Multiple sequence alignment - TraesCS3B01G396300

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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 TraesCS3B01G396300 chr3B 100.000 3825 0 0 1 3825 625328338 625332162 0.000000e+00 7064
1 TraesCS3B01G396300 chr3D 90.416 3339 170 56 2 3258 470884085 470887355 0.000000e+00 4255
2 TraesCS3B01G396300 chr3D 90.773 466 26 10 3272 3734 470887334 470887785 1.180000e-169 606
3 TraesCS3B01G396300 chr3A 91.825 1688 92 23 410 2080 613167189 613168847 0.000000e+00 2311
4 TraesCS3B01G396300 chr3A 91.818 1210 47 16 2065 3258 613168860 613170033 0.000000e+00 1639
5 TraesCS3B01G396300 chr3A 92.918 466 30 1 3272 3734 613170012 613170477 0.000000e+00 675
6 TraesCS3B01G396300 chr3A 89.409 406 32 7 70 466 613166785 613167188 5.700000e-138 501
7 TraesCS3B01G396300 chr3A 79.901 403 47 17 3328 3727 35434912 35435283 8.150000e-67 265
8 TraesCS3B01G396300 chr7D 78.402 338 45 15 3400 3736 69089165 69088855 1.080000e-45 195


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 TraesCS3B01G396300 chr3B 625328338 625332162 3824 False 7064.0 7064 100.0000 1 3825 1 chr3B.!!$F1 3824
1 TraesCS3B01G396300 chr3D 470884085 470887785 3700 False 2430.5 4255 90.5945 2 3734 2 chr3D.!!$F1 3732
2 TraesCS3B01G396300 chr3A 613166785 613170477 3692 False 1281.5 2311 91.4925 70 3734 4 chr3A.!!$F2 3664

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
586 669 0.898789 ATGGGTCTCTTCCGTCGTGT 60.899 55.000 0.00 0.0 0.00 4.49 F
782 866 1.954382 CCCTCGAGATCCACGTAATGA 59.046 52.381 15.71 0.0 0.00 2.57 F
2230 2403 1.134670 CCCTAAGCGCTAAACTCTGCT 60.135 52.381 12.05 0.0 39.89 4.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1659 1782 0.179132 CGAGACGAGACGAGAGGAGA 60.179 60.0 0.00 0.00 0.00 3.71 R
2510 2683 0.821517 ACATCACTGTATTCCGCGGA 59.178 50.0 27.28 27.28 32.49 5.54 R
3804 3996 0.820074 CGGCCTGAGTCGTATCCTCT 60.820 60.0 0.00 0.00 36.00 3.69 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 3.884037 ATCACACTTCAACCCTCCTTT 57.116 42.857 0.00 0.00 0.00 3.11
64 65 1.956477 CACACTTCAACCCTCCTTTGG 59.044 52.381 0.00 0.00 0.00 3.28
67 68 1.202770 ACTTCAACCCTCCTTTGGACG 60.203 52.381 0.00 0.00 0.00 4.79
215 219 3.573967 ACCTACCTTTTGTGCAAATCCAG 59.426 43.478 0.00 0.00 0.00 3.86
216 220 2.531522 ACCTTTTGTGCAAATCCAGC 57.468 45.000 0.00 0.00 0.00 4.85
245 249 5.221783 TGGAGATCCACTGAATATGACATGG 60.222 44.000 0.00 0.00 42.01 3.66
261 265 6.541934 TGACATGGCATTAATTTTGGATCA 57.458 33.333 0.00 0.00 0.00 2.92
262 266 6.339730 TGACATGGCATTAATTTTGGATCAC 58.660 36.000 0.00 0.00 0.00 3.06
263 267 6.154877 TGACATGGCATTAATTTTGGATCACT 59.845 34.615 0.00 0.00 0.00 3.41
264 268 6.576185 ACATGGCATTAATTTTGGATCACTC 58.424 36.000 0.00 0.00 0.00 3.51
265 269 6.154877 ACATGGCATTAATTTTGGATCACTCA 59.845 34.615 0.00 0.00 0.00 3.41
350 364 6.125029 TCCATTCAGAGGATTCCATTTTCTC 58.875 40.000 5.29 0.00 0.00 2.87
355 369 2.172717 GAGGATTCCATTTTCTCCCCGA 59.827 50.000 5.29 0.00 0.00 5.14
413 495 2.197324 GCACAGAACCCCAACCCA 59.803 61.111 0.00 0.00 0.00 4.51
457 539 4.697756 ACGGGCCCACGTGTCATG 62.698 66.667 24.92 3.98 46.64 3.07
462 544 1.377202 GCCCACGTGTCATGGACAT 60.377 57.895 15.65 0.00 44.63 3.06
494 576 2.031012 CAGCTTCCCGTCAGCACA 59.969 61.111 0.00 0.00 39.99 4.57
584 667 2.190756 GATGGGTCTCTTCCGTCGT 58.809 57.895 0.00 0.00 31.54 4.34
586 669 0.898789 ATGGGTCTCTTCCGTCGTGT 60.899 55.000 0.00 0.00 0.00 4.49
640 723 3.965026 CTCCTCCCTCCGACTGGCA 62.965 68.421 0.00 0.00 34.14 4.92
648 731 4.320456 CCGACTGGCAGCACACCT 62.320 66.667 15.89 0.00 0.00 4.00
782 866 1.954382 CCCTCGAGATCCACGTAATGA 59.046 52.381 15.71 0.00 0.00 2.57
845 930 3.474570 ATGGAGGCCGGAGCAGAC 61.475 66.667 5.05 0.00 42.56 3.51
979 1073 2.757917 GCAGCTCCTCCTCTCCGT 60.758 66.667 0.00 0.00 0.00 4.69
1188 1288 3.433343 TCCCTGTTCGGTGTTATGTCTA 58.567 45.455 0.00 0.00 0.00 2.59
