Multiple sequence alignment - TraesCS4D01G276200

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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 TraesCS4D01G276200 chr4D 100.000 3539 0 0 1 3539 447340900 447337362 0.000000e+00 6536.0
1 TraesCS4D01G276200 chr4D 87.500 64 7 1 3229 3291 355001351 355001288 4.900000e-09 73.1
2 TraesCS4D01G276200 chr4B 96.714 2861 75 8 1 2857 559857547 559854702 0.000000e+00 4745.0
3 TraesCS4D01G276200 chr4B 92.920 226 9 3 2841 3059 559854547 559854322 4.410000e-84 322.0
4 TraesCS4D01G276200 chr4B 83.951 162 7 5 3080 3241 559845404 559845262 1.710000e-28 137.0
5 TraesCS4D01G276200 chr4A 94.417 2042 95 8 659 2691 19658220 19660251 0.000000e+00 3121.0
6 TraesCS4D01G276200 chr4A 96.684 392 12 1 2693 3084 19660336 19660726 0.000000e+00 651.0
7 TraesCS4D01G276200 chr4A 87.591 548 42 15 1 531 19657624 19658162 2.340000e-171 612.0
8 TraesCS4D01G276200 chr4A 91.358 162 9 2 3080 3241 19660915 19661071 2.140000e-52 217.0
9 TraesCS4D01G276200 chr4A 97.368 38 1 0 3232 3269 96743661 96743624 8.200000e-07 65.8
10 TraesCS4D01G276200 chr6A 85.283 265 25 5 3240 3490 535277879 535278143 9.740000e-66 261.0
11 TraesCS4D01G276200 chr3A 80.812 271 39 10 3233 3490 717806581 717806851 2.150000e-47 200.0
12 TraesCS4D01G276200 chr5D 88.136 59 6 1 3241 3298 178550929 178550871 6.340000e-08 69.4
13 TraesCS4D01G276200 chr5D 100.000 28 0 0 342 369 522494658 522494685 6.000000e-03 52.8
14 TraesCS4D01G276200 chr5A 84.375 64 9 1 3236 3298 188995467 188995530 1.060000e-05 62.1
15 TraesCS4D01G276200 chr2B 92.683 41 3 0 3240 3280 13041923 13041883 3.820000e-05 60.2
16 TraesCS4D01G276200 chr1B 92.857 42 1 1 3230 3269 80957228 80957269 3.820000e-05 60.2
17 TraesCS4D01G276200 chr1B 100.000 29 0 0 3241 3269 17263270 17263298 2.000000e-03 54.7
18 TraesCS4D01G276200 chr7D 84.483 58 5 2 3242 3298 625770078 625770024 2.000000e-03 54.7


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 TraesCS4D01G276200 chr4D 447337362 447340900 3538 True 6536.00 6536 100.0000 1 3539 1 chr4D.!!$R2 3538
1 TraesCS4D01G276200 chr4B 559854322 559857547 3225 True 2533.50 4745 94.8170 1 3059 2 chr4B.!!$R2 3058
2 TraesCS4D01G276200 chr4A 19657624 19661071 3447 False 1150.25 3121 92.5125 1 3241 4 chr4A.!!$F1 3240

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
550 577 1.028905 CCTTTTTGCCGACCTCACAA 58.971 50.0 0.00 0.0 0.00 3.33 F
1186 1215 0.526739 TCGCCATCGTGGTTCGTATG 60.527 55.0 6.02 0.0 40.46 2.39 F
2124 2161 0.387565 CCAACCAAGAAAACACCGGG 59.612 55.0 6.32 0.0 0.00 5.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1640 1677 0.025898 CATGATCTGCAGTGTTCGCG 59.974 55.0 14.67 0.0 0.00 5.87 R
2487 2524 0.668535 TCAGCCATAGATCACCGTCG 59.331 55.0 0.00 0.0 0.00 5.12 R
3387 3878 0.033601 AGGCACAAGTTTGGTGACCA 60.034 50.0 0.00 0.0 45.61 4.02 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
329 333 6.529220 AGCCCTCTGTCATTTATCTGAATAC 58.471 40.000 0.00 0.00 0.00 1.89
550 577 1.028905 CCTTTTTGCCGACCTCACAA 58.971 50.000 0.00 0.00 0.00 3.33
649 676 6.100004 TGTTATCTGTTGTCCGAAAGAGATC 58.900 40.000 7.90 0.00 38.91 2.75
856 883 3.127533 GGGCTACTGGCTTGTGCG 61.128 66.667 0.00 0.00 41.46 5.34
999 1028 2.499289 AGTGAGACTTCCAGCCATACAG 59.501 50.000 0.00 0.00 0.00 2.74
1090 1119 4.457603 TCAATAACCCAACCACTTCATTCG 59.542 41.667 0.00 0.00 0.00 3.34
1121 1150 1.610522 GCTTGATCTTGCAACACCACT 59.389 47.619 0.00 0.00 0.00 4.00
1137 1166 6.590234 ACACCACTCCTTCCATTTAATTTC 57.410 37.500 0.00 0.00 0.00 2.17
1186 1215 0.526739 TCGCCATCGTGGTTCGTATG 60.527 55.000 6.02 0.00 40.46 2.39
1369 1398 6.509418 TCAACAAGGGCATCTATTTGTAAC 57.491 37.500 0.00 0.00 33.70 2.50
1640 1677 5.886960 AGAACATCAGCTTCATTGTAACC 57.113 39.130 0.00 0.00 0.00 2.85
1699 1736 2.005451 CATGCACCTTGAGTAGCACTC 58.995 52.381 8.75 8.75 45.26 3.51
1771 1808 2.887568 GATGTCGGTGCTCAGGCG 60.888 66.667 0.00 0.00 42.25 5.52
1975 2012 3.584733 AGGACTGGAAGAAAAAGCACT 57.415 42.857 0.00 0.00 37.43 4.40
1981 2018 4.336713 ACTGGAAGAAAAAGCACTGAGTTC 59.663 41.667 0.00 0.00 37.43 3.01
2091 2128 3.402110 CATCACAGGTTCAGTTACTGCA 58.598 45.455 7.61 0.00 35.70 4.41
2110 2147 2.127232 CATGCCCGGGAATCCAACC 61.127 63.158 29.31 3.60 0.00 3.77
2124 2161 0.387565 CCAACCAAGAAAACACCGGG 59.612 55.000 6.32 0.00 0.00 5.73
2151 2188 0.534877 TTGTCAACTGCAGCATCGGT 60.535 50.000 15.27 0.00 0.00 4.69
2294 2331 3.117169 AGAGATCAGTATGCCTCTCCTGT 60.117 47.826 0.00 0.00 42.16 4.00
2487 2524 7.816640 TGCCTTACTTGAACACATCTTTTATC 58.183 34.615 0.00 0.00 0.00 1.75
2691 2728 9.865321 AGTACATCATTTGGAATTTCAGAAATG 57.135 29.630 9.24 18.33 37.21 2.32
2951 3242 2.606795 CCTGCTATCTACTCTGCGCTTC 60.607 54.545 9.73 0.00 0.00 3.86
2952 3243 1.002359 TGCTATCTACTCTGCGCTTCG 60.002 52.381 9.73 0.00 0.00 3.79
2983 3274 6.486253 TCAGCTGAACAGTTCATTTACATC 57.514 37.500 15.67 1.30 39.30 3.06
3110 3601 8.822855 CCATACATAAATCAAAGTAACGCTACA 58.177 33.333 0.00 0.00 0.00 2.74
3119 3610 7.816945 TCAAAGTAACGCTACAATAGTTACC 57.183 36.000 12.33 0.00 46.63 2.85
3133 3624 7.809665 ACAATAGTTACCCATAACACGAAAAC 58.190 34.615 0.00 0.00 42.83 2.43
3143 3634 5.059221 CCATAACACGAAAACGCAATTTCTC 59.941 40.000 8.92 0.00 37.20 2.87
3147 3638 2.477375 ACGAAAACGCAATTTCTCGCTA 59.523 40.909 8.92 0.00 37.20 4.26
