0.00 0.00 5.18
3093 5320 4.711949 AGACTTGCCTGCCTGCGG 62.712 66.667 0.00 0.00 0.00 5.69
3110 5337 4.752879 GCCTACGGCGTGGCTCAA 62.753 66.667 31.91 11.20 45.26 3.02
3111 5338 2.047655 CCTACGGCGTGGCTCAAA 60.048 61.111 24.86 0.00 0.00 2.69
3112 5339 2.100631 CCTACGGCGTGGCTCAAAG 61.101 63.158 24.86 9.92 0.00 2.77
3113 5340 2.047655 TACGGCGTGGCTCAAAGG 60.048 61.111 24.86 0.00 0.00 3.11
3114 5341 3.599285 TACGGCGTGGCTCAAAGGG 62.599 63.158 24.86 0.00 0.00 3.95
3121 5348 4.766632 GGCTCAAAGGGGGCCCAG 62.767 72.222 26.86 14.08 39.96 4.45
3123 5350 3.983420 CTCAAAGGGGGCCCAGCA 61.983 66.667 26.86 1.45 38.92 4.41
3124 5351 4.299796 TCAAAGGGGGCCCAGCAC 62.300 66.667 26.86 10.72 38.92 4.40
3134 5361 4.431131 CCCAGCACGGCCCATCTT 62.431 66.667 0.00 0.00 0.00 2.40
3135 5362 2.825836 CCAGCACGGCCCATCTTC 60.826 66.667 0.00 0.00 0.00 2.87
3136 5363 2.046023 CAGCACGGCCCATCTTCA 60.046 61.111 0.00 0.00 0.00 3.02
3137 5364 2.045926 AGCACGGCCCATCTTCAC 60.046 61.111 0.00 0.00 0.00 3.18
3138 5365 3.134127 GCACGGCCCATCTTCACC 61.134 66.667 0.00 0.00 0.00 4.02
3139 5366 2.350895 CACGGCCCATCTTCACCA 59.649 61.111 0.00 0.00 0.00 4.17
3140 5367 1.303236 CACGGCCCATCTTCACCAA 60.303 57.895 0.00 0.00 0.00 3.67
3141 5368 1.303317 ACGGCCCATCTTCACCAAC 60.303 57.895 0.00 0.00 0.00 3.77
3142 5369 1.303236 CGGCCCATCTTCACCAACA 60.303 57.895 0.00 0.00 0.00 3.33
3143 5370 1.586154 CGGCCCATCTTCACCAACAC 61.586 60.000 0.00 0.00 0.00 3.32
3144 5371 0.539438 GGCCCATCTTCACCAACACA 60.539 55.000 0.00 0.00 0.00 3.72
3145 5372 1.327303 GCCCATCTTCACCAACACAA 58.673 50.000 0.00 0.00 0.00 3.33
3146 5373 1.686052 GCCCATCTTCACCAACACAAA 59.314 47.619 0.00 0.00 0.00 2.83
3147 5374 2.545742 GCCCATCTTCACCAACACAAAC 60.546 50.000 0.00 0.00 0.00 2.93
3148 5375 2.035832 CCCATCTTCACCAACACAAACC 59.964 50.000 0.00 0.00 0.00 3.27
3149 5376 2.035832 CCATCTTCACCAACACAAACCC 59.964 50.000 0.00 0.00 0.00 4.11
3150 5377 2.516227 TCTTCACCAACACAAACCCA 57.484 45.000 0.00 0.00 0.00 4.51
3151 5378 2.808919 TCTTCACCAACACAAACCCAA 58.191 42.857 0.00 0.00 0.00 4.12
3152 5379 2.757868 TCTTCACCAACACAAACCCAAG 59.242 45.455 0.00 0.00 0.00 3.61
3153 5380 2.516227 TCACCAACACAAACCCAAGA 57.484 45.000 0.00 0.00 0.00 3.02
3154 5381 2.096248 TCACCAACACAAACCCAAGAC 58.904 47.619 0.00 0.00 0.00 3.01
3155 5382 1.136110 CACCAACACAAACCCAAGACC 59.864 52.381 0.00 0.00 0.00 3.85
3156 5383 0.750249 CCAACACAAACCCAAGACCC 59.250 55.000 0.00 0.00 0.00 4.46
3157 5384 1.687996 CCAACACAAACCCAAGACCCT 60.688 52.381 0.00 0.00 0.00 4.34
3158 5385 1.681264 CAACACAAACCCAAGACCCTC 59.319 52.381 0.00 0.00 0.00 4.30
3159 5386 0.179029 ACACAAACCCAAGACCCTCG 60.179 55.000 0.00 0.00 0.00 4.63
3160 5387 1.228154 ACAAACCCAAGACCCTCGC 60.228 57.895 0.00 0.00 0.00 5.03
3161 5388 2.032071 AAACCCAAGACCCTCGCG 59.968 61.111 0.00 0.00 0.00 5.87
3162 5389 2.513259 AAACCCAAGACCCTCGCGA 61.513 57.895 9.26 9.26 0.00 5.87
3163 5390 2.450479 AAACCCAAGACCCTCGCGAG 62.450 60.000 29.06 29.06 0.00 5.03
3208 5435 2.125350 CGGAGCTTCCTCAGGCAC 60.125 66.667 0.00 0.00 39.96 5.01
3209 5436 2.125350 GGAGCTTCCTCAGGCACG 60.125 66.667 0.00 0.00 39.96 5.34
3210 5437 2.125350 GAGCTTCCTCAGGCACGG 60.125 66.667 0.00 0.00 38.03 4.94
3211 5438 4.400961 AGCTTCCTCAGGCACGGC 62.401 66.667 0.00 0.00 0.00 5.68
3228 5455 3.317109 CCTCATCAGGCTGGCTCA 58.683 61.111 15.73 0.00 30.98 4.26
3229 5456 1.153208 CCTCATCAGGCTGGCTCAC 60.153 63.158 15.73 0.00 30.98 3.51
3230 5457 1.521010 CTCATCAGGCTGGCTCACG 60.521 63.158 15.73 0.00 0.00 4.35
3231 5458 1.953231 CTCATCAGGCTGGCTCACGA 61.953 60.000 15.73 0.00 0.00 4.35
3232 5459 1.521010 CATCAGGCTGGCTCACGAG 60.521 63.158 15.73 0.00 0.00 4.18
3233 5460 2.729479 ATCAGGCTGGCTCACGAGG 61.729 63.158 15.73 0.00 0.00 4.63
3234 5461 4.463879 CAGGCTGGCTCACGAGGG 62.464 72.222 6.61 0.00 0.00 4.30
3245 5472 4.144727 ACGAGGGGGCGGAGAGAT 62.145 66.667 0.00 0.00 35.12 2.75