1192 1292 4.804139 CCTGTTCGGTGTTATGTCTATGTC 59.196 45.833 0.00 0.00 0.00 3.06
1193 1293 5.394224 TGTTCGGTGTTATGTCTATGTCA 57.606 39.130 0.00 0.00 0.00 3.58
1196 1296 6.151480 TGTTCGGTGTTATGTCTATGTCACTA 59.849 38.462 0.00 0.00 0.00 2.74
1197 1297 6.954487 TCGGTGTTATGTCTATGTCACTAT 57.046 37.500 0.00 0.00 0.00 2.12
1198 1298 6.735130 TCGGTGTTATGTCTATGTCACTATG 58.265 40.000 0.00 0.00 0.00 2.23
1199 1299 6.320418 TCGGTGTTATGTCTATGTCACTATGT 59.680 38.462 0.00 0.00 0.00 2.29
1200 1300 6.417930 CGGTGTTATGTCTATGTCACTATGTG 59.582 42.308 0.00 0.00 34.45 3.21
1201 1301 6.701841 GGTGTTATGTCTATGTCACTATGTGG 59.298 42.308 0.00 0.00 33.87 4.17
1202 1302 7.265673 GTGTTATGTCTATGTCACTATGTGGT 58.734 38.462 0.00 0.00 33.87 4.16
1203 1303 7.764443 GTGTTATGTCTATGTCACTATGTGGTT 59.236 37.037 0.00 0.00 33.87 3.67
1204 1304 7.979537 TGTTATGTCTATGTCACTATGTGGTTC 59.020 37.037 0.00 0.00 33.87 3.62
1205 1305 4.993905 TGTCTATGTCACTATGTGGTTCG 58.006 43.478 0.00 0.00 33.87 3.95
1206 1306 4.142249 TGTCTATGTCACTATGTGGTTCGG 60.142 45.833 0.00 0.00 33.87 4.30
1207 1307 4.021229 TCTATGTCACTATGTGGTTCGGT 58.979 43.478 0.00 0.00 33.87 4.69
1295 1411 4.392940 CCCTTGATTGCTAGATCGGATTT 58.607 43.478 0.00 0.00 0.00 2.17
1304 1420 5.972935 TGCTAGATCGGATTTGTCTTGTTA 58.027 37.500 0.00 0.00 0.00 2.41
1307 1423 7.011389 TGCTAGATCGGATTTGTCTTGTTATTG 59.989 37.037 0.00 0.00 0.00 1.90
1326 1442 2.615262 GATCCTTCCTCGTTCGCGCT 62.615 60.000 5.56 0.00 41.05 5.92
1348 1464 7.318205 GCGCTATGATTTTAGTTTTCGTATGAC 59.682 37.037 0.00 0.00 0.00 3.06
1364 1482 4.003788 ACGCCCCGTCTGTTGGAG 62.004 66.667 0.00 0.00 33.69 3.86
1449 1569 6.008960 ACCGATTATCTTAGAGTATCCCGTT 58.991 40.000 0.00 0.00 33.66 4.44
1485 1605 2.555732 ATTTGGGGGATTCATGCTGT 57.444 45.000 0.00 0.00 0.00 4.40
1502 1622 2.812011 GCTGTGATGTTTTCTTACGGGT 59.188 45.455 0.00 0.00 0.00 5.28
1510 1630 4.069304 TGTTTTCTTACGGGTGAAGGATG 58.931 43.478 0.00 0.00 0.00 3.51
1548 1671 3.380320 CCATCTAATTTGGACGTTTCCCC 59.620 47.826 0.00 0.00 42.01 4.81
1556 1679 2.458620 TGGACGTTTCCCCTTTTTGTT 58.541 42.857 0.00 0.00 42.01 2.83
1603 1726 2.271800 CAGGACTTGTACGCCATTCTC 58.728 52.381 0.00 0.00 0.00 2.87
1633 1756 2.034687 AACGGCAATGCTCAGGCT 59.965 55.556 4.82 0.00 39.59 4.58
1712 1845 3.377172 CCTTTTTGCCATTCCGGTACTAG 59.623 47.826 0.00 0.00 36.97 2.57
1713 1846 3.706600 TTTTGCCATTCCGGTACTAGT 57.293 42.857 0.00 0.00 36.97 2.57
1714 1847 4.822685 TTTTGCCATTCCGGTACTAGTA 57.177 40.909 0.00 0.00 36.97 1.82
1715 1848 3.806625 TTGCCATTCCGGTACTAGTAC 57.193 47.619 22.53 22.53 36.97 2.73
1719 1852 3.254411 GCCATTCCGGTACTAGTACTACC 59.746 52.174 27.71 16.43 36.36 3.18
1850 1989 7.116233 CCAAACTCAAAAACATTTAATCCCTCG 59.884 37.037 0.00 0.00 0.00 4.63
1964 2105 7.882271 GGAGAAGAGATATAATTTCACTGCCAT 59.118 37.037 0.00 0.00 0.00 4.40
2023 2164 7.359181 GGTTGCAATTTTCATACTTGTACAAGC 60.359 37.037 30.97 16.19 41.99 4.01
2025 2166 7.083858 TGCAATTTTCATACTTGTACAAGCTC 58.916 34.615 30.97 8.60 41.99 4.09
2093 2262 9.997172 AATTTCTATTTCTTATTCTTGTCCCCT 57.003 29.630 0.00 0.00 0.00 4.79
2195 2368 2.673368 CGAGTAGGCCAGTTTCAATCAC 59.327 50.000 5.01 0.00 0.00 3.06
2230 2403 1.134670 CCCTAAGCGCTAAACTCTGCT 60.135 52.381 12.05 0.00 39.89 4.24
2232 2405 2.611518 CTAAGCGCTAAACTCTGCTGT 58.388 47.619 12.05 0.00 37.81 4.40
2338 2511 5.686841 TGAGAAATGCAACGACAGAAAAATG 59.313 36.000 0.00 0.00 0.00 2.32
2341 2514 3.347958 TGCAACGACAGAAAAATGACC 57.652 42.857 0.00 0.00 0.00 4.02
2418 2591 5.245531 CCGCACAACATATACCAAGGATAT 58.754 41.667 0.00 0.00 0.00 1.63
2443 2616 4.021229 AGTATGACTCGGTTGGTACATCA 58.979 43.478 0.00 0.00 39.30 3.07
2510 2683 1.747709 CAGCTCTGCACCTAAGCAAT 58.252 50.000 7.99 0.00 45.13 3.56
2625 2801 1.136110 AGGCAACCAAGGTTTTGAACG 59.864 47.619 0.79 0.00 36.36 3.95
2631 2807 3.258228 ACCAAGGTTTTGAACGCTTTTG 58.742 40.909 0.00 0.00 36.36 2.44