3170 3661 3.328382 TGCAAGTAATAGTGGTCGCTT 57.672 42.857 0.00 0.00 0.00 4.68
3175 3666 1.852895 GTAATAGTGGTCGCTTGCTCG 59.147 52.381 0.00 0.00 0.00 5.03
3176 3667 1.084370 AATAGTGGTCGCTTGCTCGC 61.084 55.000 0.00 0.00 0.00 5.03
3177 3668 2.907897 ATAGTGGTCGCTTGCTCGCC 62.908 60.000 0.00 0.00 0.00 5.54
3200 3691 2.515901 GGTGCCCTGTTGTGGTCT 59.484 61.111 0.00 0.00 0.00 3.85
3218 3709 4.101119 TGGTCTAGGCCAATAGCTAAACTC 59.899 45.833 15.36 0.00 43.05 3.01
3227 3718 2.838386 TAGCTAAACTCGCCTACACG 57.162 50.000 0.00 0.00 0.00 4.49
3256 3747 7.542534 TTTTGTTTACTAGTACATATGCCCG 57.457 36.000 0.91 0.00 0.00 6.13
3257 3748 5.857471 TGTTTACTAGTACATATGCCCGT 57.143 39.130 0.91 0.00 0.00 5.28
3258 3749 5.593968 TGTTTACTAGTACATATGCCCGTG 58.406 41.667 0.91 0.00 0.00 4.94
3259 3750 2.814280 ACTAGTACATATGCCCGTGC 57.186 50.000 1.58 0.00 38.26 5.34
3260 3751 1.000607 ACTAGTACATATGCCCGTGCG 60.001 52.381 1.58 0.00 41.78 5.34
3261 3752 1.000607 CTAGTACATATGCCCGTGCGT 60.001 52.381 1.58 0.00 41.78 5.24
3262 3753 0.177141 AGTACATATGCCCGTGCGTT 59.823 50.000 1.58 0.00 41.78 4.84
3263 3754 0.303493 GTACATATGCCCGTGCGTTG 59.697 55.000 1.58 0.00 41.78 4.10
3264 3755 1.433053 TACATATGCCCGTGCGTTGC 61.433 55.000 1.58 0.00 41.78 4.17
3265 3756 2.437537 ATATGCCCGTGCGTTGCA 60.438 55.556 8.11 8.11 41.78 4.08
3266 3757 2.043405 ATATGCCCGTGCGTTGCAA 61.043 52.632 0.00 0.00 41.47 4.08
3267 3758 2.265073 ATATGCCCGTGCGTTGCAAC 62.265 55.000 19.89 19.89 41.47 4.17
3283 3774 4.355543 TGCAACGAAAGAGATAATTGGC 57.644 40.909 0.00 0.00 0.00 4.52
3284 3775 3.181511 TGCAACGAAAGAGATAATTGGCG 60.182 43.478 0.00 0.00 0.00 5.69
3285 3776 3.181510 GCAACGAAAGAGATAATTGGCGT 60.182 43.478 0.00 0.00 0.00 5.68
3286 3777 4.334443 CAACGAAAGAGATAATTGGCGTG 58.666 43.478 0.00 0.00 0.00 5.34
3287 3778 3.596214 ACGAAAGAGATAATTGGCGTGT 58.404 40.909 0.00 0.00 0.00 4.49
3288 3779 3.617263 ACGAAAGAGATAATTGGCGTGTC 59.383 43.478 0.00 0.00 0.00 3.67
3289 3780 3.001330 CGAAAGAGATAATTGGCGTGTCC 59.999 47.826 0.00 0.00 0.00 4.02
3290 3781 3.627395 AAGAGATAATTGGCGTGTCCA 57.373 42.857 0.00 0.00 44.85 4.02
3291 3782 2.906354 AGAGATAATTGGCGTGTCCAC 58.094 47.619 0.00 0.00 46.55 4.02
3292 3783 2.236146 AGAGATAATTGGCGTGTCCACA 59.764 45.455 0.00 0.00 46.55 4.17
3293 3784 3.006940 GAGATAATTGGCGTGTCCACAA 58.993 45.455 0.00 0.00 46.55 3.33
3294 3785 3.417101 AGATAATTGGCGTGTCCACAAA 58.583 40.909 0.00 0.00 46.55 2.83
3295 3786 3.823873 AGATAATTGGCGTGTCCACAAAA 59.176 39.130 0.00 0.00 46.55 2.44
3296 3787 4.462483 AGATAATTGGCGTGTCCACAAAAT 59.538 37.500 0.00 0.00 46.55 1.82
3297 3788 2.437200 ATTGGCGTGTCCACAAAATG 57.563 45.000 0.00 0.00 46.55 2.32
3310 3801 5.138125 CCACAAAATGGCATTTACAGAGT 57.862 39.130 24.58 15.01 43.24 3.24
3311 3802 4.925054 CCACAAAATGGCATTTACAGAGTG 59.075 41.667 24.58 22.89 43.24 3.51
3312 3803 5.278907 CCACAAAATGGCATTTACAGAGTGA 60.279 40.000 24.58 0.00 43.24 3.41
3313 3804 5.860182 CACAAAATGGCATTTACAGAGTGAG 59.140 40.000 24.58 13.03 0.00 3.51
3314 3805 5.047802 ACAAAATGGCATTTACAGAGTGAGG 60.048 40.000 24.58 7.82 0.00 3.86
3315 3806 4.574674 AATGGCATTTACAGAGTGAGGA 57.425 40.909 6.96 0.00 0.00 3.71
3316 3807 3.616956 TGGCATTTACAGAGTGAGGAG 57.383 47.619 0.00 0.00 0.00 3.69
3317 3808 2.906389 TGGCATTTACAGAGTGAGGAGT 59.094 45.455 0.00 0.00 0.00 3.85
3318 3809 3.055819 TGGCATTTACAGAGTGAGGAGTC 60.056 47.826 0.00 0.00 0.00 3.36
3319 3810 3.182967 GCATTTACAGAGTGAGGAGTCG 58.817 50.000 0.00 0.00 0.00 4.18
3320 3811 3.182967 CATTTACAGAGTGAGGAGTCGC 58.817 50.000 0.00 0.00 0.00 5.19
3321 3812 0.803117 TTACAGAGTGAGGAGTCGCG 59.197 55.000 0.00 0.00 38.32 5.87
3322 3813 1.025113 TACAGAGTGAGGAGTCGCGG 61.025 60.000 6.13 0.00 38.32 6.46
3323 3814 2.034376 AGAGTGAGGAGTCGCGGT 59.966 61.111 6.13 0.00 38.32 5.68
3324 3815 2.041686 AGAGTGAGGAGTCGCGGTC 61.042 63.158 6.13 3.15 38.32 4.79
3325 3816 2.034376 AGTGAGGAGTCGCGGTCT 59.966 61.111 6.13 5.20 38.32 3.85
3326 3817 1.587933 GAGTGAGGAGTCGCGGTCTT 61.588 60.000 6.13 0.00 38.32 3.01
3327 3818 1.153997 GTGAGGAGTCGCGGTCTTC 60.154 63.158 6.13 10.32 0.00 2.87
3328 3819 1.303398 TGAGGAGTCGCGGTCTTCT 60.303 57.895 17.80 15.00 0.00 2.85
3329 3820 1.306642 TGAGGAGTCGCGGTCTTCTC 61.307 60.000 23.73 23.73 37.88 2.87
3330 3821 2.100603 GGAGTCGCGGTCTTCTCG 59.899 66.667 6.13 0.00 0.00 4.04
3337 3828 2.962569 CGGTCTTCTCGCAGGTCA 59.037 61.111 0.00 0.00 0.00 4.02
3338 3829 1.513158 CGGTCTTCTCGCAGGTCAT 59.487 57.895 0.00 0.00 0.00 3.06
3339 3830 0.803768 CGGTCTTCTCGCAGGTCATG 60.804 60.000 0.00 0.00 0.00 3.07
3340 3831 0.247736 GGTCTTCTCGCAGGTCATGT 59.752 55.000 0.00 0.00 0.00 3.21
3341 3832 1.354040 GTCTTCTCGCAGGTCATGTG 58.646 55.000 0.00 0.00 41.00 3.21
3342 3833 0.969149 TCTTCTCGCAGGTCATGTGT 59.031 50.000 0.00 0.00 40.47 3.72
3343 3834 1.344438 TCTTCTCGCAGGTCATGTGTT 59.656 47.619 0.00 0.00 40.47 3.32
3344 3835 1.462283 CTTCTCGCAGGTCATGTGTTG 59.538 52.381 0.00 0.00 40.47 3.33
3345 3836 0.950555 TCTCGCAGGTCATGTGTTGC 60.951 55.000 0.00 0.37 40.47 4.17
3346 3837 1.915614 CTCGCAGGTCATGTGTTGCC 61.916 60.000 10.76 0.56 40.47 4.52
3347 3838 2.260154 CGCAGGTCATGTGTTGCCA 61.260 57.895 10.76 0.00 34.56 4.92
3348 3839 1.582968 GCAGGTCATGTGTTGCCAG 59.417 57.895 0.00 0.00 0.00 4.85
3349 3840 1.582968 CAGGTCATGTGTTGCCAGC 59.417 57.895 0.00 0.00 0.00 4.85