3246 5473 3.299190 CGAGGGGGCGGAGAGATC 61.299 72.222 0.00 0.00 0.00 2.75
3247 5474 2.123251 GAGGGGGCGGAGAGATCA 60.123 66.667 0.00 0.00 0.00 2.92
3248 5475 1.762460 GAGGGGGCGGAGAGATCAA 60.762 63.158 0.00 0.00 0.00 2.57
3249 5476 1.753368 GAGGGGGCGGAGAGATCAAG 61.753 65.000 0.00 0.00 0.00 3.02
3250 5477 2.812619 GGGGGCGGAGAGATCAAGG 61.813 68.421 0.00 0.00 0.00 3.61
3251 5478 1.762460 GGGGCGGAGAGATCAAGGA 60.762 63.158 0.00 0.00 0.00 3.36
3252 5479 1.745264 GGGCGGAGAGATCAAGGAG 59.255 63.158 0.00 0.00 0.00 3.69
3253 5480 1.745264 GGCGGAGAGATCAAGGAGG 59.255 63.158 0.00 0.00 0.00 4.30
3254 5481 1.745264 GCGGAGAGATCAAGGAGGG 59.255 63.158 0.00 0.00 0.00 4.30
3255 5482 1.753368 GCGGAGAGATCAAGGAGGGG 61.753 65.000 0.00 0.00 0.00 4.79
3256 5483 0.397816 CGGAGAGATCAAGGAGGGGT 60.398 60.000 0.00 0.00 0.00 4.95
3257 5484 1.133450 CGGAGAGATCAAGGAGGGGTA 60.133 57.143 0.00 0.00 0.00 3.69
3258 5485 2.321719 GGAGAGATCAAGGAGGGGTAC 58.678 57.143 0.00 0.00 0.00 3.34
3275 5502 2.124983 CCTCACGAGGTGCCCATG 60.125 66.667 4.83 0.00 43.61 3.66
3276 5503 2.124983 CTCACGAGGTGCCCATGG 60.125 66.667 4.14 4.14 32.98 3.66
3294 5521 3.084579 CGCAAGCCATGACGACTC 58.915 61.111 0.00 0.00 32.61 3.36
3295 5522 1.737735 CGCAAGCCATGACGACTCA 60.738 57.895 0.00 0.00 32.61 3.41
3296 5523 1.690283 CGCAAGCCATGACGACTCAG 61.690 60.000 0.00 0.00 32.61 3.35
3297 5524 1.364626 GCAAGCCATGACGACTCAGG 61.365 60.000 0.00 0.00 0.00 3.86
3300 5527 2.202797 CCATGACGACTCAGGGCG 60.203 66.667 0.00 0.00 41.35 6.13
3301 5528 2.887568 CATGACGACTCAGGGCGC 60.888 66.667 0.00 0.00 0.00 6.53
3302 5529 4.148825 ATGACGACTCAGGGCGCC 62.149 66.667 21.18 21.18 0.00 6.53
3304 5531 4.803426 GACGACTCAGGGCGCCAG 62.803 72.222 30.85 20.04 0.00 4.85
3337 5564 2.815647 CGCAGCGTCCTCCTTTCC 60.816 66.667 6.65 0.00 0.00 3.13
3338 5565 2.665603 GCAGCGTCCTCCTTTCCT 59.334 61.111 0.00 0.00 0.00 3.36
3339 5566 1.448717 GCAGCGTCCTCCTTTCCTC 60.449 63.158 0.00 0.00 0.00 3.71
3340 5567 1.893919 GCAGCGTCCTCCTTTCCTCT 61.894 60.000 0.00 0.00 0.00 3.69
3341 5568 0.610687 CAGCGTCCTCCTTTCCTCTT 59.389 55.000 0.00 0.00 0.00 2.85
3342 5569 1.002544 CAGCGTCCTCCTTTCCTCTTT 59.997 52.381 0.00 0.00 0.00 2.52
3343 5570 1.002544 AGCGTCCTCCTTTCCTCTTTG 59.997 52.381 0.00 0.00 0.00 2.77
3344 5571 1.946283 GCGTCCTCCTTTCCTCTTTGG 60.946 57.143 0.00 0.00 37.10 3.28
3345 5572 1.348036 CGTCCTCCTTTCCTCTTTGGT 59.652 52.381 0.00 0.00 37.07 3.67
3346 5573 2.784347 GTCCTCCTTTCCTCTTTGGTG 58.216 52.381 0.00 0.00 37.07 4.17
3347 5574 1.073923 TCCTCCTTTCCTCTTTGGTGC 59.926 52.381 0.00 0.00 37.07 5.01
3348 5575 1.202927 CCTCCTTTCCTCTTTGGTGCA 60.203 52.381 0.00 0.00 37.07 4.57
3349 5576 2.586425 CTCCTTTCCTCTTTGGTGCAA 58.414 47.619 0.00 0.00 37.07 4.08
3350 5577 2.958355 CTCCTTTCCTCTTTGGTGCAAA 59.042 45.455 0.00 0.00 37.07 3.68
3355 5582 2.354902 CTCTTTGGTGCAAAGGGGG 58.645 57.895 0.00 0.00 45.21 5.40
3356 5583 1.820010 CTCTTTGGTGCAAAGGGGGC 61.820 60.000 0.00 0.00 45.21 5.80
3357 5584 2.041508 TTTGGTGCAAAGGGGGCA 60.042 55.556 0.00 0.00 39.32 5.36
3358 5585 1.690633 TTTGGTGCAAAGGGGGCAA 60.691 52.632 0.00 0.00 43.91 4.52
3359 5586 1.694133 TTTGGTGCAAAGGGGGCAAG 61.694 55.000 0.00 0.00 43.91 4.01
3360 5587 4.007644 GGTGCAAAGGGGGCAAGC 62.008 66.667 0.00 0.00 43.91 4.01
3361 5588 4.362476 GTGCAAAGGGGGCAAGCG 62.362 66.667 0.00 0.00 43.91 4.68
3364 5591 4.060038 CAAAGGGGGCAAGCGCAG 62.060 66.667 11.47 2.01 41.24 5.18
3387 5614 1.742768 GGAGTACCGAGGCATCAGG 59.257 63.158 0.00 3.36 0.00 3.86
3388 5615 1.068250 GAGTACCGAGGCATCAGGC 59.932 63.158 8.76 0.00 43.74 4.85
3407 5634 1.782044 CAAAGGTTGCCATTTCGGTG 58.218 50.000 0.00 0.00 36.97 4.94
3408 5635 0.033366 AAAGGTTGCCATTTCGGTGC 59.967 50.000 0.00 0.00 36.97 5.01
3409 5636 1.112315 AAGGTTGCCATTTCGGTGCA 61.112 50.000 0.00 0.00 36.97 4.57
3410 5637 1.112315 AGGTTGCCATTTCGGTGCAA 61.112 50.000 0.00 0.00 42.28 4.08