2634 2810 4.153296 CCAAGGTTTTGAACGCTTTTGTTT 59.847 37.500 0.00 0.00 36.36 2.83
2638 2814 4.779023 GGTTTTGAACGCTTTTGTTTTTCG 59.221 37.500 0.00 0.00 30.75 3.46
2705 2881 2.294074 GCGATTGGTGGCAAGGTATAA 58.706 47.619 0.00 0.00 0.00 0.98
2744 2920 8.984891 TTGGACATATGTTATTTTTGAAGCTG 57.015 30.769 10.30 0.00 0.00 4.24
2763 2939 7.557358 TGAAGCTGTTTGGACATATGTTATGAT 59.443 33.333 10.30 0.00 34.72 2.45
2890 3074 5.724854 ACAAGGACCTTACTAGCTATTGGAA 59.275 40.000 6.38 0.00 0.00 3.53
2932 3116 2.251818 TGGTCTTGCTCTCTGCTTACT 58.748 47.619 0.00 0.00 43.37 2.24
2947 3131 8.300286 TCTCTGCTTACTTGTGATATGCTATAC 58.700 37.037 0.00 0.00 0.00 1.47
2979 3163 7.118245 TCAGCTTACATAGGCAATCGATAATTG 59.882 37.037 0.00 0.00 46.37 2.32
3048 3232 0.519077 CTTTTGCTCACTTCGCCTCC 59.481 55.000 0.00 0.00 0.00 4.30
3077 3261 2.749280 ATCGTGTTCACAGATGCTGA 57.251 45.000 0.82 0.00 35.18 4.26
3102 3286 9.591404 GATCTTTATCAGAAAGCGAACATATTG 57.409 33.333 0.00 0.00 34.16 1.90
3183 3367 9.871238 GAATTACTCGAAGCTTAATATGGGATA 57.129 33.333 0.00 0.00 0.00 2.59
3229 3413 8.044060 TGAAATATTTCACATTCTCACCTGTC 57.956 34.615 23.86 0.00 41.88 3.51
3251 3439 2.237143 TGTGTGAAATTTGCCCAAACCA 59.763 40.909 0.00 0.00 32.51 3.67
3252 3440 3.274288 GTGTGAAATTTGCCCAAACCAA 58.726 40.909 0.00 0.00 32.51 3.67
3253 3441 3.691609 GTGTGAAATTTGCCCAAACCAAA 59.308 39.130 0.00 0.00 36.70 3.28
3254 3442 4.156739 GTGTGAAATTTGCCCAAACCAAAA 59.843 37.500 0.00 0.00 35.97 2.44
3255 3443 4.952335 TGTGAAATTTGCCCAAACCAAAAT 59.048 33.333 0.00 0.00 35.97 1.82
3256 3444 5.420104 TGTGAAATTTGCCCAAACCAAAATT 59.580 32.000 0.00 0.00 35.97 1.82
3257 3445 5.976534 GTGAAATTTGCCCAAACCAAAATTC 59.023 36.000 0.00 7.39 40.17 2.17
3258 3446 5.653769 TGAAATTTGCCCAAACCAAAATTCA 59.346 32.000 11.25 11.25 43.88 2.57
3259 3447 6.153340 TGAAATTTGCCCAAACCAAAATTCAA 59.847 30.769 12.35 1.37 43.50 2.69
3260 3448 6.535963 AATTTGCCCAAACCAAAATTCAAA 57.464 29.167 0.00 0.00 35.97 2.69
3261 3449 5.982890 TTTGCCCAAACCAAAATTCAAAA 57.017 30.435 0.00 0.00 29.93 2.44
3262 3450 5.982890 TTGCCCAAACCAAAATTCAAAAA 57.017 30.435 0.00 0.00 0.00 1.94
3307 3495 4.263683 CCCAAATTCTTCTCCCAGTTCTCT 60.264 45.833 0.00 0.00 0.00 3.10
3415 3607 1.904287 AGGCTTTAACGTCAATGGCA 58.096 45.000 12.58 0.00 32.52 4.92
3451 3643 1.003233 AGTAACTAGCTGTGGGGTTGC 59.997 52.381 0.00 0.00 0.00 4.17
3497 3689 8.999431 GTTGTGGTTGAGATAAGATAACAAAGA 58.001 33.333 0.00 0.00 0.00 2.52
3511 3703 9.525826 AAGATAACAAAGATCACTTGGAAGAAT 57.474 29.630 11.09 0.04 36.39 2.40
3517 3709 9.220767 ACAAAGATCACTTGGAAGAATAGTAAC 57.779 33.333 11.09 0.00 36.39 2.50
3688 3880 2.479566 AGTATGCTCACCACTTGTGG 57.520 50.000 17.34 17.34 45.48 4.17
3709 3901 5.949952 GTGGGGATGTTCCTTTAAGTTGTAT 59.050 40.000 0.00 0.00 36.57 2.29
3710 3902 6.436218 GTGGGGATGTTCCTTTAAGTTGTATT 59.564 38.462 0.00 0.00 36.57 1.89
3711 3903 6.435904 TGGGGATGTTCCTTTAAGTTGTATTG 59.564 38.462 0.00 0.00 36.57 1.90
3712 3904 6.330278 GGGATGTTCCTTTAAGTTGTATTGC 58.670 40.000 0.00 0.00 36.57 3.56
3713 3905 6.152831 GGGATGTTCCTTTAAGTTGTATTGCT 59.847 38.462 0.00 0.00 36.57 3.91
3714 3906 7.309805 GGGATGTTCCTTTAAGTTGTATTGCTT 60.310 37.037 0.00 0.00 36.57 3.91
3715 3907 7.542130 GGATGTTCCTTTAAGTTGTATTGCTTG 59.458 37.037 0.00 0.00 32.53 4.01
3716 3908 6.212955 TGTTCCTTTAAGTTGTATTGCTTGC 58.787 36.000 0.00 0.00 0.00 4.01
3717 3909 6.040391 TGTTCCTTTAAGTTGTATTGCTTGCT 59.960 34.615 0.00 0.00 0.00 3.91
3718 3910 7.229707 TGTTCCTTTAAGTTGTATTGCTTGCTA 59.770 33.333 0.00 0.00 0.00 3.49
3719 3911 7.938140 TCCTTTAAGTTGTATTGCTTGCTAT 57.062 32.000 0.00 0.00 0.00 2.97
3720 3912 7.761409 TCCTTTAAGTTGTATTGCTTGCTATG 58.239 34.615 0.17 0.00 0.00 2.23
3721 3913 6.473455 CCTTTAAGTTGTATTGCTTGCTATGC 59.527 38.462 0.17 0.00 0.00 3.14
3722 3914 4.376340 AAGTTGTATTGCTTGCTATGCC 57.624 40.909 0.17 0.00 0.00 4.40
3723 3915 3.355378 AGTTGTATTGCTTGCTATGCCA 58.645 40.909 0.17 0.00 0.00 4.92