3350 3841 1.151221 AGGTCATGTGTTGCCAGCA 59.849 52.632 0.00 0.00 0.00 4.41
3351 3842 0.467844 AGGTCATGTGTTGCCAGCAA 60.468 50.000 0.00 0.00 0.00 3.91
3352 3843 0.038892 GGTCATGTGTTGCCAGCAAG 60.039 55.000 5.07 0.00 36.52 4.01
3353 3844 0.953727 GTCATGTGTTGCCAGCAAGA 59.046 50.000 5.07 0.93 36.52 3.02
3354 3845 1.542915 GTCATGTGTTGCCAGCAAGAT 59.457 47.619 5.07 0.00 36.52 2.40
3355 3846 1.814394 TCATGTGTTGCCAGCAAGATC 59.186 47.619 5.07 0.82 36.52 2.75
3356 3847 1.816835 CATGTGTTGCCAGCAAGATCT 59.183 47.619 5.07 0.00 36.52 2.75
3357 3848 1.985473 TGTGTTGCCAGCAAGATCTT 58.015 45.000 5.07 0.88 36.52 2.40
3358 3849 1.610038 TGTGTTGCCAGCAAGATCTTG 59.390 47.619 27.82 27.82 43.14 3.02
3359 3850 1.068055 GTGTTGCCAGCAAGATCTTGG 60.068 52.381 31.41 20.15 40.74 3.61
3368 3859 3.017265 GCAAGATCTTGGTGTTTGTGG 57.983 47.619 31.41 7.54 40.74 4.17
3369 3860 2.288395 GCAAGATCTTGGTGTTTGTGGG 60.288 50.000 31.41 7.06 40.74 4.61
3370 3861 3.221771 CAAGATCTTGGTGTTTGTGGGA 58.778 45.455 25.14 0.00 36.95 4.37
3371 3862 3.593442 AGATCTTGGTGTTTGTGGGAA 57.407 42.857 0.00 0.00 0.00 3.97
3372 3863 4.118168 AGATCTTGGTGTTTGTGGGAAT 57.882 40.909 0.00 0.00 0.00 3.01
3373 3864 3.828451 AGATCTTGGTGTTTGTGGGAATG 59.172 43.478 0.00 0.00 0.00 2.67
3374 3865 3.304911 TCTTGGTGTTTGTGGGAATGA 57.695 42.857 0.00 0.00 0.00 2.57
3375 3866 3.843422 TCTTGGTGTTTGTGGGAATGAT 58.157 40.909 0.00 0.00 0.00 2.45
3376 3867 3.826157 TCTTGGTGTTTGTGGGAATGATC 59.174 43.478 0.00 0.00 0.00 2.92
3377 3868 3.235750 TGGTGTTTGTGGGAATGATCA 57.764 42.857 0.00 0.00 0.00 2.92
3378 3869 3.156293 TGGTGTTTGTGGGAATGATCAG 58.844 45.455 0.09 0.00 0.00 2.90
3379 3870 2.094545 GGTGTTTGTGGGAATGATCAGC 60.095 50.000 0.09 0.00 0.00 4.26
3380 3871 2.821969 GTGTTTGTGGGAATGATCAGCT 59.178 45.455 0.09 0.00 0.00 4.24
3381 3872 3.256631 GTGTTTGTGGGAATGATCAGCTT 59.743 43.478 0.09 0.00 0.00 3.74
3382 3873 3.256383 TGTTTGTGGGAATGATCAGCTTG 59.744 43.478 0.09 0.00 0.00 4.01
3383 3874 2.133281 TGTGGGAATGATCAGCTTGG 57.867 50.000 0.09 0.00 0.00 3.61
3384 3875 1.355381 TGTGGGAATGATCAGCTTGGT 59.645 47.619 0.09 0.00 0.00 3.67
3385 3876 2.575735 TGTGGGAATGATCAGCTTGGTA 59.424 45.455 0.09 0.00 0.00 3.25
3386 3877 3.209410 GTGGGAATGATCAGCTTGGTAG 58.791 50.000 0.09 0.00 0.00 3.18
3387 3878 2.846206 TGGGAATGATCAGCTTGGTAGT 59.154 45.455 0.09 0.00 0.00 2.73
3388 3879 3.209410 GGGAATGATCAGCTTGGTAGTG 58.791 50.000 0.09 0.00 0.00 2.74
3389 3880 3.209410 GGAATGATCAGCTTGGTAGTGG 58.791 50.000 0.09 0.00 0.00 4.00
3390 3881 3.370953 GGAATGATCAGCTTGGTAGTGGT 60.371 47.826 0.09 0.00 0.00 4.16
3391 3882 3.550437 ATGATCAGCTTGGTAGTGGTC 57.450 47.619 0.09 0.00 0.00 4.02
3392 3883 2.256306 TGATCAGCTTGGTAGTGGTCA 58.744 47.619 0.00 0.00 0.00 4.02
3393 3884 2.028112 TGATCAGCTTGGTAGTGGTCAC 60.028 50.000 0.00 0.00 0.00 3.67
3394 3885 0.685097 TCAGCTTGGTAGTGGTCACC 59.315 55.000 0.00 0.00 36.54 4.02
3395 3886 0.396435 CAGCTTGGTAGTGGTCACCA 59.604 55.000 0.00 0.00 44.35 4.17
3401 3892 2.925724 TGGTAGTGGTCACCAAACTTG 58.074 47.619 0.00 0.00 43.08 3.16
3402 3893 2.240160 TGGTAGTGGTCACCAAACTTGT 59.760 45.455 0.00 0.00 43.08 3.16
3403 3894 2.616842 GGTAGTGGTCACCAAACTTGTG 59.383 50.000 0.00 0.00 34.18 3.33
3404 3895 1.102978 AGTGGTCACCAAACTTGTGC 58.897 50.000 0.00 0.00 34.18 4.57
3405 3896 0.102300 GTGGTCACCAAACTTGTGCC 59.898 55.000 0.00 0.00 34.18 5.01
3406 3897 0.033601 TGGTCACCAAACTTGTGCCT 60.034 50.000 0.00 0.00 0.00 4.75
3407 3898 1.213182 TGGTCACCAAACTTGTGCCTA 59.787 47.619 0.00 0.00 0.00 3.93
3408 3899 1.880027 GGTCACCAAACTTGTGCCTAG 59.120 52.381 0.00 0.00 0.00 3.02
3409 3900 2.572290 GTCACCAAACTTGTGCCTAGT 58.428 47.619 0.00 0.00 0.00 2.57
3410 3901 2.949644 GTCACCAAACTTGTGCCTAGTT 59.050 45.455 0.00 0.00 37.43 2.24
3411 3902 3.380320 GTCACCAAACTTGTGCCTAGTTT 59.620 43.478 8.24 8.24 44.38 2.66
3412 3903 4.020543 TCACCAAACTTGTGCCTAGTTTT 58.979 39.130 10.38 0.00 42.32 2.43
3413 3904 4.464597 TCACCAAACTTGTGCCTAGTTTTT 59.535 37.500 10.38 1.97 42.32 1.94
3428 3919 4.687464 TTTTTCCTCCGAGTCCGC 57.313 55.556 0.00 0.00 0.00 5.54
3429 3920 1.004200 TTTTTCCTCCGAGTCCGCC 60.004 57.895 0.00 0.00 0.00 6.13
3430 3921 1.477685 TTTTTCCTCCGAGTCCGCCT 61.478 55.000 0.00 0.00 0.00 5.52
3431 3922 1.477685 TTTTCCTCCGAGTCCGCCTT 61.478 55.000 0.00 0.00 0.00 4.35
3432 3923 1.885163 TTTCCTCCGAGTCCGCCTTC 61.885 60.000 0.00 0.00 0.00 3.46
3433 3924 3.068691 CCTCCGAGTCCGCCTTCA 61.069 66.667 0.00 0.00 0.00 3.02
3434 3925 2.427245 CCTCCGAGTCCGCCTTCAT 61.427 63.158 0.00 0.00 0.00 2.57
3435 3926 1.066587 CTCCGAGTCCGCCTTCATC 59.933 63.158 0.00 0.00 0.00 2.92
3436 3927 1.379977 TCCGAGTCCGCCTTCATCT 60.380 57.895 0.00 0.00 0.00 2.90
3437 3928 1.066587 CCGAGTCCGCCTTCATCTC 59.933 63.158 0.00 0.00 0.00 2.75
3438 3929 1.298713 CGAGTCCGCCTTCATCTCG 60.299 63.158 0.00 0.00 41.02 4.04
3439 3930 1.066587 GAGTCCGCCTTCATCTCGG 59.933 63.158 0.00 0.00 44.16 4.63
3440 3931 1.668101 GAGTCCGCCTTCATCTCGGT 61.668 60.000 0.00 0.00 43.35 4.69
3441 3932 1.519455 GTCCGCCTTCATCTCGGTG 60.519 63.158 0.00 0.00 43.35 4.94
3442 3933 2.202932 CCGCCTTCATCTCGGTGG 60.203 66.667 0.00 0.00 43.85 4.61
3443 3934 2.579201 CGCCTTCATCTCGGTGGT 59.421 61.111 0.00 0.00 0.00 4.16
3444 3935 1.811266 CGCCTTCATCTCGGTGGTG 60.811 63.158 0.00 0.00 0.00 4.17