3412 5639 1.007964 TTGCCATTTCGGTGCAACG 60.008 52.632 20.47 20.47 39.86 4.10
3413 5640 1.448119 TTGCCATTTCGGTGCAACGA 61.448 50.000 25.58 25.58 39.86 3.85
3414 5641 1.154225 GCCATTTCGGTGCAACGAG 60.154 57.895 27.66 16.71 44.47 4.18
3415 5642 1.573829 GCCATTTCGGTGCAACGAGA 61.574 55.000 27.66 24.05 44.47 4.04
3416 5643 0.165944 CCATTTCGGTGCAACGAGAC 59.834 55.000 27.66 0.00 44.47 3.36
3417 5644 0.165944 CATTTCGGTGCAACGAGACC 59.834 55.000 27.66 2.32 44.47 3.85
3418 5645 0.250124 ATTTCGGTGCAACGAGACCA 60.250 50.000 27.66 9.89 44.47 4.02
3419 5646 0.462225 TTTCGGTGCAACGAGACCAA 60.462 50.000 27.66 15.98 44.47 3.67
3420 5647 0.878523 TTCGGTGCAACGAGACCAAG 60.879 55.000 27.66 0.00 44.47 3.61
3421 5648 1.300620 CGGTGCAACGAGACCAAGA 60.301 57.895 22.23 0.00 38.12 3.02
3422 5649 1.557443 CGGTGCAACGAGACCAAGAC 61.557 60.000 22.23 0.00 38.12 3.01
3423 5650 1.228657 GGTGCAACGAGACCAAGACC 61.229 60.000 0.00 0.00 38.12 3.85
3424 5651 0.531974 GTGCAACGAGACCAAGACCA 60.532 55.000 0.00 0.00 0.00 4.02
3425 5652 0.249868 TGCAACGAGACCAAGACCAG 60.250 55.000 0.00 0.00 0.00 4.00
3426 5653 0.951040 GCAACGAGACCAAGACCAGG 60.951 60.000 0.00 0.00 0.00 4.45
3427 5654 0.679505 CAACGAGACCAAGACCAGGA 59.320 55.000 0.00 0.00 0.00 3.86
3428 5655 0.969894 AACGAGACCAAGACCAGGAG 59.030 55.000 0.00 0.00 0.00 3.69
3429 5656 0.900647 ACGAGACCAAGACCAGGAGG 60.901 60.000 0.00 0.00 42.21 4.30
3430 5657 0.612174 CGAGACCAAGACCAGGAGGA 60.612 60.000 0.00 0.00 38.69 3.71
3431 5658 0.899019 GAGACCAAGACCAGGAGGAC 59.101 60.000 0.00 0.00 38.69 3.85
3432 5659 0.489567 AGACCAAGACCAGGAGGACT 59.510 55.000 0.00 0.00 41.82 3.85
3433 5660 1.717077 AGACCAAGACCAGGAGGACTA 59.283 52.381 0.00 0.00 39.03 2.59
3434 5661 1.826096 GACCAAGACCAGGAGGACTAC 59.174 57.143 0.00 0.00 39.03 2.73
3435 5662 0.818296 CCAAGACCAGGAGGACTACG 59.182 60.000 0.00 0.00 39.03 3.51
3436 5663 1.616187 CCAAGACCAGGAGGACTACGA 60.616 57.143 0.00 0.00 39.03 3.43
3437 5664 1.746220 CAAGACCAGGAGGACTACGAG 59.254 57.143 0.00 0.00 39.03 4.18
3438 5665 1.287217 AGACCAGGAGGACTACGAGA 58.713 55.000 0.00 0.00 38.17 4.04
3439 5666 1.065272 AGACCAGGAGGACTACGAGAC 60.065 57.143 0.00 0.00 38.17 3.36
3440 5667 0.392729 ACCAGGAGGACTACGAGACG 60.393 60.000 0.00 0.00 38.69 4.18
3441 5668 1.096386 CCAGGAGGACTACGAGACGG 61.096 65.000 0.00 0.00 36.89 4.79
3442 5669 0.107800 CAGGAGGACTACGAGACGGA 60.108 60.000 0.00 0.00 0.00 4.69
3443 5670 0.178533 AGGAGGACTACGAGACGGAG 59.821 60.000 1.68 1.68 44.37 4.63
3444 5671 0.814812 GGAGGACTACGAGACGGAGG 60.815 65.000 8.24 0.00 42.90 4.30
3445 5672 0.107752 GAGGACTACGAGACGGAGGT 60.108 60.000 8.24 0.00 42.90 3.85
3446 5673 0.107752 AGGACTACGAGACGGAGGTC 60.108 60.000 8.24 6.60 42.90 3.85
3447 5674 0.392193 GGACTACGAGACGGAGGTCA 60.392 60.000 8.24 0.00 42.90 4.02
3448 5675 1.666054 GACTACGAGACGGAGGTCAT 58.334 55.000 8.24 0.00 42.90 3.06
3449 5676 1.598601 GACTACGAGACGGAGGTCATC 59.401 57.143 8.24 0.00 42.90 2.92
3450 5677 0.582482 CTACGAGACGGAGGTCATCG 59.418 60.000 11.62 11.62 45.92 3.84
3451 5678 1.376942 ACGAGACGGAGGTCATCGT 60.377 57.895 12.51 12.51 45.92 3.73
3452 5679 1.062685 CGAGACGGAGGTCATCGTG 59.937 63.158 0.00 0.00 45.92 4.35
3453 5680 1.433879 GAGACGGAGGTCATCGTGG 59.566 63.158 0.00 0.00 45.92 4.94
3454 5681 1.001269 AGACGGAGGTCATCGTGGA 60.001 57.895 0.00 0.00 45.92 4.02
3455 5682 1.032657 AGACGGAGGTCATCGTGGAG 61.033 60.000 0.00 0.00 45.92 3.86
3456 5683 2.105128 CGGAGGTCATCGTGGAGC 59.895 66.667 1.05 1.05 35.57 4.70
3457 5684 2.501610 GGAGGTCATCGTGGAGCC 59.498 66.667 5.01 0.00 35.95 4.70
3458 5685 2.501610 GAGGTCATCGTGGAGCCC 59.498 66.667 5.01 0.00 35.95 5.19
3459 5686 2.284625 AGGTCATCGTGGAGCCCA 60.285 61.111 5.01 0.00 35.95 5.36
3460 5687 1.899437 GAGGTCATCGTGGAGCCCAA 61.899 60.000 0.00 0.00 34.18 4.12
3461 5688 1.450312 GGTCATCGTGGAGCCCAAG 60.450 63.158 0.00 0.00 34.18 3.61