3724 3916 3.956199 AGTTGTATTGCTTGCTATGCCAT 59.044 39.130 0.17 0.00 0.00 4.40
3725 3917 4.403432 AGTTGTATTGCTTGCTATGCCATT 59.597 37.500 0.17 0.00 0.00 3.16
3726 3918 5.593909 AGTTGTATTGCTTGCTATGCCATTA 59.406 36.000 0.17 0.00 0.00 1.90
3727 3919 5.437289 TGTATTGCTTGCTATGCCATTAC 57.563 39.130 0.17 0.00 0.00 1.89
3728 3920 5.132502 TGTATTGCTTGCTATGCCATTACT 58.867 37.500 0.17 0.00 0.00 2.24
3729 3921 5.593909 TGTATTGCTTGCTATGCCATTACTT 59.406 36.000 0.17 0.00 0.00 2.24
3730 3922 5.603170 ATTGCTTGCTATGCCATTACTTT 57.397 34.783 0.00 0.00 0.00 2.66
3731 3923 4.637483 TGCTTGCTATGCCATTACTTTC 57.363 40.909 0.00 0.00 0.00 2.62
3732 3924 3.065233 TGCTTGCTATGCCATTACTTTCG 59.935 43.478 0.00 0.00 0.00 3.46
3733 3925 3.065371 GCTTGCTATGCCATTACTTTCGT 59.935 43.478 0.00 0.00 0.00 3.85
3734 3926 4.438744 GCTTGCTATGCCATTACTTTCGTT 60.439 41.667 0.00 0.00 0.00 3.85
3735 3927 4.875544 TGCTATGCCATTACTTTCGTTC 57.124 40.909 0.00 0.00 0.00 3.95
3736 3928 4.513442 TGCTATGCCATTACTTTCGTTCT 58.487 39.130 0.00 0.00 0.00 3.01
3737 3929 4.570772 TGCTATGCCATTACTTTCGTTCTC 59.429 41.667 0.00 0.00 0.00 2.87
3738 3930 4.811557 GCTATGCCATTACTTTCGTTCTCT 59.188 41.667 0.00 0.00 0.00 3.10
3739 3931 5.277058 GCTATGCCATTACTTTCGTTCTCTG 60.277 44.000 0.00 0.00 0.00 3.35
3740 3932 4.002906 TGCCATTACTTTCGTTCTCTGT 57.997 40.909 0.00 0.00 0.00 3.41
3741 3933 4.385825 TGCCATTACTTTCGTTCTCTGTT 58.614 39.130 0.00 0.00 0.00 3.16
3742 3934 4.451096 TGCCATTACTTTCGTTCTCTGTTC 59.549 41.667 0.00 0.00 0.00 3.18
3743 3935 4.142881 GCCATTACTTTCGTTCTCTGTTCC 60.143 45.833 0.00 0.00 0.00 3.62
3744 3936 5.238583 CCATTACTTTCGTTCTCTGTTCCT 58.761 41.667 0.00 0.00 0.00 3.36
3745 3937 5.701290 CCATTACTTTCGTTCTCTGTTCCTT 59.299 40.000 0.00 0.00 0.00 3.36
3746 3938 6.204882 CCATTACTTTCGTTCTCTGTTCCTTT 59.795 38.462 0.00 0.00 0.00 3.11
3747 3939 7.386848 CCATTACTTTCGTTCTCTGTTCCTTTA 59.613 37.037 0.00 0.00 0.00 1.85
3748 3940 8.770828 CATTACTTTCGTTCTCTGTTCCTTTAA 58.229 33.333 0.00 0.00 0.00 1.52
3749 3941 6.846325 ACTTTCGTTCTCTGTTCCTTTAAG 57.154 37.500 0.00 0.00 0.00 1.85
3750 3942 6.346896 ACTTTCGTTCTCTGTTCCTTTAAGT 58.653 36.000 0.00 0.00 0.00 2.24
3751 3943 6.822170 ACTTTCGTTCTCTGTTCCTTTAAGTT 59.178 34.615 0.00 0.00 0.00 2.66
3752 3944 6.598753 TTCGTTCTCTGTTCCTTTAAGTTG 57.401 37.500 0.00 0.00 0.00 3.16
3753 3945 5.054477 TCGTTCTCTGTTCCTTTAAGTTGG 58.946 41.667 0.00 0.00 0.00 3.77
3754 3946 5.054477 CGTTCTCTGTTCCTTTAAGTTGGA 58.946 41.667 0.00 0.00 0.00 3.53
3780 3972 5.878116 TGCTTGCTATACCATTACTTTCGTT 59.122 36.000 0.00 0.00 0.00 3.85
3781 3973 6.373216 TGCTTGCTATACCATTACTTTCGTTT 59.627 34.615 0.00 0.00 0.00 3.60
3782 3974 7.094549 TGCTTGCTATACCATTACTTTCGTTTT 60.095 33.333 0.00 0.00 0.00 2.43
3783 3975 7.218204 GCTTGCTATACCATTACTTTCGTTTTG 59.782 37.037 0.00 0.00 0.00 2.44
3784 3976 7.908827 TGCTATACCATTACTTTCGTTTTGA 57.091 32.000 0.00 0.00 0.00 2.69
3785 3977 7.970384 TGCTATACCATTACTTTCGTTTTGAG 58.030 34.615 0.00 0.00 0.00 3.02
3786 3978 7.820386 TGCTATACCATTACTTTCGTTTTGAGA 59.180 33.333 0.00 0.00 0.00 3.27
3787 3979 8.662141 GCTATACCATTACTTTCGTTTTGAGAA 58.338 33.333 0.00 0.00 0.00 2.87
3790 3982 7.090953 ACCATTACTTTCGTTTTGAGAAACA 57.909 32.000 3.33 0.00 44.25 2.83
3791 3983 7.193595 ACCATTACTTTCGTTTTGAGAAACAG 58.806 34.615 3.33 0.00 44.25 3.16
3792 3984 7.066525 ACCATTACTTTCGTTTTGAGAAACAGA 59.933 33.333 3.33 0.00 44.25 3.41
3793 3985 7.913297 CCATTACTTTCGTTTTGAGAAACAGAA 59.087 33.333 3.33 4.71 44.25 3.02
3794 3986 9.450807 CATTACTTTCGTTTTGAGAAACAGAAT 57.549 29.630 3.33 0.00 44.25 2.40
3797 3989 8.836959 ACTTTCGTTTTGAGAAACAGAATTAC 57.163 30.769 3.33 0.00 44.25 1.89
3798 3990 8.674607 ACTTTCGTTTTGAGAAACAGAATTACT 58.325 29.630 3.33 0.00 44.25 2.24
3799 3991 9.159470 CTTTCGTTTTGAGAAACAGAATTACTC 57.841 33.333 3.33 0.00 44.25 2.59