3445 3936 1.296715 GCCTTCATCTCGGTGGTGT 59.703 57.895 0.00 0.00 0.00 4.16
3446 3937 0.321653 GCCTTCATCTCGGTGGTGTT 60.322 55.000 0.00 0.00 0.00 3.32
3447 3938 1.726853 CCTTCATCTCGGTGGTGTTC 58.273 55.000 0.00 0.00 0.00 3.18
3448 3939 1.676014 CCTTCATCTCGGTGGTGTTCC 60.676 57.143 0.00 0.00 0.00 3.62
3449 3940 0.323629 TTCATCTCGGTGGTGTTCCC 59.676 55.000 0.00 0.00 0.00 3.97
3450 3941 0.544357 TCATCTCGGTGGTGTTCCCT 60.544 55.000 0.00 0.00 0.00 4.20
3451 3942 1.191535 CATCTCGGTGGTGTTCCCTA 58.808 55.000 0.00 0.00 0.00 3.53
3452 3943 1.134788 CATCTCGGTGGTGTTCCCTAC 60.135 57.143 0.00 0.00 0.00 3.18
3453 3944 1.214589 CTCGGTGGTGTTCCCTACG 59.785 63.158 0.00 0.00 35.34 3.51
3454 3945 1.530013 CTCGGTGGTGTTCCCTACGT 61.530 60.000 0.00 0.00 35.47 3.57
3455 3946 1.114722 TCGGTGGTGTTCCCTACGTT 61.115 55.000 0.00 0.00 35.47 3.99
3456 3947 0.947180 CGGTGGTGTTCCCTACGTTG 60.947 60.000 0.00 0.00 0.00 4.10
3457 3948 1.232621 GGTGGTGTTCCCTACGTTGC 61.233 60.000 0.00 0.00 0.00 4.17
3458 3949 1.071814 TGGTGTTCCCTACGTTGCC 59.928 57.895 0.00 0.00 0.00 4.52
3459 3950 1.071814 GGTGTTCCCTACGTTGCCA 59.928 57.895 0.00 0.00 0.00 4.92
3460 3951 0.322187 GGTGTTCCCTACGTTGCCAT 60.322 55.000 0.00 0.00 0.00 4.40
3461 3952 1.530323 GTGTTCCCTACGTTGCCATT 58.470 50.000 0.00 0.00 0.00 3.16
3462 3953 1.199097 GTGTTCCCTACGTTGCCATTG 59.801 52.381 0.00 0.00 0.00 2.82
3463 3954 0.808755 GTTCCCTACGTTGCCATTGG 59.191 55.000 0.00 0.00 0.00 3.16
3464 3955 0.322997 TTCCCTACGTTGCCATTGGG 60.323 55.000 4.53 0.00 36.14 4.12
3465 3956 1.752694 CCCTACGTTGCCATTGGGG 60.753 63.158 4.53 0.00 40.85 4.96
3466 3957 1.301623 CCTACGTTGCCATTGGGGA 59.698 57.895 4.53 0.00 40.01 4.81
3467 3958 0.106719 CCTACGTTGCCATTGGGGAT 60.107 55.000 4.53 0.00 40.01 3.85
3468 3959 1.308998 CTACGTTGCCATTGGGGATC 58.691 55.000 4.53 0.00 40.01 3.36
3469 3960 0.106918 TACGTTGCCATTGGGGATCC 60.107 55.000 1.92 1.92 40.01 3.36
3470 3961 1.379710 CGTTGCCATTGGGGATCCA 60.380 57.895 15.23 0.00 42.25 3.41
3471 3962 1.386525 CGTTGCCATTGGGGATCCAG 61.387 60.000 15.23 0.00 45.04 3.86
3472 3963 1.044790 GTTGCCATTGGGGATCCAGG 61.045 60.000 15.23 7.98 45.04 4.45
3473 3964 1.220518 TTGCCATTGGGGATCCAGGA 61.221 55.000 15.23 0.00 45.04 3.86
3474 3965 1.152368 GCCATTGGGGATCCAGGAG 59.848 63.158 15.23 0.00 45.04 3.69
3475 3966 1.849116 CCATTGGGGATCCAGGAGG 59.151 63.158 15.23 4.58 45.04 4.30
3476 3967 0.995675 CCATTGGGGATCCAGGAGGT 60.996 60.000 15.23 0.00 45.04 3.85
3477 3968 0.929244 CATTGGGGATCCAGGAGGTT 59.071 55.000 15.23 0.00 45.04 3.50
3478 3969 0.929244 ATTGGGGATCCAGGAGGTTG 59.071 55.000 15.23 0.00 45.04 3.77
3479 3970 0.477597 TTGGGGATCCAGGAGGTTGT 60.478 55.000 15.23 0.00 45.04 3.32
3480 3971 0.419865 TGGGGATCCAGGAGGTTGTA 59.580 55.000 15.23 0.00 38.32 2.41
3481 3972 1.010793 TGGGGATCCAGGAGGTTGTAT 59.989 52.381 15.23 0.00 38.32 2.29
3482 3973 2.251605 TGGGGATCCAGGAGGTTGTATA 59.748 50.000 15.23 0.00 38.32 1.47
3483 3974 2.907042 GGGGATCCAGGAGGTTGTATAG 59.093 54.545 15.23 0.00 35.89 1.31
3484 3975 3.588569 GGGATCCAGGAGGTTGTATAGT 58.411 50.000 15.23 0.00 35.89 2.12
3485 3976 3.325135 GGGATCCAGGAGGTTGTATAGTG 59.675 52.174 15.23 0.00 35.89 2.74
3486 3977 3.325135 GGATCCAGGAGGTTGTATAGTGG 59.675 52.174 6.95 0.00 35.89 4.00
3487 3978 3.484953 TCCAGGAGGTTGTATAGTGGT 57.515 47.619 0.00 0.00 35.89 4.16
3488 3979 3.104512 TCCAGGAGGTTGTATAGTGGTG 58.895 50.000 0.00 0.00 35.89 4.17
3489 3980 3.104512 CCAGGAGGTTGTATAGTGGTGA 58.895 50.000 0.00 0.00 0.00 4.02
3490 3981 3.118738 CCAGGAGGTTGTATAGTGGTGAC 60.119 52.174 0.00 0.00 0.00 3.67
3491 3982 3.769844 CAGGAGGTTGTATAGTGGTGACT 59.230 47.826 0.00 0.00 36.07 3.41
3492 3983 4.024670 AGGAGGTTGTATAGTGGTGACTC 58.975 47.826 0.00 0.00 33.21 3.36
3493 3984 4.024670 GGAGGTTGTATAGTGGTGACTCT 58.975 47.826 0.00 0.00 37.95 3.24
3494 3985 4.098196 GGAGGTTGTATAGTGGTGACTCTC 59.902 50.000 0.00 0.00 35.43 3.20
3495 3986 4.936802 AGGTTGTATAGTGGTGACTCTCT 58.063 43.478 0.00 0.00 35.43 3.10
3496 3987 5.334421 AGGTTGTATAGTGGTGACTCTCTT 58.666 41.667 0.00 0.00 35.43 2.85
3497 3988 5.419471 AGGTTGTATAGTGGTGACTCTCTTC 59.581 44.000 0.00 0.00 35.43 2.87
3498 3989 5.419471 GGTTGTATAGTGGTGACTCTCTTCT 59.581 44.000 0.00 0.00 35.43 2.85
3499 3990 6.404954 GGTTGTATAGTGGTGACTCTCTTCTC 60.405 46.154 0.00 0.00 35.43 2.87
3500 3991 5.194432 TGTATAGTGGTGACTCTCTTCTCC 58.806 45.833 0.00 0.00 35.43 3.71
3501 3992 1.540267 AGTGGTGACTCTCTTCTCCG 58.460 55.000 0.00 0.00 32.66 4.63
3502 3993 1.074084 AGTGGTGACTCTCTTCTCCGA 59.926 52.381 0.00 0.00 32.66 4.55
3503 3994 1.200484 GTGGTGACTCTCTTCTCCGAC 59.800 57.143 0.00 0.00 32.66 4.79
3504 3995 1.202891 TGGTGACTCTCTTCTCCGACA 60.203 52.381 0.00 0.00 32.66 4.35
3505 3996 1.470890 GGTGACTCTCTTCTCCGACAG 59.529 57.143 0.00 0.00 0.00 3.51
3506 3997 1.135517 GTGACTCTCTTCTCCGACAGC 60.136 57.143 0.00 0.00 0.00 4.40
3507 3998 0.098025 GACTCTCTTCTCCGACAGCG 59.902 60.000 0.00 0.00 37.24 5.18
3508 3999 0.606944 ACTCTCTTCTCCGACAGCGT 60.607 55.000 0.00 0.00 35.23 5.07
3509 4000 0.523966 CTCTCTTCTCCGACAGCGTT 59.476 55.000 0.00 0.00 35.23 4.84
3510 4001 0.241213 TCTCTTCTCCGACAGCGTTG 59.759 55.000 0.00 0.00 35.23 4.10
3511 4002 0.734253 CTCTTCTCCGACAGCGTTGG 60.734 60.000 3.74 8.24 38.40 3.77
3512 4003 1.176619 TCTTCTCCGACAGCGTTGGA 61.177 55.000 14.42 14.42 43.20 3.53