3462 5689 1.596934 GTCATCGTGGAGCCCAAGA 59.403 57.895 11.08 11.08 45.06 3.02
3463 5690 0.741221 GTCATCGTGGAGCCCAAGAC 60.741 60.000 10.94 6.75 43.94 3.01
3464 5691 1.811266 CATCGTGGAGCCCAAGACG 60.811 63.158 10.94 4.71 43.94 4.18
3465 5692 3.019003 ATCGTGGAGCCCAAGACGG 62.019 63.158 10.94 0.00 43.94 4.79
3472 5699 3.195698 GCCCAAGACGGCGTCATC 61.196 66.667 37.71 19.13 39.64 2.92
3473 5700 2.264480 CCCAAGACGGCGTCATCA 59.736 61.111 37.71 0.00 34.60 3.07
3474 5701 2.100631 CCCAAGACGGCGTCATCAC 61.101 63.158 37.71 15.05 34.60 3.06
3475 5702 2.100631 CCAAGACGGCGTCATCACC 61.101 63.158 37.71 14.29 34.60 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
45 46 0.320697 ACTGAACCCGTGCCTAAGAC 59.679 55.000 0.00 0.00 0.00 3.01
62 63 2.040278 AGCAGGCAGGGCTCTACT 59.960 61.111 0.00 0.00 36.81 2.57
79 80 4.555709 ACAGCACGGCGGGTTTGA 62.556 61.111 19.71 0.00 0.00 2.69
89 90 2.789339 CGTAACTATGGATGACAGCACG 59.211 50.000 0.00 0.00 0.00 5.34
90 91 3.782046 ACGTAACTATGGATGACAGCAC 58.218 45.455 0.00 0.00 0.00 4.40
93 94 4.034048 GGCAAACGTAACTATGGATGACAG 59.966 45.833 0.00 0.00 0.00 3.51
254 255 4.707934 TGTCTCATGTCCGTTCTATTACCA 59.292 41.667 0.00 0.00 0.00 3.25
258 259 4.122776 GCATGTCTCATGTCCGTTCTATT 58.877 43.478 10.68 0.00 0.00 1.73
291 292 6.735130 AGCCTGTTTTGAATTGTACAACTAC 58.265 36.000 11.22 6.04 0.00 2.73
295 296 7.548097 TGTTTAGCCTGTTTTGAATTGTACAA 58.452 30.769 11.41 11.41 0.00 2.41
354 355 8.606040 AATCTTTTGGTTGGTTTCATACATTG 57.394 30.769 0.00 0.00 0.00 2.82
376 377 5.389935 CGTTCTGCCTTTCACTTGAGTAATC 60.390 44.000 0.00 0.00 0.00 1.75
448 771 0.110419 TTTCAGCAATTTCGACCGCG 60.110 50.000 0.00 0.00 39.35 6.46
518 841 5.643777 AGCGCATCTCTAGTGTTATTTGTTT 59.356 36.000 11.47 0.00 0.00 2.83
814 1142 9.136952 GGAAGAAATACGTCGTTATAGCATATT 57.863 33.333 1.78 0.00 0.00 1.28
876 1204 3.908213 TGGGAACTTAATTTTTCAGCGC 58.092 40.909 0.00 0.00 0.00 5.92
910 1238 4.407496 TTTTATACAAAACACCGAGCCG 57.593 40.909 0.00 0.00 0.00 5.52
963 1291 1.470494 GATGCGAGCGATGAGGATAGA 59.530 52.381 0.00 0.00 0.00 1.98
1011 1339 0.532573 TGAGGTGCTTGAGATCGGAC 59.467 55.000 0.00 0.00 0.00 4.79
1083 1411 3.934391 GACGGCGGCTGCTAGTGTT 62.934 63.158 18.85 0.00 42.25 3.32
1123 1451 1.202582 CTCGTCTATAGGGGCAATCCG 59.797 57.143 0.00 0.00 36.01 4.18
1169 1497 2.290960 GCCAAGAGTAGGTTGATGGGTT 60.291 50.000 0.00 0.00 0.00 4.11
1176 1504 0.036732 TGGCAGCCAAGAGTAGGTTG 59.963 55.000 13.33 0.00 39.98 3.77
1218 1546 5.938279 TGACGTATGAGGTAGGAGTAGATT 58.062 41.667 0.00 0.00 0.00 2.40
1373 1705 0.319900 AGAGCGCTCAATCACACGTT 60.320 50.000 36.87 11.42 0.00 3.99
1407 1739 2.652530 GCAGGTGGCACCAATGTG 59.347 61.111 36.28 26.06 41.95 3.21
1529 1861 1.153369 ACGTGGATCGCATCAAGGG 60.153 57.895 0.00 0.00 44.19 3.95
1609 1942 2.962253 GTCTCGCAGCGCATACCC 60.962 66.667 10.87 0.00 0.00 3.69
1614 1947 4.419939 ATGTCGTCTCGCAGCGCA 62.420 61.111 10.87 0.72 0.00 6.09
1625 1958 1.076533 GTTGATCACGCGGATGTCGT 61.077 55.000 12.47 0.00 41.72 4.34
1626 1959 1.631072 GTTGATCACGCGGATGTCG 59.369 57.895 12.47 0.00 36.00 4.35
1694 2027 2.950309 GGAATGATCTGCAGCATGTTCT 59.050 45.455 9.47 0.00 39.31 3.01
1762 2095 3.312421 CGCACATTCCCCTTGTAGTATTG 59.688 47.826 0.00 0.00 0.00 1.90
1853 2186 2.597510 GCTTGAACCGGGCCTTGT 60.598 61.111 6.32 0.00 0.00 3.16
1903 2236 1.153628 ACCGGTAAGCAGCGTCATC 60.154 57.895 4.49 0.00 44.06 2.92
1923 2256 4.122776 CAGGATCATCCTCTTGGTAAACG 58.877 47.826 1.94 0.00 45.66 3.60
1998 4190 0.537143 TCATGTTGGCCTTGAGCGTT 60.537 50.000 3.32 0.00 45.17 4.84
2413 4608 1.347243 TGGATGCAGCTAGCCCATGA 61.347 55.000 19.67 6.67 44.83 3.07
2489 4684 3.125487 TGTTGTAGTTTGTCCACGTTGTG 59.875 43.478 0.00 0.00 0.00 3.33
2491 4686 4.201871 ACATGTTGTAGTTTGTCCACGTTG 60.202 41.667 0.00 0.00 0.00 4.10
2492 4687 3.942748 ACATGTTGTAGTTTGTCCACGTT 59.057 39.130 0.00 0.00 0.00 3.99
2493 4688 3.311322 CACATGTTGTAGTTTGTCCACGT 59.689 43.478 0.00 0.00 0.00 4.49