3800 3992 6.873656 TCGTTTTGAGAAACAGAATTACTCG 58.126 36.000 3.33 0.00 44.25 4.18
3801 3993 6.698329 TCGTTTTGAGAAACAGAATTACTCGA 59.302 34.615 3.33 0.00 44.25 4.04
3802 3994 7.223193 TCGTTTTGAGAAACAGAATTACTCGAA 59.777 33.333 0.00 0.00 44.25 3.71
3803 3995 7.849026 CGTTTTGAGAAACAGAATTACTCGAAA 59.151 33.333 0.00 0.00 44.25 3.46
3804 3996 9.498307 GTTTTGAGAAACAGAATTACTCGAAAA 57.502 29.630 0.00 0.00 43.65 2.29
3805 3997 9.716507 TTTTGAGAAACAGAATTACTCGAAAAG 57.283 29.630 0.00 0.00 37.75 2.27
3806 3998 8.657074 TTGAGAAACAGAATTACTCGAAAAGA 57.343 30.769 0.00 0.00 0.00 2.52
3818 4010 4.617808 CTCGAAAAGAGGATACGACTCA 57.382 45.455 0.00 0.00 43.20 3.41
3819 4011 4.593157 CTCGAAAAGAGGATACGACTCAG 58.407 47.826 0.00 0.00 43.20 3.35
3820 4012 3.377485 TCGAAAAGAGGATACGACTCAGG 59.623 47.826 0.00 0.00 46.39 3.86
3821 4013 3.449632 GAAAAGAGGATACGACTCAGGC 58.550 50.000 0.00 0.00 46.39 4.85
3822 4014 1.404843 AAGAGGATACGACTCAGGCC 58.595 55.000 0.00 0.00 46.39 5.19
3823 4015 0.820074 AGAGGATACGACTCAGGCCG 60.820 60.000 0.00 0.00 46.39 6.13
3824 4016 1.076923 AGGATACGACTCAGGCCGT 60.077 57.895 0.00 0.00 46.39 5.68
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
43 44 2.422803 CCAAAGGAGGGTTGAAGTGTGA 60.423 50.000 0.00 0.00 0.00 3.58
62 63 8.560355 TTCAAATTTCTATGATCTTTCGTCCA 57.440 30.769 0.00 0.00 0.00 4.02
64 65 8.669243 ACCTTCAAATTTCTATGATCTTTCGTC 58.331 33.333 0.00 0.00 0.00 4.20
231 235 8.984764 CCAAAATTAATGCCATGTCATATTCAG 58.015 33.333 0.00 0.00 0.00 3.02
376 390 0.666374 AAAGACCAAAAGGGCGTTCG 59.334 50.000 0.00 0.00 42.05 3.95
377 391 1.868109 GCAAAGACCAAAAGGGCGTTC 60.868 52.381 0.00 0.00 42.05 3.95
380 394 0.597377 GTGCAAAGACCAAAAGGGCG 60.597 55.000 0.00 0.00 42.05 6.13
381 395 0.463620 TGTGCAAAGACCAAAAGGGC 59.536 50.000 0.00 0.00 42.05 5.19
382 396 2.031120 TCTGTGCAAAGACCAAAAGGG 58.969 47.619 1.21 0.00 44.81 3.95
385 409 2.167487 GGGTTCTGTGCAAAGACCAAAA 59.833 45.455 20.47 0.34 0.00 2.44
413 495 2.989166 GGAATTCCGTCGAAACTAACGT 59.011 45.455 9.17 0.00 37.19 3.99
440 522 4.697756 CATGACACGTGGGCCCGT 62.698 66.667 21.57 9.63 42.87 5.28
494 576 2.434359 GGCTTTACGGCGCTGAGT 60.434 61.111 25.98 15.71 0.00 3.41
525 607 4.379243 CTGCACCGGGTCGAGCTT 62.379 66.667 15.18 0.00 0.00 3.74
584 667 0.885879 AAGGACGTGACGCTGATACA 59.114 50.000 4.25 0.00 0.00 2.29
586 669 2.602878 GAAAAGGACGTGACGCTGATA 58.397 47.619 4.25 0.00 0.00 2.15
623 706 3.965026 CTGCCAGTCGGAGGGAGGA 62.965 68.421 0.02 0.00 40.53 3.71
640 723 1.370064 GAACGTGGGTAGGTGTGCT 59.630 57.895 0.00 0.00 0.00 4.40
648 731 4.360964 CGGTGGCGAACGTGGGTA 62.361 66.667 0.00 0.00 0.00 3.69
685 768 2.664851 CGCCGTTCAGGTTCAGCA 60.665 61.111 0.00 0.00 43.70 4.41
807 891 1.309499 CGTGCCCCGCATTTAAAGGA 61.309 55.000 3.61 0.00 41.91 3.36
845 930 1.919956 AACTACTCGACTCGTGGCGG 61.920 60.000 13.46 6.29 0.00 6.13
1188 1288 2.354704 CCACCGAACCACATAGTGACAT 60.355 50.000 0.00 0.00 35.23 3.06
1192 1292 1.024579 GGCCACCGAACCACATAGTG 61.025 60.000 0.00 0.00 0.00 2.74
1193 1293 1.298667 GGCCACCGAACCACATAGT 59.701 57.895 0.00 0.00 0.00 2.12
1273 1389 3.692257 ATCCGATCTAGCAATCAAGGG 57.308 47.619 0.00 0.00 0.00 3.95
1275 1391 5.757320 AGACAAATCCGATCTAGCAATCAAG 59.243 40.000 0.00 0.00 0.00 3.02
1277 1393 5.282055 AGACAAATCCGATCTAGCAATCA 57.718 39.130 0.00 0.00 0.00 2.57
1295 1411 5.046591 ACGAGGAAGGATCAATAACAAGACA 60.047 40.000 0.00 0.00 0.00 3.41
1304 1420 1.802880 CGCGAACGAGGAAGGATCAAT 60.803 52.381 0.00 0.00 43.93 2.57
1307 1423 2.231618 GCGCGAACGAGGAAGGATC 61.232 63.158 12.10 0.00 43.93 3.36
1326 1442 7.254522 GGGCGTCATACGAAAACTAAAATCATA 60.255 37.037 3.22 0.00 46.05 2.15
1348 1464 4.003788 ACTCCAACAGACGGGGCG 62.004 66.667 0.00 0.00 0.00 6.13
1364 1482 7.011482 AGTCTACCAAAATTCTCGCATATTCAC 59.989 37.037 0.00 0.00 0.00 3.18
1449 1569 8.290277 TCCCCCAAATTAATAAGGCTTATTACA 58.710 33.333 30.03 22.66 37.70 2.41