3513 4004 1.006571 TTCTCCGACAGCGTTGGAC 60.007 57.895 12.03 0.00 40.82 4.02
3514 4005 1.740332 TTCTCCGACAGCGTTGGACA 61.740 55.000 12.03 2.23 40.82 4.02
3515 4006 1.300620 CTCCGACAGCGTTGGACAA 60.301 57.895 12.03 0.00 40.82 3.18
3516 4007 0.878523 CTCCGACAGCGTTGGACAAA 60.879 55.000 12.03 0.00 40.82 2.83
3517 4008 0.878523 TCCGACAGCGTTGGACAAAG 60.879 55.000 12.03 0.00 40.82 2.77
3518 4009 0.878523 CCGACAGCGTTGGACAAAGA 60.879 55.000 3.74 0.00 39.36 2.52
3519 4010 0.232303 CGACAGCGTTGGACAAAGAC 59.768 55.000 3.74 0.00 0.00 3.01
3520 4011 1.583054 GACAGCGTTGGACAAAGACT 58.417 50.000 3.74 0.00 0.00 3.24
3521 4012 1.940613 GACAGCGTTGGACAAAGACTT 59.059 47.619 3.74 0.00 0.00 3.01
3522 4013 1.940613 ACAGCGTTGGACAAAGACTTC 59.059 47.619 3.74 0.00 0.00 3.01
3523 4014 1.264288 CAGCGTTGGACAAAGACTTCC 59.736 52.381 2.19 0.00 0.00 3.46
3524 4015 1.134220 AGCGTTGGACAAAGACTTCCA 60.134 47.619 2.19 0.00 40.30 3.53
3525 4016 1.264288 GCGTTGGACAAAGACTTCCAG 59.736 52.381 2.19 0.00 42.93 3.86
3526 4017 2.561569 CGTTGGACAAAGACTTCCAGT 58.438 47.619 0.00 0.00 42.93 4.00
3527 4018 2.943033 CGTTGGACAAAGACTTCCAGTT 59.057 45.455 0.00 0.00 42.93 3.16
3528 4019 3.377172 CGTTGGACAAAGACTTCCAGTTT 59.623 43.478 0.00 0.00 42.93 2.66
3529 4020 4.142469 CGTTGGACAAAGACTTCCAGTTTT 60.142 41.667 0.00 0.00 42.93 2.43
3530 4021 4.981806 TGGACAAAGACTTCCAGTTTTG 57.018 40.909 0.00 8.65 36.96 2.44
3531 4022 4.340617 TGGACAAAGACTTCCAGTTTTGT 58.659 39.130 12.78 12.78 39.60 2.83
3532 4023 5.502079 TGGACAAAGACTTCCAGTTTTGTA 58.498 37.500 12.84 2.70 38.39 2.41
3533 4024 5.588648 TGGACAAAGACTTCCAGTTTTGTAG 59.411 40.000 12.84 0.00 38.39 2.74
3534 4025 5.589050 GGACAAAGACTTCCAGTTTTGTAGT 59.411 40.000 12.84 0.00 38.39 2.73
3535 4026 6.238402 GGACAAAGACTTCCAGTTTTGTAGTC 60.238 42.308 12.84 0.00 38.39 2.59
3536 4027 6.177610 ACAAAGACTTCCAGTTTTGTAGTCA 58.822 36.000 11.90 0.00 37.50 3.41
3537 4028 6.316390 ACAAAGACTTCCAGTTTTGTAGTCAG 59.684 38.462 11.90 0.00 37.50 3.51
3538 4029 4.962155 AGACTTCCAGTTTTGTAGTCAGG 58.038 43.478 0.00 0.00 36.93 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
98 100 1.377725 GGCCTGCAGCACATACAGT 60.378 57.895 8.66 0.00 46.50 3.55
174 178 3.243367 TGAATGTTTTCTTTCCAGTGCCG 60.243 43.478 0.00 0.00 34.40 5.69
252 256 4.657436 AGCTAGACGAATTCTAAGTGGG 57.343 45.455 3.52 0.00 36.32 4.61
456 476 6.014242 ACCATCACAAGACAGAGATAAACAGA 60.014 38.462 0.00 0.00 0.00 3.41
465 485 2.288457 ACGTCACCATCACAAGACAGAG 60.288 50.000 0.00 0.00 0.00 3.35
649 676 3.193263 CGAAAGAGGTGTGAGGATGATG 58.807 50.000 0.00 0.00 0.00 3.07
856 883 0.320771 TCTTCAAGCTTGAGACGCCC 60.321 55.000 27.02 0.00 38.61 6.13
999 1028 1.099879 AGATGGCTTTGGCGCTCATC 61.100 55.000 7.64 11.03 39.81 2.92
1090 1119 2.292103 AGATCAAGCAGAGCTCGAAC 57.708 50.000 8.37 1.55 39.11 3.95
1121 1150 8.950007 AACTGTAAGGAAATTAAATGGAAGGA 57.050 30.769 0.00 0.00 39.30 3.36
1186 1215 1.936547 GAAATCATCACAGAGCGGGTC 59.063 52.381 0.00 0.00 0.00 4.46
1640 1677 0.025898 CATGATCTGCAGTGTTCGCG 59.974 55.000 14.67 0.00 0.00 5.87
1699 1736 8.253810 TGGTGTCAAGATGATTAAGAGAGTTAG 58.746 37.037 0.00 0.00 0.00 2.34
1975 2012 4.451096 GCAAGGAATTAGTGAACGAACTCA 59.549 41.667 0.00 0.00 0.00 3.41
1981 2018 3.751175 TGGAAGCAAGGAATTAGTGAACG 59.249 43.478 0.00 0.00 0.00 3.95
2076 2113 2.154462 GCATGTGCAGTAACTGAACCT 58.846 47.619 0.00 0.00 39.19 3.50
2091 2128 1.379843 GTTGGATTCCCGGGCATGT 60.380 57.895 18.49 0.03 34.29 3.21
2110 2147 5.385509 AATGAATACCCGGTGTTTTCTTG 57.614 39.130 19.16 0.00 36.31 3.02
2124 2161 4.797471 TGCTGCAGTTGACAAATGAATAC 58.203 39.130 19.19 5.01 0.00 1.89
2151 2188 2.751731 CCATATCCACCCGGTGCCA 61.752 63.158 12.54 0.77 31.34 4.92
2294 2331 6.109156 TGATTCCAGAAAACACTAGCAGTA 57.891 37.500 0.00 0.00 0.00 2.74
2487 2524 0.668535 TCAGCCATAGATCACCGTCG 59.331 55.000 0.00 0.00 0.00 5.12
2566 2603 4.631377 TGCTTGTCTGTGATACAATGCTAC 59.369 41.667 0.00 0.00 36.33 3.58
2660 2697 9.143631 CTGAAATTCCAAATGATGTACTTTTCC 57.856 33.333 0.00 0.00 0.00 3.13
2691 2728 9.013490 CAATCCAATCTTTGTCGAAATCAATAC 57.987 33.333 0.00 0.00 0.00 1.89
2893 3184 6.425417 TGTGTATTCAGAACGATTTGCAACTA 59.575 34.615 0.00 0.00 0.00 2.24
2951 3242 2.002586 CTGTTCAGCTGATGTTACCCG 58.997 52.381 19.04 3.02 0.00 5.28
2952 3243 3.059352 ACTGTTCAGCTGATGTTACCC 57.941 47.619 19.04 0.66 0.00 3.69
2983 3274 2.352651 CACCTCACCAGTTATTCATGCG 59.647 50.000 0.00 0.00 0.00 4.73
3110 3601 6.402442 GCGTTTTCGTGTTATGGGTAACTATT 60.402 38.462 0.73 0.00 46.03 1.73
3119 3610 4.915085 AGAAATTGCGTTTTCGTGTTATGG 59.085 37.500 5.76 0.00 46.03 2.74
3147 3638 4.261801 AGCGACCACTATTACTTGCAATT 58.738 39.130 0.00 0.00 0.00 2.32
3153 3644 3.522553 GAGCAAGCGACCACTATTACTT 58.477 45.455 0.00 0.00 0.00 2.24
3170 3661 4.735132 GCACCGTGTAGGCGAGCA 62.735 66.667 0.00 0.00 46.52 4.26
3200 3691 2.224209 GGCGAGTTTAGCTATTGGCCTA 60.224 50.000 3.32 0.00 43.05 3.93
3241 3732 1.000607 ACGCACGGGCATATGTACTAG 60.001 52.381 11.77 0.00 41.24 2.57
3242 3733 1.034356 ACGCACGGGCATATGTACTA 58.966 50.000 11.77 0.00 41.24 1.82
3243 3734 0.177141 AACGCACGGGCATATGTACT 59.823 50.000 11.77 0.00 41.24 2.73
3244 3735 0.303493 CAACGCACGGGCATATGTAC 59.697 55.000 11.77 0.00 41.24 2.90
3245 3736 1.433053 GCAACGCACGGGCATATGTA 61.433 55.000 11.77 0.00 41.24 2.29