2495 4690 5.493133 TTCACATGTTGTAGTTTGTCCAC 57.507 39.130 0.00 0.00 0.00 4.02
2533 4734 7.492994 GGTCCACTCAGCTAGTTTTATTCTTAG 59.507 40.741 0.00 0.00 35.76 2.18
2608 4809 6.451064 AGGAATTCCATAAAAACGTCCATC 57.549 37.500 26.22 0.00 38.89 3.51
2610 4811 7.573469 CGTTTAGGAATTCCATAAAAACGTCCA 60.573 37.037 32.27 12.97 40.71 4.02
2671 4875 8.314021 TGTAGTATTCTTTCTCTGAGCATTTGA 58.686 33.333 0.00 0.00 0.00 2.69
2672 4876 8.386606 GTGTAGTATTCTTTCTCTGAGCATTTG 58.613 37.037 0.00 0.00 0.00 2.32
2678 4882 7.079182 AGTCGTGTAGTATTCTTTCTCTGAG 57.921 40.000 0.00 0.00 0.00 3.35
2771 4983 9.719355 ACCTGTAGTTCAAAATTTTCAAACTTT 57.281 25.926 23.28 10.72 32.71 2.66
2799 5012 3.369175 TGGAGATGTGCTGTAGATGAGT 58.631 45.455 0.00 0.00 0.00 3.41
2800 5013 4.099113 TCTTGGAGATGTGCTGTAGATGAG 59.901 45.833 0.00 0.00 0.00 2.90
2807 5020 3.777106 TTCTTCTTGGAGATGTGCTGT 57.223 42.857 0.00 0.00 0.00 4.40
2929 5142 3.220110 CTGGATGCCAAGCAGATACATT 58.780 45.455 0.00 0.00 43.65 2.71
2937 5150 2.512692 ATTGTACTGGATGCCAAGCA 57.487 45.000 0.00 0.00 44.86 3.91
2943 5156 5.671493 ACTAGTGGTAATTGTACTGGATGC 58.329 41.667 0.00 0.00 0.00 3.91
2960 5187 5.923733 AATCTAAGGTGACTGGACTAGTG 57.076 43.478 0.00 0.00 42.68 2.74
2986 5213 7.279536 CACTTGCTGTACATGATAGATGACTTT 59.720 37.037 0.00 0.00 0.00 2.66
2990 5217 5.052481 GCACTTGCTGTACATGATAGATGA 58.948 41.667 0.00 0.00 38.21 2.92
3013 5240 9.383519 TCTATTTCATGCTAGAAAGGTAACAAG 57.616 33.333 0.00 0.00 40.49 3.16
3030 5257 6.276847 GCCGATAATCCTCGATCTATTTCAT 58.723 40.000 0.00 0.00 41.12 2.57
3048 5275 0.177141 CCTTTCCCAGAACGCCGATA 59.823 55.000 0.00 0.00 0.00 2.92
3051 5278 2.746277 CCCTTTCCCAGAACGCCG 60.746 66.667 0.00 0.00 0.00 6.46
3052 5279 2.361230 CCCCTTTCCCAGAACGCC 60.361 66.667 0.00 0.00 0.00 5.68
3053 5280 2.361230 CCCCCTTTCCCAGAACGC 60.361 66.667 0.00 0.00 0.00 4.84
3054 5281 1.002502 GACCCCCTTTCCCAGAACG 60.003 63.158 0.00 0.00 0.00 3.95
3055 5282 1.383019 GGACCCCCTTTCCCAGAAC 59.617 63.158 0.00 0.00 0.00 3.01
3056 5283 3.931707 GGACCCCCTTTCCCAGAA 58.068 61.111 0.00 0.00 0.00 3.02
3070 5297 2.360475 GCAGGCAAGTCTGGGGAC 60.360 66.667 3.62 0.00 42.41 4.46
3071 5298 3.650950 GGCAGGCAAGTCTGGGGA 61.651 66.667 3.62 0.00 35.43 4.81
3072 5299 3.655211 AGGCAGGCAAGTCTGGGG 61.655 66.667 3.62 0.00 35.43 4.96
3073 5300 2.360852 CAGGCAGGCAAGTCTGGG 60.361 66.667 3.62 0.00 37.58 4.45
3074 5301 3.060615 GCAGGCAGGCAAGTCTGG 61.061 66.667 12.46 0.00 41.45 3.86
3075 5302 3.429141 CGCAGGCAGGCAAGTCTG 61.429 66.667 7.14 7.14 43.93 3.51
3076 5303 4.711949 CCGCAGGCAGGCAAGTCT 62.712 66.667 0.00 0.00 46.14 3.24
3095 5322 2.100631 CCTTTGAGCCACGCCGTAG 61.101 63.158 0.00 0.00 0.00 3.51
3096 5323 2.047655 CCTTTGAGCCACGCCGTA 60.048 61.111 0.00 0.00 0.00 4.02
3104 5331 4.766632 CTGGGCCCCCTTTGAGCC 62.767 72.222 22.27 0.00 46.37 4.70
3106 5333 3.983420 TGCTGGGCCCCCTTTGAG 61.983 66.667 22.27 10.13 36.94 3.02
3107 5334 4.299796 GTGCTGGGCCCCCTTTGA 62.300 66.667 22.27 0.00 36.94 2.69
3117 5344 4.431131 AAGATGGGCCGTGCTGGG 62.431 66.667 1.02 0.00 38.63 4.45
3118 5345 2.825836 GAAGATGGGCCGTGCTGG 60.826 66.667 1.02 0.00 42.50 4.85
3119 5346 2.046023 TGAAGATGGGCCGTGCTG 60.046 61.111 1.02 0.00 0.00 4.41
3120 5347 2.045926 GTGAAGATGGGCCGTGCT 60.046 61.111 1.02 0.00 0.00 4.40
3121 5348 3.134127 GGTGAAGATGGGCCGTGC 61.134 66.667 1.02 0.00 0.00 5.34
3122 5349 1.303236 TTGGTGAAGATGGGCCGTG 60.303 57.895 1.02 0.00 0.00 4.94
3123 5350 1.303317 GTTGGTGAAGATGGGCCGT 60.303 57.895 0.00 0.00 0.00 5.68
3124 5351 1.303236 TGTTGGTGAAGATGGGCCG 60.303 57.895 0.00 0.00 0.00 6.13
3125 5352 0.539438 TGTGTTGGTGAAGATGGGCC 60.539 55.000 0.00 0.00 0.00 5.80
3126 5353 1.327303 TTGTGTTGGTGAAGATGGGC 58.673 50.000 0.00 0.00 0.00 5.36
3127 5354 2.035832 GGTTTGTGTTGGTGAAGATGGG 59.964 50.000 0.00 0.00 0.00 4.00
3128 5355 2.035832 GGGTTTGTGTTGGTGAAGATGG 59.964 50.000 0.00 0.00 0.00 3.51