1485 1605 4.069304 CCTTCACCCGTAAGAAAACATCA 58.931 43.478 0.00 0.00 43.02 3.07
1502 1622 5.450826 GCAACATCACAATATGCATCCTTCA 60.451 40.000 0.19 0.00 37.00 3.02
1548 1671 9.097672 CGTTTACCTTGAAAACAAAACAAAAAG 57.902 29.630 0.00 0.00 36.78 2.27
1556 1679 4.451629 TGCCGTTTACCTTGAAAACAAA 57.548 36.364 0.00 0.00 36.78 2.83
1603 1726 2.335712 GCCGTTCTGCCCCTTGAAG 61.336 63.158 0.00 0.00 0.00 3.02
1633 1756 2.301583 TGTGCAACTACCTGTCATGCTA 59.698 45.455 0.00 0.00 38.04 3.49
1659 1782 0.179132 CGAGACGAGACGAGAGGAGA 60.179 60.000 0.00 0.00 0.00 3.71
1712 1845 2.925563 CGTTCCATTTCCACGGTAGTAC 59.074 50.000 0.00 0.00 0.00 2.73
1713 1846 2.094078 CCGTTCCATTTCCACGGTAGTA 60.094 50.000 1.74 0.00 46.90 1.82
1714 1847 1.338389 CCGTTCCATTTCCACGGTAGT 60.338 52.381 1.74 0.00 46.90 2.73
1715 1848 1.365699 CCGTTCCATTTCCACGGTAG 58.634 55.000 1.74 0.00 46.90 3.18
1719 1852 3.267483 ACTATTCCGTTCCATTTCCACG 58.733 45.455 0.00 0.00 0.00 4.94
1785 1924 2.426024 CTCGGCACTAAGTAACCTGCTA 59.574 50.000 0.00 0.00 0.00 3.49
1894 2033 2.094906 GCTTTGCTGATCAACTGATGCA 60.095 45.455 0.00 0.00 34.37 3.96
1982 2123 1.135575 GCAACCAAAGATGAAGGCTCG 60.136 52.381 0.00 0.00 0.00 5.03
1987 2128 6.847956 TGAAAATTGCAACCAAAGATGAAG 57.152 33.333 0.00 0.00 34.05 3.02
2161 2331 3.802948 CCTACTCGTAGGCTTGTCAAT 57.197 47.619 9.99 0.00 45.36 2.57
2195 2368 1.025812 TAGGGTTGTGGCGTTTGTTG 58.974 50.000 0.00 0.00 0.00 3.33
2230 2403 6.374053 CCCATAATGTGTTGACATGACTAACA 59.626 38.462 0.00 4.93 42.30 2.41
2232 2405 6.480763 ACCCATAATGTGTTGACATGACTAA 58.519 36.000 0.00 0.00 42.30 2.24
2338 2511 8.946085 TCTGTAAGACAAATCAATATGTTGGTC 58.054 33.333 2.06 2.32 38.67 4.02
2418 2591 3.827876 TGTACCAACCGAGTCATACTTGA 59.172 43.478 0.00 0.00 31.05 3.02
2443 2616 4.402155 TGCACAGAAGAACCAAAACAAGAT 59.598 37.500 0.00 0.00 0.00 2.40
2510 2683 0.821517 ACATCACTGTATTCCGCGGA 59.178 50.000 27.28 27.28 32.49 5.54
2589 2762 5.303078 TGGTTGCCTAAAGTGCTGATTAAAA 59.697 36.000 0.00 0.00 0.00 1.52
2590 2763 4.830046 TGGTTGCCTAAAGTGCTGATTAAA 59.170 37.500 0.00 0.00 0.00 1.52
2625 2801 6.620253 TGTACTGAAACGAAAAACAAAAGC 57.380 33.333 0.00 0.00 0.00 3.51
2631 2807 5.032220 CCACCTTGTACTGAAACGAAAAAC 58.968 41.667 0.00 0.00 0.00 2.43
2634 2810 4.139859 TCCACCTTGTACTGAAACGAAA 57.860 40.909 0.00 0.00 0.00 3.46
2638 2814 6.371825 CCTTCTTATCCACCTTGTACTGAAAC 59.628 42.308 0.00 0.00 0.00 2.78
2720 2896 8.121305 ACAGCTTCAAAAATAACATATGTCCA 57.879 30.769 9.23 0.39 0.00 4.02
2721 2897 8.986477 AACAGCTTCAAAAATAACATATGTCC 57.014 30.769 9.23 0.00 0.00 4.02
2723 2899 9.206870 CCAAACAGCTTCAAAAATAACATATGT 57.793 29.630 1.41 1.41 0.00 2.29
2724 2900 9.421806 TCCAAACAGCTTCAAAAATAACATATG 57.578 29.630 0.00 0.00 0.00 1.78
2725 2901 9.423061 GTCCAAACAGCTTCAAAAATAACATAT 57.577 29.630 0.00 0.00 0.00 1.78
2726 2902 8.417106 TGTCCAAACAGCTTCAAAAATAACATA 58.583 29.630 0.00 0.00 0.00 2.29
2727 2903 7.271511 TGTCCAAACAGCTTCAAAAATAACAT 58.728 30.769 0.00 0.00 0.00 2.71
2728 2904 6.634805 TGTCCAAACAGCTTCAAAAATAACA 58.365 32.000 0.00 0.00 0.00 2.41
2729 2905 7.713764 ATGTCCAAACAGCTTCAAAAATAAC 57.286 32.000 0.00 0.00 39.20 1.89
2730 2906 9.421806 CATATGTCCAAACAGCTTCAAAAATAA 57.578 29.630 0.00 0.00 39.20 1.40
2731 2907 8.584157 ACATATGTCCAAACAGCTTCAAAAATA 58.416 29.630 1.41 0.00 39.20 1.40
2732 2908 7.444299 ACATATGTCCAAACAGCTTCAAAAAT 58.556 30.769 1.41 0.00 39.20 1.82
2733 2909 6.815089 ACATATGTCCAAACAGCTTCAAAAA 58.185 32.000 1.41 0.00 39.20 1.94
2734 2910 6.403866 ACATATGTCCAAACAGCTTCAAAA 57.596 33.333 1.41 0.00 39.20 2.44
2735 2911 6.403866 AACATATGTCCAAACAGCTTCAAA 57.596 33.333 9.23 0.00 39.20 2.69
2736 2912 7.392953 TCATAACATATGTCCAAACAGCTTCAA 59.607 33.333 9.23 0.00 39.20 2.69
2737 2913 6.883756 TCATAACATATGTCCAAACAGCTTCA 59.116 34.615 9.23 0.00 39.20 3.02
2738 2914 7.320443 TCATAACATATGTCCAAACAGCTTC 57.680 36.000 9.23 0.00 39.20 3.86