3246 3737 2.760159 GCAACGCACGGGCATATGT 61.760 57.895 11.77 0.00 41.24 2.29
3247 3738 2.024588 GCAACGCACGGGCATATG 59.975 61.111 11.77 6.17 41.24 1.78
3248 3739 2.043405 TTGCAACGCACGGGCATAT 61.043 52.632 11.77 0.00 38.71 1.78
3249 3740 2.669910 TTGCAACGCACGGGCATA 60.670 55.556 11.77 0.00 38.71 3.14
3250 3741 4.341502 GTTGCAACGCACGGGCAT 62.342 61.111 14.90 0.00 38.71 4.40
3260 3751 4.558860 GCCAATTATCTCTTTCGTTGCAAC 59.441 41.667 19.89 19.89 0.00 4.17
3261 3752 4.671508 CGCCAATTATCTCTTTCGTTGCAA 60.672 41.667 0.00 0.00 0.00 4.08
3262 3753 3.181511 CGCCAATTATCTCTTTCGTTGCA 60.182 43.478 0.00 0.00 0.00 4.08
3263 3754 3.181510 ACGCCAATTATCTCTTTCGTTGC 60.182 43.478 0.00 0.00 0.00 4.17
3264 3755 4.142902 ACACGCCAATTATCTCTTTCGTTG 60.143 41.667 0.00 0.00 0.00 4.10
3265 3756 4.000988 ACACGCCAATTATCTCTTTCGTT 58.999 39.130 0.00 0.00 0.00 3.85
3266 3757 3.596214 ACACGCCAATTATCTCTTTCGT 58.404 40.909 0.00 0.00 0.00 3.85
3267 3758 3.001330 GGACACGCCAATTATCTCTTTCG 59.999 47.826 0.00 0.00 36.34 3.46
3268 3759 3.938963 TGGACACGCCAATTATCTCTTTC 59.061 43.478 0.00 0.00 45.87 2.62
3269 3760 3.950397 TGGACACGCCAATTATCTCTTT 58.050 40.909 0.00 0.00 45.87 2.52
3270 3761 3.627395 TGGACACGCCAATTATCTCTT 57.373 42.857 0.00 0.00 45.87 2.85
3289 3780 5.771469 TCACTCTGTAAATGCCATTTTGTG 58.229 37.500 8.15 9.80 33.82 3.33
3290 3781 5.047802 CCTCACTCTGTAAATGCCATTTTGT 60.048 40.000 8.15 0.00 33.82 2.83
3291 3782 5.183713 TCCTCACTCTGTAAATGCCATTTTG 59.816 40.000 8.15 0.00 33.82 2.44
3292 3783 5.324409 TCCTCACTCTGTAAATGCCATTTT 58.676 37.500 8.15 0.00 33.82 1.82
3293 3784 4.922206 TCCTCACTCTGTAAATGCCATTT 58.078 39.130 7.93 7.93 36.29 2.32
3294 3785 4.018960 ACTCCTCACTCTGTAAATGCCATT 60.019 41.667 0.00 0.00 0.00 3.16
3295 3786 3.521126 ACTCCTCACTCTGTAAATGCCAT 59.479 43.478 0.00 0.00 0.00 4.40
3296 3787 2.906389 ACTCCTCACTCTGTAAATGCCA 59.094 45.455 0.00 0.00 0.00 4.92
3297 3788 3.526534 GACTCCTCACTCTGTAAATGCC 58.473 50.000 0.00 0.00 0.00 4.40
3298 3789 3.182967 CGACTCCTCACTCTGTAAATGC 58.817 50.000 0.00 0.00 0.00 3.56
3299 3790 3.182967 GCGACTCCTCACTCTGTAAATG 58.817 50.000 0.00 0.00 0.00 2.32
3300 3791 2.159366 CGCGACTCCTCACTCTGTAAAT 60.159 50.000 0.00 0.00 0.00 1.40
3301 3792 1.199327 CGCGACTCCTCACTCTGTAAA 59.801 52.381 0.00 0.00 0.00 2.01
3302 3793 0.803117 CGCGACTCCTCACTCTGTAA 59.197 55.000 0.00 0.00 0.00 2.41
3303 3794 1.025113 CCGCGACTCCTCACTCTGTA 61.025 60.000 8.23 0.00 0.00 2.74
3304 3795 2.336478 CCGCGACTCCTCACTCTGT 61.336 63.158 8.23 0.00 0.00 3.41
3305 3796 2.259875 GACCGCGACTCCTCACTCTG 62.260 65.000 8.23 0.00 0.00 3.35
3306 3797 2.034376 ACCGCGACTCCTCACTCT 59.966 61.111 8.23 0.00 0.00 3.24
3307 3798 1.587933 AAGACCGCGACTCCTCACTC 61.588 60.000 8.23 0.00 0.00 3.51
3308 3799 1.587933 GAAGACCGCGACTCCTCACT 61.588 60.000 8.23 0.00 0.00 3.41
3309 3800 1.153997 GAAGACCGCGACTCCTCAC 60.154 63.158 8.23 0.00 0.00 3.51
3310 3801 1.303398 AGAAGACCGCGACTCCTCA 60.303 57.895 8.23 0.00 0.00 3.86
3311 3802 1.430228 GAGAAGACCGCGACTCCTC 59.570 63.158 8.23 5.66 0.00 3.71
3312 3803 2.400158 CGAGAAGACCGCGACTCCT 61.400 63.158 8.23 0.00 40.62 3.69
3313 3804 2.100603 CGAGAAGACCGCGACTCC 59.899 66.667 8.23 0.00 40.62 3.85
3314 3805 2.577378 GCGAGAAGACCGCGACTC 60.577 66.667 8.23 0.72 43.28 3.36
3320 3811 0.803768 CATGACCTGCGAGAAGACCG 60.804 60.000 0.00 0.00 0.00 4.79
3321 3812 0.247736 ACATGACCTGCGAGAAGACC 59.752 55.000 0.00 0.00 0.00 3.85
3322 3813 1.337260 ACACATGACCTGCGAGAAGAC 60.337 52.381 0.00 0.00 0.00 3.01
3323 3814 0.969149 ACACATGACCTGCGAGAAGA 59.031 50.000 0.00 0.00 0.00 2.87
3324 3815 1.462283 CAACACATGACCTGCGAGAAG 59.538 52.381 0.00 0.00 0.00 2.85
3325 3816 1.511850 CAACACATGACCTGCGAGAA 58.488 50.000 0.00 0.00 0.00 2.87
3326 3817 0.950555 GCAACACATGACCTGCGAGA 60.951 55.000 0.00 0.00 0.00 4.04
3327 3818 1.499056 GCAACACATGACCTGCGAG 59.501 57.895 0.00 0.00 0.00 5.03
3328 3819 1.965930 GGCAACACATGACCTGCGA 60.966 57.895 0.00 0.00 35.60 5.10
3329 3820 2.191354 CTGGCAACACATGACCTGCG 62.191 60.000 0.00 0.00 46.17 5.18
3330 3821 1.582968 CTGGCAACACATGACCTGC 59.417 57.895 0.00 4.37 46.17 4.85
3331 3822 1.174078 TGCTGGCAACACATGACCTG 61.174 55.000 0.00 0.00 46.17 4.00
3332 3823 0.467844 TTGCTGGCAACACATGACCT 60.468 50.000 0.00 0.00 46.17 3.85
3333 3824 0.038892 CTTGCTGGCAACACATGACC 60.039 55.000 0.00 0.00 46.17 4.02
3334 3825 0.953727 TCTTGCTGGCAACACATGAC 59.046 50.000 0.00 0.00 46.17 3.06
3335 3826 1.814394 GATCTTGCTGGCAACACATGA 59.186 47.619 0.00 0.76 46.17 3.07
3336 3827 1.816835 AGATCTTGCTGGCAACACATG 59.183 47.619 3.72 0.00 46.17 3.21
3337 3828 2.211250 AGATCTTGCTGGCAACACAT 57.789 45.000 3.72 0.00 46.17 3.21
3338 3829 1.610038 CAAGATCTTGCTGGCAACACA 59.390 47.619 21.96 0.00 44.67 3.72
3339 3830 1.068055 CCAAGATCTTGCTGGCAACAC 60.068 52.381 27.01 0.00 39.70 3.32
3340 3831 1.250328 CCAAGATCTTGCTGGCAACA 58.750 50.000 27.01 0.00 41.38 3.33
3341 3832 1.068055 CACCAAGATCTTGCTGGCAAC 60.068 52.381 27.01 0.00 39.16 4.17
3342 3833 1.250328 CACCAAGATCTTGCTGGCAA 58.750 50.000 27.01 7.78 39.16 4.52
3343 3834 0.111061 ACACCAAGATCTTGCTGGCA 59.889 50.000 26.81 0.00 39.16 4.92
3344 3835 1.251251 AACACCAAGATCTTGCTGGC 58.749 50.000 26.81 0.00 39.16 4.85
3345 3836 2.624838 ACAAACACCAAGATCTTGCTGG 59.375 45.455 26.81 19.37 39.16 4.85