3129 5356 2.692557 TGGGTTTGTGTTGGTGAAGATG 59.307 45.455 0.00 0.00 0.00 2.90
3130 5357 3.025322 TGGGTTTGTGTTGGTGAAGAT 57.975 42.857 0.00 0.00 0.00 2.40
3131 5358 2.516227 TGGGTTTGTGTTGGTGAAGA 57.484 45.000 0.00 0.00 0.00 2.87
3132 5359 2.757868 TCTTGGGTTTGTGTTGGTGAAG 59.242 45.455 0.00 0.00 0.00 3.02
3133 5360 2.494073 GTCTTGGGTTTGTGTTGGTGAA 59.506 45.455 0.00 0.00 0.00 3.18
3134 5361 2.096248 GTCTTGGGTTTGTGTTGGTGA 58.904 47.619 0.00 0.00 0.00 4.02
3135 5362 1.136110 GGTCTTGGGTTTGTGTTGGTG 59.864 52.381 0.00 0.00 0.00 4.17
3136 5363 1.480789 GGTCTTGGGTTTGTGTTGGT 58.519 50.000 0.00 0.00 0.00 3.67
3137 5364 0.750249 GGGTCTTGGGTTTGTGTTGG 59.250 55.000 0.00 0.00 0.00 3.77
3138 5365 1.681264 GAGGGTCTTGGGTTTGTGTTG 59.319 52.381 0.00 0.00 0.00 3.33
3139 5366 1.749286 CGAGGGTCTTGGGTTTGTGTT 60.749 52.381 0.00 0.00 0.00 3.32
3140 5367 0.179029 CGAGGGTCTTGGGTTTGTGT 60.179 55.000 0.00 0.00 0.00 3.72
3141 5368 1.515521 GCGAGGGTCTTGGGTTTGTG 61.516 60.000 0.00 0.00 0.00 3.33
3142 5369 1.228154 GCGAGGGTCTTGGGTTTGT 60.228 57.895 0.00 0.00 0.00 2.83
3143 5370 2.325082 CGCGAGGGTCTTGGGTTTG 61.325 63.158 0.00 0.00 0.00 2.93
3144 5371 2.032071 CGCGAGGGTCTTGGGTTT 59.968 61.111 0.00 0.00 0.00 3.27
3145 5372 2.920912 TCGCGAGGGTCTTGGGTT 60.921 61.111 3.71 0.00 0.00 4.11
3146 5373 3.382832 CTCGCGAGGGTCTTGGGT 61.383 66.667 28.40 0.00 0.00 4.51
3147 5374 4.148825 CCTCGCGAGGGTCTTGGG 62.149 72.222 41.47 19.14 44.87 4.12
3184 5411 4.117661 AGGAAGCTCCGCGTCGTC 62.118 66.667 4.92 1.45 42.75 4.20
3185 5412 4.117661 GAGGAAGCTCCGCGTCGT 62.118 66.667 4.92 0.00 42.75 4.34
3186 5413 4.116328 TGAGGAAGCTCCGCGTCG 62.116 66.667 4.92 0.00 42.75 5.12
3187 5414 2.202676 CTGAGGAAGCTCCGCGTC 60.203 66.667 4.92 0.00 42.75 5.19
3188 5415 3.764466 CCTGAGGAAGCTCCGCGT 61.764 66.667 4.92 0.00 42.75 6.01
3190 5417 4.087892 TGCCTGAGGAAGCTCCGC 62.088 66.667 0.65 0.00 42.75 5.54
3191 5418 2.125350 GTGCCTGAGGAAGCTCCG 60.125 66.667 0.65 0.00 42.75 4.63
3192 5419 2.125350 CGTGCCTGAGGAAGCTCC 60.125 66.667 0.65 0.00 36.58 4.70
3193 5420 2.125350 CCGTGCCTGAGGAAGCTC 60.125 66.667 0.65 0.00 0.00 4.09
3194 5421 4.400961 GCCGTGCCTGAGGAAGCT 62.401 66.667 0.65 0.00 0.00 3.74
3211 5438 1.153208 GTGAGCCAGCCTGATGAGG 60.153 63.158 0.00 0.00 43.19 3.86
3212 5439 1.521010 CGTGAGCCAGCCTGATGAG 60.521 63.158 0.00 0.00 0.00 2.90
3213 5440 1.953231 CTCGTGAGCCAGCCTGATGA 61.953 60.000 0.00 0.00 0.00 2.92
3214 5441 1.521010 CTCGTGAGCCAGCCTGATG 60.521 63.158 0.00 0.00 0.00 3.07
3215 5442 2.729479 CCTCGTGAGCCAGCCTGAT 61.729 63.158 0.00 0.00 0.00 2.90
3216 5443 3.385384 CCTCGTGAGCCAGCCTGA 61.385 66.667 0.00 0.00 0.00 3.86
3217 5444 4.463879 CCCTCGTGAGCCAGCCTG 62.464 72.222 0.00 0.00 0.00 4.85
3228 5455 4.144727 ATCTCTCCGCCCCCTCGT 62.145 66.667 0.00 0.00 0.00 4.18
3229 5456 3.299190 GATCTCTCCGCCCCCTCG 61.299 72.222 0.00 0.00 0.00 4.63
3230 5457 1.753368 CTTGATCTCTCCGCCCCCTC 61.753 65.000 0.00 0.00 0.00 4.30
3231 5458 1.764054 CTTGATCTCTCCGCCCCCT 60.764 63.158 0.00 0.00 0.00 4.79
3232 5459 2.812619 CCTTGATCTCTCCGCCCCC 61.813 68.421 0.00 0.00 0.00 5.40
3233 5460 1.753368 CTCCTTGATCTCTCCGCCCC 61.753 65.000 0.00 0.00 0.00 5.80
3234 5461 1.745264 CTCCTTGATCTCTCCGCCC 59.255 63.158 0.00 0.00 0.00 6.13
3235 5462 1.745264 CCTCCTTGATCTCTCCGCC 59.255 63.158 0.00 0.00 0.00 6.13
3236 5463 1.745264 CCCTCCTTGATCTCTCCGC 59.255 63.158 0.00 0.00 0.00 5.54
3237 5464 0.397816 ACCCCTCCTTGATCTCTCCG 60.398 60.000 0.00 0.00 0.00 4.63
3238 5465 2.321719 GTACCCCTCCTTGATCTCTCC 58.678 57.143 0.00 0.00 0.00 3.71
3239 5466 2.090999 AGGTACCCCTCCTTGATCTCTC 60.091 54.545 8.74 0.00 35.62 3.20
3240 5467 1.940957 AGGTACCCCTCCTTGATCTCT 59.059 52.381 8.74 0.00 35.62 3.10
3241 5468 2.480642 AGGTACCCCTCCTTGATCTC 57.519 55.000 8.74 0.00 35.62 2.75
3276 5503 3.088500 GAGTCGTCATGGCTTGCGC 62.089 63.158 0.00 0.00 0.00 6.09