2739 2915 7.886629 ATCATAACATATGTCCAAACAGCTT 57.113 32.000 9.23 0.00 39.20 3.74
2740 2916 7.557358 TCAATCATAACATATGTCCAAACAGCT 59.443 33.333 9.23 0.00 39.20 4.24
2741 2917 7.706159 TCAATCATAACATATGTCCAAACAGC 58.294 34.615 9.23 0.00 39.20 4.40
2742 2918 8.896744 ACTCAATCATAACATATGTCCAAACAG 58.103 33.333 9.23 2.04 39.20 3.16
2743 2919 8.806429 ACTCAATCATAACATATGTCCAAACA 57.194 30.769 9.23 0.00 40.38 2.83
2803 2979 4.620097 GCTTAGTAGTAAAACGAGCCTGGT 60.620 45.833 0.00 0.00 31.42 4.00
2932 3116 9.948964 AGCTGAATAATGTATAGCATATCACAA 57.051 29.630 0.00 0.00 36.67 3.33
2947 3131 7.118245 TCGATTGCCTATGTAAGCTGAATAATG 59.882 37.037 0.00 0.00 0.00 1.90
2979 3163 0.106894 CCCCCTATCGCTTTCCAGAC 59.893 60.000 0.00 0.00 0.00 3.51
3048 3232 2.666022 TGTGAACACGATAACTGATGCG 59.334 45.455 0.00 0.00 0.00 4.73
3077 3261 9.113838 ACAATATGTTCGCTTTCTGATAAAGAT 57.886 29.630 1.78 0.00 33.93 2.40
3102 3286 5.050363 TGACTTCTGAAACAAAGTATGCGAC 60.050 40.000 0.00 0.00 35.90 5.19
3218 3402 3.904800 TTTCACACAGACAGGTGAGAA 57.095 42.857 0.00 1.41 44.12 2.87
3227 3411 3.451141 TTGGGCAAATTTCACACAGAC 57.549 42.857 0.00 0.00 0.00 3.51
3228 3412 3.431486 GGTTTGGGCAAATTTCACACAGA 60.431 43.478 0.00 0.00 32.36 3.41
3229 3413 2.871633 GGTTTGGGCAAATTTCACACAG 59.128 45.455 0.00 0.00 32.36 3.66
3264 3452 7.423844 TTGGGTTTGGGCAATTTTAATTTTT 57.576 28.000 0.00 0.00 0.00 1.94
3265 3453 7.423844 TTTGGGTTTGGGCAATTTTAATTTT 57.576 28.000 0.00 0.00 0.00 1.82
3266 3454 7.609097 ATTTGGGTTTGGGCAATTTTAATTT 57.391 28.000 0.00 0.00 0.00 1.82
3267 3455 7.508636 AGAATTTGGGTTTGGGCAATTTTAATT 59.491 29.630 0.00 0.00 0.00 1.40
3268 3456 7.009550 AGAATTTGGGTTTGGGCAATTTTAAT 58.990 30.769 0.00 0.00 0.00 1.40
3269 3457 6.368805 AGAATTTGGGTTTGGGCAATTTTAA 58.631 32.000 0.00 0.00 0.00 1.52
3270 3458 5.946486 AGAATTTGGGTTTGGGCAATTTTA 58.054 33.333 0.00 0.00 0.00 1.52
3271 3459 4.802307 AGAATTTGGGTTTGGGCAATTTT 58.198 34.783 0.00 0.00 0.00 1.82
3272 3460 4.451891 AGAATTTGGGTTTGGGCAATTT 57.548 36.364 0.00 0.00 0.00 1.82
3273 3461 4.104579 AGAAGAATTTGGGTTTGGGCAATT 59.895 37.500 0.00 0.00 0.00 2.32
3274 3462 3.652387 AGAAGAATTTGGGTTTGGGCAAT 59.348 39.130 0.00 0.00 0.00 3.56
3275 3463 3.044894 AGAAGAATTTGGGTTTGGGCAA 58.955 40.909 0.00 0.00 0.00 4.52
3276 3464 2.632512 GAGAAGAATTTGGGTTTGGGCA 59.367 45.455 0.00 0.00 0.00 5.36
3277 3465 2.028112 GGAGAAGAATTTGGGTTTGGGC 60.028 50.000 0.00 0.00 0.00 5.36
3278 3466 2.567169 GGGAGAAGAATTTGGGTTTGGG 59.433 50.000 0.00 0.00 0.00 4.12
3279 3467 3.238597 TGGGAGAAGAATTTGGGTTTGG 58.761 45.455 0.00 0.00 0.00 3.28
3280 3468 3.897505 ACTGGGAGAAGAATTTGGGTTTG 59.102 43.478 0.00 0.00 0.00 2.93
3281 3469 4.199002 ACTGGGAGAAGAATTTGGGTTT 57.801 40.909 0.00 0.00 0.00 3.27
3282 3470 3.903530 ACTGGGAGAAGAATTTGGGTT 57.096 42.857 0.00 0.00 0.00 4.11
3283 3471 3.399305 AGAACTGGGAGAAGAATTTGGGT 59.601 43.478 0.00 0.00 0.00 4.51
3284 3472 4.013050 GAGAACTGGGAGAAGAATTTGGG 58.987 47.826 0.00 0.00 0.00 4.12
3285 3473 4.916183 AGAGAACTGGGAGAAGAATTTGG 58.084 43.478 0.00 0.00 0.00 3.28
3364 3553 5.575218 GGCAACACGGGTGAATAAATAAAAG 59.425 40.000 5.71 0.00 0.00 2.27
3369 3561 2.491693 CTGGCAACACGGGTGAATAAAT 59.508 45.455 5.71 0.00 46.17 1.40
3451 3643 7.063426 CCACAACTACATCATTGTACTGTACAG 59.937 40.741 21.44 21.44 40.24 2.74
3497 3689 6.154706 AGGACGTTACTATTCTTCCAAGTGAT 59.845 38.462 0.00 0.00 0.00 3.06
3503 3695 3.449737 CCCAGGACGTTACTATTCTTCCA 59.550 47.826 0.00 0.00 0.00 3.53
3511 3703 4.560513 CGGTTTTTACCCAGGACGTTACTA 60.561 45.833 0.00 0.00 0.00 1.82
3517 3709 2.289010 ACTACGGTTTTTACCCAGGACG 60.289 50.000 0.00 0.00 0.00 4.79
3570 3762 3.967332 TGACCCTAAACTCCCTAAACG 57.033 47.619 0.00 0.00 0.00 3.60
3571 3763 5.379187 TGTTTGACCCTAAACTCCCTAAAC 58.621 41.667 0.00 0.00 40.36 2.01
3688 3880 6.152831 AGCAATACAACTTAAAGGAACATCCC 59.847 38.462 0.00 0.00 37.19 3.85