3346 3837 3.551454 CCACAAACACCAAGATCTTGCTG 60.551 47.826 27.01 25.06 39.16 4.41
3347 3838 2.624838 CCACAAACACCAAGATCTTGCT 59.375 45.455 27.01 13.39 39.16 3.91
3348 3839 2.288395 CCCACAAACACCAAGATCTTGC 60.288 50.000 27.01 0.00 39.16 4.01
3349 3840 3.221771 TCCCACAAACACCAAGATCTTG 58.778 45.455 25.75 25.75 40.13 3.02
3350 3841 3.593442 TCCCACAAACACCAAGATCTT 57.407 42.857 0.88 0.88 0.00 2.40
3351 3842 3.593442 TTCCCACAAACACCAAGATCT 57.407 42.857 0.00 0.00 0.00 2.75
3352 3843 3.826157 TCATTCCCACAAACACCAAGATC 59.174 43.478 0.00 0.00 0.00 2.75
3353 3844 3.843422 TCATTCCCACAAACACCAAGAT 58.157 40.909 0.00 0.00 0.00 2.40
3354 3845 3.304911 TCATTCCCACAAACACCAAGA 57.695 42.857 0.00 0.00 0.00 3.02
3355 3846 3.573538 TGATCATTCCCACAAACACCAAG 59.426 43.478 0.00 0.00 0.00 3.61
3356 3847 3.570540 TGATCATTCCCACAAACACCAA 58.429 40.909 0.00 0.00 0.00 3.67
3357 3848 3.156293 CTGATCATTCCCACAAACACCA 58.844 45.455 0.00 0.00 0.00 4.17
3358 3849 2.094545 GCTGATCATTCCCACAAACACC 60.095 50.000 0.00 0.00 0.00 4.16
3359 3850 2.821969 AGCTGATCATTCCCACAAACAC 59.178 45.455 0.00 0.00 0.00 3.32
3360 3851 3.159213 AGCTGATCATTCCCACAAACA 57.841 42.857 0.00 0.00 0.00 2.83
3361 3852 3.367703 CCAAGCTGATCATTCCCACAAAC 60.368 47.826 0.00 0.00 0.00 2.93
3362 3853 2.827322 CCAAGCTGATCATTCCCACAAA 59.173 45.455 0.00 0.00 0.00 2.83
3363 3854 2.225091 ACCAAGCTGATCATTCCCACAA 60.225 45.455 0.00 0.00 0.00 3.33
3364 3855 1.355381 ACCAAGCTGATCATTCCCACA 59.645 47.619 0.00 0.00 0.00 4.17
3365 3856 2.134789 ACCAAGCTGATCATTCCCAC 57.865 50.000 0.00 0.00 0.00 4.61
3366 3857 2.846206 ACTACCAAGCTGATCATTCCCA 59.154 45.455 0.00 0.00 0.00 4.37
3367 3858 3.209410 CACTACCAAGCTGATCATTCCC 58.791 50.000 0.00 0.00 0.00 3.97
3368 3859 3.209410 CCACTACCAAGCTGATCATTCC 58.791 50.000 0.00 0.00 0.00 3.01
3369 3860 3.873952 GACCACTACCAAGCTGATCATTC 59.126 47.826 0.00 0.00 0.00 2.67
3370 3861 3.264193 TGACCACTACCAAGCTGATCATT 59.736 43.478 0.00 0.00 0.00 2.57
3371 3862 2.840038 TGACCACTACCAAGCTGATCAT 59.160 45.455 0.00 0.00 0.00 2.45
3372 3863 2.028112 GTGACCACTACCAAGCTGATCA 60.028 50.000 0.00 0.00 0.00 2.92
3373 3864 2.622436 GTGACCACTACCAAGCTGATC 58.378 52.381 0.00 0.00 0.00 2.92
3374 3865 1.279271 GGTGACCACTACCAAGCTGAT 59.721 52.381 0.00 0.00 38.12 2.90
3375 3866 0.685097 GGTGACCACTACCAAGCTGA 59.315 55.000 0.00 0.00 38.12 4.26
3376 3867 0.396435 TGGTGACCACTACCAAGCTG 59.604 55.000 0.00 0.00 44.79 4.24
3377 3868 2.848608 TGGTGACCACTACCAAGCT 58.151 52.632 0.00 0.00 44.79 3.74
3381 3872 2.240160 ACAAGTTTGGTGACCACTACCA 59.760 45.455 2.46 0.00 46.01 3.25
3382 3873 2.616842 CACAAGTTTGGTGACCACTACC 59.383 50.000 2.46 0.00 38.54 3.18
3383 3874 2.032924 GCACAAGTTTGGTGACCACTAC 59.967 50.000 2.46 5.83 38.54 2.73
3384 3875 2.294074 GCACAAGTTTGGTGACCACTA 58.706 47.619 2.46 0.00 38.54 2.74
3385 3876 1.102978 GCACAAGTTTGGTGACCACT 58.897 50.000 2.46 0.00 38.54 4.00
3386 3877 0.102300 GGCACAAGTTTGGTGACCAC 59.898 55.000 2.46 0.00 38.37 4.16
3387 3878 0.033601 AGGCACAAGTTTGGTGACCA 60.034 50.000 0.00 0.00 45.61 4.02
3388 3879 1.880027 CTAGGCACAAGTTTGGTGACC 59.120 52.381 0.00 0.00 45.61 4.02
3389 3880 2.572290 ACTAGGCACAAGTTTGGTGAC 58.428 47.619 0.00 0.00 44.80 3.67
3390 3881 3.290948 AACTAGGCACAAGTTTGGTGA 57.709 42.857 0.00 0.00 38.54 4.02
3391 3882 4.385358 AAAACTAGGCACAAGTTTGGTG 57.615 40.909 11.70 0.00 44.35 4.17
3411 3902 1.004200 GGCGGACTCGGAGGAAAAA 60.004 57.895 10.23 0.00 36.79 1.94
3412 3903 1.477685 AAGGCGGACTCGGAGGAAAA 61.478 55.000 10.23 0.00 36.79 2.29
3413 3904 1.885163 GAAGGCGGACTCGGAGGAAA 61.885 60.000 10.23 0.00 36.79 3.13
3414 3905 2.283676 AAGGCGGACTCGGAGGAA 60.284 61.111 10.23 0.00 36.79 3.36
3415 3906 2.754658 GAAGGCGGACTCGGAGGA 60.755 66.667 10.23 0.00 36.79 3.71
3416 3907 2.356818 GATGAAGGCGGACTCGGAGG 62.357 65.000 10.23 0.00 36.79 4.30
3417 3908 1.066587 GATGAAGGCGGACTCGGAG 59.933 63.158 2.83 2.83 36.79 4.63
3418 3909 1.379977 AGATGAAGGCGGACTCGGA 60.380 57.895 0.00 0.00 36.79 4.55
3419 3910 1.066587 GAGATGAAGGCGGACTCGG 59.933 63.158 0.00 0.00 36.79 4.63
3420 3911 1.298713 CGAGATGAAGGCGGACTCG 60.299 63.158 0.00 0.00 42.77 4.18
3421 3912 4.719997 CGAGATGAAGGCGGACTC 57.280 61.111 0.00 0.00 0.00 3.36
3426 3917 1.811266 CACCACCGAGATGAAGGCG 60.811 63.158 0.00 0.00 0.00 5.52
3427 3918 0.321653 AACACCACCGAGATGAAGGC 60.322 55.000 0.00 0.00 0.00 4.35
3428 3919 1.676014 GGAACACCACCGAGATGAAGG 60.676 57.143 0.00 0.00 0.00 3.46
3429 3920 1.676014 GGGAACACCACCGAGATGAAG 60.676 57.143 0.00 0.00 39.85 3.02
3430 3921 0.323629 GGGAACACCACCGAGATGAA 59.676 55.000 0.00 0.00 39.85 2.57
3431 3922 0.544357 AGGGAACACCACCGAGATGA 60.544 55.000 0.00 0.00 43.89 2.92
3432 3923 1.134788 GTAGGGAACACCACCGAGATG 60.135 57.143 0.00 0.00 43.89 2.90
3433 3924 1.192428 GTAGGGAACACCACCGAGAT 58.808 55.000 0.00 0.00 43.89 2.75
3434 3925 1.246056 CGTAGGGAACACCACCGAGA 61.246 60.000 0.00 0.00 43.89 4.04
3435 3926 1.214589 CGTAGGGAACACCACCGAG 59.785 63.158 0.00 0.00 43.89 4.63
3436 3927 1.114722 AACGTAGGGAACACCACCGA 61.115 55.000 0.00 0.00 43.89 4.69
3437 3928 0.947180 CAACGTAGGGAACACCACCG 60.947 60.000 0.00 0.00 43.89 4.94
3438 3929 1.232621 GCAACGTAGGGAACACCACC 61.233 60.000 0.00 0.00 43.89 4.61
3439 3930 1.232621 GGCAACGTAGGGAACACCAC 61.233 60.000 0.00 0.00 43.89 4.16