3277 5504 1.690283 CTGAGTCGTCATGGCTTGCG 61.690 60.000 0.00 9.67 30.18 4.85
3278 5505 1.364626 CCTGAGTCGTCATGGCTTGC 61.365 60.000 0.00 0.00 30.18 4.01
3279 5506 0.742281 CCCTGAGTCGTCATGGCTTG 60.742 60.000 0.00 0.00 32.38 4.01
3280 5507 1.599047 CCCTGAGTCGTCATGGCTT 59.401 57.895 0.00 0.00 32.38 4.35
3281 5508 3.303189 CCCTGAGTCGTCATGGCT 58.697 61.111 0.00 0.00 32.38 4.75
3283 5510 2.202797 CGCCCTGAGTCGTCATGG 60.203 66.667 0.00 0.00 40.55 3.66
3284 5511 2.887568 GCGCCCTGAGTCGTCATG 60.888 66.667 0.00 0.00 30.18 3.07
3285 5512 4.148825 GGCGCCCTGAGTCGTCAT 62.149 66.667 18.11 0.00 30.18 3.06
3287 5514 4.803426 CTGGCGCCCTGAGTCGTC 62.803 72.222 26.77 0.00 0.00 4.20
3319 5546 3.491652 GAAAGGAGGACGCTGCGC 61.492 66.667 23.51 14.60 0.00 6.09
3320 5547 2.815647 GGAAAGGAGGACGCTGCG 60.816 66.667 21.91 21.91 0.00 5.18
3321 5548 1.448717 GAGGAAAGGAGGACGCTGC 60.449 63.158 0.00 0.00 0.00 5.25
3322 5549 0.610687 AAGAGGAAAGGAGGACGCTG 59.389 55.000 0.00 0.00 0.00 5.18
3323 5550 1.002544 CAAAGAGGAAAGGAGGACGCT 59.997 52.381 0.00 0.00 0.00 5.07
3324 5551 1.443802 CAAAGAGGAAAGGAGGACGC 58.556 55.000 0.00 0.00 0.00 5.19
3325 5552 1.348036 ACCAAAGAGGAAAGGAGGACG 59.652 52.381 0.00 0.00 41.22 4.79
3326 5553 2.784347 CACCAAAGAGGAAAGGAGGAC 58.216 52.381 0.00 0.00 41.22 3.85
3327 5554 1.073923 GCACCAAAGAGGAAAGGAGGA 59.926 52.381 0.00 0.00 41.22 3.71
3328 5555 1.202927 TGCACCAAAGAGGAAAGGAGG 60.203 52.381 0.00 0.00 41.22 4.30
3329 5556 2.276732 TGCACCAAAGAGGAAAGGAG 57.723 50.000 0.00 0.00 41.22 3.69
3330 5557 2.746279 TTGCACCAAAGAGGAAAGGA 57.254 45.000 0.00 0.00 41.22 3.36
3340 5567 1.690633 TTGCCCCCTTTGCACCAAA 60.691 52.632 0.00 0.00 38.72 3.28
3341 5568 2.041508 TTGCCCCCTTTGCACCAA 60.042 55.556 0.00 0.00 38.72 3.67
3342 5569 2.523902 CTTGCCCCCTTTGCACCA 60.524 61.111 0.00 0.00 38.72 4.17
3343 5570 4.007644 GCTTGCCCCCTTTGCACC 62.008 66.667 0.00 0.00 38.72 5.01
3344 5571 4.362476 CGCTTGCCCCCTTTGCAC 62.362 66.667 0.00 0.00 38.72 4.57
3347 5574 4.060038 CTGCGCTTGCCCCCTTTG 62.060 66.667 9.73 0.00 38.03 2.77
3369 5596 1.742768 CCTGATGCCTCGGTACTCC 59.257 63.158 0.00 0.00 0.00 3.85
3370 5597 1.068250 GCCTGATGCCTCGGTACTC 59.932 63.158 0.00 0.00 0.00 2.59
3371 5598 1.264749 TTGCCTGATGCCTCGGTACT 61.265 55.000 0.00 0.00 40.16 2.73
3372 5599 0.392461 TTTGCCTGATGCCTCGGTAC 60.392 55.000 0.00 0.00 40.16 3.34
3373 5600 0.107703 CTTTGCCTGATGCCTCGGTA 60.108 55.000 0.00 0.00 40.16 4.02
3374 5601 1.377725 CTTTGCCTGATGCCTCGGT 60.378 57.895 0.00 0.00 40.16 4.69
3375 5602 2.117156 CCTTTGCCTGATGCCTCGG 61.117 63.158 0.00 0.00 40.16 4.63
3376 5603 0.962356 AACCTTTGCCTGATGCCTCG 60.962 55.000 0.00 0.00 40.16 4.63
3377 5604 0.529378 CAACCTTTGCCTGATGCCTC 59.471 55.000 0.00 0.00 40.16 4.70
3378 5605 2.662309 CAACCTTTGCCTGATGCCT 58.338 52.632 0.00 0.00 40.16 4.75
3388 5615 1.782044 CACCGAAATGGCAACCTTTG 58.218 50.000 0.00 0.00 43.94 2.77
3389 5616 0.033366 GCACCGAAATGGCAACCTTT 59.967 50.000 0.00 0.00 43.94 3.11
3390 5617 1.112315 TGCACCGAAATGGCAACCTT 61.112 50.000 0.00 0.00 43.94 3.50
3391 5618 1.112315 TTGCACCGAAATGGCAACCT 61.112 50.000 0.00 0.00 42.12 3.50
3392 5619 1.365633 TTGCACCGAAATGGCAACC 59.634 52.632 0.00 0.00 42.12 3.77
3394 5621 1.007964 CGTTGCACCGAAATGGCAA 60.008 52.632 0.00 0.00 44.50 4.52
3395 5622 1.851021 CTCGTTGCACCGAAATGGCA 61.851 55.000 8.00 0.00 43.94 4.92
3396 5623 1.154225 CTCGTTGCACCGAAATGGC 60.154 57.895 8.00 0.00 43.94 4.40
3397 5624 0.165944 GTCTCGTTGCACCGAAATGG 59.834 55.000 8.00 0.00 46.41 3.16
3398 5625 0.165944 GGTCTCGTTGCACCGAAATG 59.834 55.000 8.00 0.00 36.24 2.32
3399 5626 0.250124 TGGTCTCGTTGCACCGAAAT 60.250 50.000 8.00 0.00 36.24 2.17
3400 5627 0.462225 TTGGTCTCGTTGCACCGAAA 60.462 50.000 8.00 0.00 36.24 3.46
3401 5628 0.878523 CTTGGTCTCGTTGCACCGAA 60.879 55.000 8.00 0.00 36.24 4.30
3402 5629 1.300620 CTTGGTCTCGTTGCACCGA 60.301 57.895 6.10 6.10 35.15 4.69
3403 5630 1.300620 TCTTGGTCTCGTTGCACCG 60.301 57.895 0.00 0.00 35.15 4.94
3404 5631 1.228657 GGTCTTGGTCTCGTTGCACC 61.229 60.000 0.00 0.00 0.00 5.01
3405 5632 0.531974 TGGTCTTGGTCTCGTTGCAC 60.532 55.000 0.00 0.00 0.00 4.57
3406 5633 0.249868 CTGGTCTTGGTCTCGTTGCA 60.250 55.000 0.00 0.00 0.00 4.08
3407 5634 0.951040 CCTGGTCTTGGTCTCGTTGC 60.951 60.000 0.00 0.00 0.00 4.17
3408 5635 0.679505 TCCTGGTCTTGGTCTCGTTG 59.320 55.000 0.00 0.00 0.00 4.10
3409 5636 0.969894 CTCCTGGTCTTGGTCTCGTT 59.030 55.000 0.00 0.00 0.00 3.85
3410 5637 0.900647 CCTCCTGGTCTTGGTCTCGT 60.901 60.000 0.00 0.00 0.00 4.18
3411 5638 0.612174 TCCTCCTGGTCTTGGTCTCG 60.612 60.000 0.00 0.00 34.23 4.04
3412 5639 0.899019 GTCCTCCTGGTCTTGGTCTC 59.101 60.000 0.00 0.00 34.23 3.36
3413 5640 0.489567 AGTCCTCCTGGTCTTGGTCT 59.510 55.000 0.00 0.00 34.23 3.85
3414 5641 1.826096 GTAGTCCTCCTGGTCTTGGTC 59.174 57.143 0.00 0.00 33.85 4.02
3415 5642 1.891450 CGTAGTCCTCCTGGTCTTGGT 60.891 57.143 0.00 0.00 33.85 3.67
3416 5643 0.818296 CGTAGTCCTCCTGGTCTTGG 59.182 60.000 0.00 0.00 33.85 3.61
3417 5644 1.746220 CTCGTAGTCCTCCTGGTCTTG 59.254 57.143 0.00 0.00 33.85 3.02
3418 5645 1.634459 TCTCGTAGTCCTCCTGGTCTT 59.366 52.381 0.00 0.00 33.85 3.01
3419 5646 1.065272 GTCTCGTAGTCCTCCTGGTCT 60.065 57.143 0.00 0.00 35.89 3.85
3420 5647 1.381522 GTCTCGTAGTCCTCCTGGTC 58.618 60.000 0.00 0.00 34.23 4.02
3421 5648 0.392729 CGTCTCGTAGTCCTCCTGGT 60.393 60.000 0.00 0.00 34.23 4.00
3422 5649 1.096386 CCGTCTCGTAGTCCTCCTGG 61.096 65.000 0.00 0.00 0.00 4.45
3423 5650 0.107800 TCCGTCTCGTAGTCCTCCTG 60.108 60.000 0.00 0.00 0.00 3.86
3424 5651 0.178533 CTCCGTCTCGTAGTCCTCCT 59.821 60.000 0.00 0.00 0.00 3.69
3425 5652 0.814812 CCTCCGTCTCGTAGTCCTCC 60.815 65.000 0.00 0.00 0.00 4.30
3426 5653 0.107752 ACCTCCGTCTCGTAGTCCTC 60.108 60.000 0.00 0.00 0.00 3.71
3427 5654 0.107752 GACCTCCGTCTCGTAGTCCT 60.108 60.000 0.00 0.00 35.99 3.85
3428 5655 0.392193 TGACCTCCGTCTCGTAGTCC 60.392 60.000 0.00 0.00 39.94 3.85
3429 5656 1.598601 GATGACCTCCGTCTCGTAGTC 59.401 57.143 0.00 0.00 39.94 2.59
3430 5657 1.666054 GATGACCTCCGTCTCGTAGT 58.334 55.000 0.00 0.00 39.94 2.73
3431 5658 0.582482 CGATGACCTCCGTCTCGTAG 59.418 60.000 0.00 0.00 39.94 3.51
3432 5659 0.107993 ACGATGACCTCCGTCTCGTA 60.108 55.000 12.67 0.00 44.05 3.43
3433 5660 1.376942 ACGATGACCTCCGTCTCGT 60.377 57.895 10.07 10.07 42.61 4.18
3434 5661 1.062685 CACGATGACCTCCGTCTCG 59.937 63.158 0.00 9.17 41.42 4.04
3435 5662 1.030488 TCCACGATGACCTCCGTCTC 61.030 60.000 0.00 0.00 39.94 3.36
3436 5663 1.001269 TCCACGATGACCTCCGTCT 60.001 57.895 0.00 0.00 39.94 4.18
3437 5664 1.433879 CTCCACGATGACCTCCGTC 59.566 63.158 0.00 0.00 36.83 4.79
3438 5665 2.711922 GCTCCACGATGACCTCCGT 61.712 63.158 0.00 0.00 39.88 4.69
3439 5666 2.105128 GCTCCACGATGACCTCCG 59.895 66.667 0.00 0.00 0.00 4.63
3440 5667 2.501610 GGCTCCACGATGACCTCC 59.498 66.667 0.00 0.00 0.00 4.30
3441 5668 1.899437 TTGGGCTCCACGATGACCTC 61.899 60.000 0.00 0.00 30.78 3.85
3442 5669 1.903877 CTTGGGCTCCACGATGACCT 61.904 60.000 0.00 0.00 30.78 3.85
3443 5670 1.450312 CTTGGGCTCCACGATGACC 60.450 63.158 0.00 0.00 30.78 4.02
3444 5671 0.741221 GTCTTGGGCTCCACGATGAC 60.741 60.000 4.20 3.28 34.39 3.06
3445 5672 1.596934 GTCTTGGGCTCCACGATGA 59.403 57.895 4.20 0.00 34.39 2.92
3446 5673 1.811266 CGTCTTGGGCTCCACGATG 60.811 63.158 4.20 5.06 34.39 3.84
3447 5674 2.579201 CGTCTTGGGCTCCACGAT 59.421 61.111 4.20 0.00 34.39 3.73
3448 5675 3.691342 CCGTCTTGGGCTCCACGA 61.691 66.667 1.59 0.00 30.78 4.35
3456 5683 2.100631 GTGATGACGCCGTCTTGGG 61.101 63.158 19.12 0.00 38.63 4.12
3457 5684 2.100631 GGTGATGACGCCGTCTTGG 61.101 63.158 19.12 0.00 42.50 3.61
3458 5685 3.474806 GGTGATGACGCCGTCTTG 58.525 61.111 19.12 0.00 36.93 3.02


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

AutoCloner maintained by Alex Coulton.