3440 3931 1.071814 GGCAACGTAGGGAACACCA 59.928 57.895 0.00 0.00 43.89 4.17
3441 3932 0.322187 ATGGCAACGTAGGGAACACC 60.322 55.000 0.00 0.00 42.51 4.16
3442 3933 1.199097 CAATGGCAACGTAGGGAACAC 59.801 52.381 0.00 0.00 42.51 3.32
3443 3934 1.529226 CAATGGCAACGTAGGGAACA 58.471 50.000 0.00 0.00 42.51 3.18
3444 3935 0.808755 CCAATGGCAACGTAGGGAAC 59.191 55.000 0.00 0.00 42.51 3.62
3445 3936 0.322997 CCCAATGGCAACGTAGGGAA 60.323 55.000 0.00 0.00 43.70 3.97
3446 3937 1.301623 CCCAATGGCAACGTAGGGA 59.698 57.895 0.00 0.00 43.70 4.20
3447 3938 1.752694 CCCCAATGGCAACGTAGGG 60.753 63.158 0.00 0.00 41.51 3.53
3448 3939 0.106719 ATCCCCAATGGCAACGTAGG 60.107 55.000 0.00 0.00 42.51 3.18
3449 3940 1.308998 GATCCCCAATGGCAACGTAG 58.691 55.000 0.00 0.00 42.51 3.51
3450 3941 0.106918 GGATCCCCAATGGCAACGTA 60.107 55.000 0.00 0.00 42.51 3.57
3451 3942 1.379843 GGATCCCCAATGGCAACGT 60.380 57.895 0.00 0.00 42.51 3.99
3452 3943 1.379710 TGGATCCCCAATGGCAACG 60.380 57.895 9.90 0.00 40.09 4.10
3453 3944 1.044790 CCTGGATCCCCAATGGCAAC 61.045 60.000 9.90 0.00 42.98 4.17
3454 3945 1.220518 TCCTGGATCCCCAATGGCAA 61.221 55.000 9.90 0.00 42.98 4.52
3455 3946 1.622132 TCCTGGATCCCCAATGGCA 60.622 57.895 9.90 0.00 42.98 4.92
3456 3947 1.152368 CTCCTGGATCCCCAATGGC 59.848 63.158 9.90 0.00 42.98 4.40
3457 3948 0.995675 ACCTCCTGGATCCCCAATGG 60.996 60.000 9.90 7.75 42.98 3.16
3458 3949 0.929244 AACCTCCTGGATCCCCAATG 59.071 55.000 9.90 0.00 42.98 2.82
3459 3950 0.929244 CAACCTCCTGGATCCCCAAT 59.071 55.000 9.90 0.00 42.98 3.16
3460 3951 0.477597 ACAACCTCCTGGATCCCCAA 60.478 55.000 9.90 0.00 42.98 4.12
3461 3952 0.419865 TACAACCTCCTGGATCCCCA 59.580 55.000 9.90 0.00 40.95 4.96
3462 3953 1.821088 ATACAACCTCCTGGATCCCC 58.179 55.000 9.90 0.00 37.04 4.81
3463 3954 3.325135 CACTATACAACCTCCTGGATCCC 59.675 52.174 9.90 0.00 37.04 3.85
3464 3955 3.325135 CCACTATACAACCTCCTGGATCC 59.675 52.174 4.20 4.20 37.04 3.36
3465 3956 3.967987 ACCACTATACAACCTCCTGGATC 59.032 47.826 0.00 0.00 37.04 3.36
3466 3957 3.711704 CACCACTATACAACCTCCTGGAT 59.288 47.826 0.00 0.00 37.04 3.41
3467 3958 3.104512 CACCACTATACAACCTCCTGGA 58.895 50.000 0.00 0.00 37.04 3.86
3468 3959 3.104512 TCACCACTATACAACCTCCTGG 58.895 50.000 0.00 0.00 39.83 4.45
3469 3960 3.769844 AGTCACCACTATACAACCTCCTG 59.230 47.826 0.00 0.00 0.00 3.86
3470 3961 4.024670 GAGTCACCACTATACAACCTCCT 58.975 47.826 0.00 0.00 30.63 3.69
3471 3962 4.024670 AGAGTCACCACTATACAACCTCC 58.975 47.826 0.00 0.00 30.63 4.30
3472 3963 4.951094 AGAGAGTCACCACTATACAACCTC 59.049 45.833 0.00 0.00 30.63 3.85
3473 3964 4.936802 AGAGAGTCACCACTATACAACCT 58.063 43.478 0.00 0.00 30.63 3.50
3474 3965 5.419471 AGAAGAGAGTCACCACTATACAACC 59.581 44.000 0.00 0.00 30.63 3.77
3475 3966 6.404954 GGAGAAGAGAGTCACCACTATACAAC 60.405 46.154 0.00 0.00 30.63 3.32
3476 3967 5.652891 GGAGAAGAGAGTCACCACTATACAA 59.347 44.000 0.00 0.00 30.63 2.41
3477 3968 5.194432 GGAGAAGAGAGTCACCACTATACA 58.806 45.833 0.00 0.00 30.63 2.29
3478 3969 4.273969 CGGAGAAGAGAGTCACCACTATAC 59.726 50.000 0.00 0.00 30.63 1.47
3479 3970 4.163649 TCGGAGAAGAGAGTCACCACTATA 59.836 45.833 0.00 0.00 30.63 1.31
3480 3971 3.054287 TCGGAGAAGAGAGTCACCACTAT 60.054 47.826 0.00 0.00 30.63 2.12
3481 3972 2.305052 TCGGAGAAGAGAGTCACCACTA 59.695 50.000 0.00 0.00 30.63 2.74
3482 3973 1.074084 TCGGAGAAGAGAGTCACCACT 59.926 52.381 0.00 0.00 34.57 4.00
3483 3974 1.200484 GTCGGAGAAGAGAGTCACCAC 59.800 57.143 0.00 0.00 39.69 4.16
3484 3975 1.202891 TGTCGGAGAAGAGAGTCACCA 60.203 52.381 0.00 0.00 39.69 4.17
3485 3976 1.470890 CTGTCGGAGAAGAGAGTCACC 59.529 57.143 0.00 0.00 39.69 4.02
3486 3977 1.135517 GCTGTCGGAGAAGAGAGTCAC 60.136 57.143 0.00 0.00 39.69 3.67
3487 3978 1.169577 GCTGTCGGAGAAGAGAGTCA 58.830 55.000 0.00 0.00 39.69 3.41
3488 3979 0.098025 CGCTGTCGGAGAAGAGAGTC 59.902 60.000 0.00 0.00 39.69 3.36
3489 3980 0.606944 ACGCTGTCGGAGAAGAGAGT 60.607 55.000 0.00 0.00 39.69 3.24
3490 3981 0.523966 AACGCTGTCGGAGAAGAGAG 59.476 55.000 0.00 0.00 39.69 3.20
3491 3982 0.241213 CAACGCTGTCGGAGAAGAGA 59.759 55.000 0.00 0.00 39.69 3.10
3492 3983 0.734253 CCAACGCTGTCGGAGAAGAG 60.734 60.000 0.00 0.00 39.69 2.85
3493 3984 1.176619 TCCAACGCTGTCGGAGAAGA 61.177 55.000 0.00 0.00 39.69 2.87
3494 3985 1.009389 GTCCAACGCTGTCGGAGAAG 61.009 60.000 0.00 0.00 39.69 2.85
3495 3986 1.006571 GTCCAACGCTGTCGGAGAA 60.007 57.895 0.00 0.00 39.69 2.87
3496 3987 1.740332 TTGTCCAACGCTGTCGGAGA 61.740 55.000 0.00 0.00 40.69 3.71
3497 3988 0.878523 TTTGTCCAACGCTGTCGGAG 60.879 55.000 0.00 0.00 40.69 4.63
3498 3989 0.878523 CTTTGTCCAACGCTGTCGGA 60.879 55.000 0.00 0.00 40.69 4.55
3499 3990 0.878523 TCTTTGTCCAACGCTGTCGG 60.879 55.000 0.00 0.00 40.69 4.79
3500 3991 0.232303 GTCTTTGTCCAACGCTGTCG 59.768 55.000 0.00 0.00 42.43 4.35
3501 3992 1.583054 AGTCTTTGTCCAACGCTGTC 58.417 50.000 0.00 0.00 0.00 3.51
3502 3993 1.940613 GAAGTCTTTGTCCAACGCTGT 59.059 47.619 0.00 0.00 0.00 4.40
3503 3994 1.264288 GGAAGTCTTTGTCCAACGCTG 59.736 52.381 0.00 0.00 33.79 5.18
3504 3995 1.134220 TGGAAGTCTTTGTCCAACGCT 60.134 47.619 0.00 0.00 41.02 5.07
3505 3996 1.264288 CTGGAAGTCTTTGTCCAACGC 59.736 52.381 0.00 0.00 43.32 4.84


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

AutoCloner maintained by Alex Coulton.