3709 3901 4.438608 CGAAAGTAATGGCATAGCAAGCAA 60.439 41.667 0.00 0.00 0.00 3.91
3710 3902 3.065233 CGAAAGTAATGGCATAGCAAGCA 59.935 43.478 0.00 0.00 0.00 3.91
3711 3903 3.065371 ACGAAAGTAATGGCATAGCAAGC 59.935 43.478 0.00 0.00 46.88 4.01
3712 3904 4.882671 ACGAAAGTAATGGCATAGCAAG 57.117 40.909 0.00 0.00 46.88 4.01
3727 3919 6.846325 ACTTAAAGGAACAGAGAACGAAAG 57.154 37.500 0.00 0.00 0.00 2.62
3728 3920 6.037830 CCAACTTAAAGGAACAGAGAACGAAA 59.962 38.462 0.00 0.00 0.00 3.46
3729 3921 5.526111 CCAACTTAAAGGAACAGAGAACGAA 59.474 40.000 0.00 0.00 0.00 3.85
3730 3922 5.054477 CCAACTTAAAGGAACAGAGAACGA 58.946 41.667 0.00 0.00 0.00 3.85
3731 3923 5.054477 TCCAACTTAAAGGAACAGAGAACG 58.946 41.667 0.00 0.00 0.00 3.95
3732 3924 7.363431 CAATCCAACTTAAAGGAACAGAGAAC 58.637 38.462 0.00 0.00 37.48 3.01
3733 3925 6.016276 GCAATCCAACTTAAAGGAACAGAGAA 60.016 38.462 0.00 0.00 37.48 2.87
3734 3926 5.473504 GCAATCCAACTTAAAGGAACAGAGA 59.526 40.000 0.00 0.00 37.48 3.10
3735 3927 5.474876 AGCAATCCAACTTAAAGGAACAGAG 59.525 40.000 0.00 0.00 37.48 3.35
3736 3928 5.385198 AGCAATCCAACTTAAAGGAACAGA 58.615 37.500 0.00 0.00 37.48 3.41
3737 3929 5.712152 AGCAATCCAACTTAAAGGAACAG 57.288 39.130 0.00 0.00 37.48 3.16
3738 3930 5.738783 GCAAGCAATCCAACTTAAAGGAACA 60.739 40.000 0.00 0.00 37.48 3.18
3739 3931 4.686091 GCAAGCAATCCAACTTAAAGGAAC 59.314 41.667 0.00 0.00 37.48 3.62
3740 3932 4.588528 AGCAAGCAATCCAACTTAAAGGAA 59.411 37.500 0.00 0.00 37.48 3.36
3741 3933 4.151883 AGCAAGCAATCCAACTTAAAGGA 58.848 39.130 0.00 0.00 38.50 3.36
3742 3934 4.525912 AGCAAGCAATCCAACTTAAAGG 57.474 40.909 0.00 0.00 0.00 3.11
3743 3935 7.148086 TGGTATAGCAAGCAATCCAACTTAAAG 60.148 37.037 1.19 0.00 0.00 1.85
3744 3936 6.661377 TGGTATAGCAAGCAATCCAACTTAAA 59.339 34.615 1.19 0.00 0.00 1.52
3745 3937 6.184068 TGGTATAGCAAGCAATCCAACTTAA 58.816 36.000 1.19 0.00 0.00 1.85
3746 3938 5.750524 TGGTATAGCAAGCAATCCAACTTA 58.249 37.500 1.19 0.00 0.00 2.24
3747 3939 4.599041 TGGTATAGCAAGCAATCCAACTT 58.401 39.130 1.19 0.00 0.00 2.66
3748 3940 4.235079 TGGTATAGCAAGCAATCCAACT 57.765 40.909 1.19 0.00 0.00 3.16
3749 3941 5.520376 AATGGTATAGCAAGCAATCCAAC 57.480 39.130 8.98 0.00 0.00 3.77
3750 3942 6.364701 AGTAATGGTATAGCAAGCAATCCAA 58.635 36.000 8.98 0.00 0.00 3.53
3751 3943 5.940617 AGTAATGGTATAGCAAGCAATCCA 58.059 37.500 8.98 0.00 0.00 3.41
3752 3944 6.884280 AAGTAATGGTATAGCAAGCAATCC 57.116 37.500 8.98 0.00 0.00 3.01
3753 3945 7.072030 CGAAAGTAATGGTATAGCAAGCAATC 58.928 38.462 8.98 3.36 0.00 2.67
3754 3946 6.542370 ACGAAAGTAATGGTATAGCAAGCAAT 59.458 34.615 8.98 0.00 46.88 3.56
3780 3972 9.104965 TCTTTTCGAGTAATTCTGTTTCTCAAA 57.895 29.630 0.00 0.00 0.00 2.69
3781 3973 8.657074 TCTTTTCGAGTAATTCTGTTTCTCAA 57.343 30.769 0.00 0.00 0.00 3.02
3782 3974 7.385205 CCTCTTTTCGAGTAATTCTGTTTCTCA 59.615 37.037 0.00 0.00 38.11 3.27
3783 3975 7.599245 TCCTCTTTTCGAGTAATTCTGTTTCTC 59.401 37.037 0.00 0.00 38.11 2.87
3784 3976 7.442656 TCCTCTTTTCGAGTAATTCTGTTTCT 58.557 34.615 0.00 0.00 38.11 2.52
3785 3977 7.653767 TCCTCTTTTCGAGTAATTCTGTTTC 57.346 36.000 0.00 0.00 38.11 2.78
3786 3978 9.152595 GTATCCTCTTTTCGAGTAATTCTGTTT 57.847 33.333 0.00 0.00 38.11 2.83
3787 3979 7.488471 CGTATCCTCTTTTCGAGTAATTCTGTT 59.512 37.037 0.00 0.00 38.11 3.16
3788 3980 6.973474 CGTATCCTCTTTTCGAGTAATTCTGT 59.027 38.462 0.00 0.00 38.11 3.41
3789 3981 7.166142 GTCGTATCCTCTTTTCGAGTAATTCTG 59.834 40.741 0.00 0.00 38.11 3.02
3790 3982 7.067251 AGTCGTATCCTCTTTTCGAGTAATTCT 59.933 37.037 0.00 0.00 38.11 2.40
3791 3983 7.194962 AGTCGTATCCTCTTTTCGAGTAATTC 58.805 38.462 0.00 0.00 38.11 2.17
3792 3984 7.098074 AGTCGTATCCTCTTTTCGAGTAATT 57.902 36.000 0.00 0.00 38.11 1.40
3793 3985 6.318144 TGAGTCGTATCCTCTTTTCGAGTAAT 59.682 38.462 0.00 0.00 38.11 1.89
3794 3986 5.645067 TGAGTCGTATCCTCTTTTCGAGTAA 59.355 40.000 0.00 0.00 38.11 2.24
3795 3987 5.181009 TGAGTCGTATCCTCTTTTCGAGTA 58.819 41.667 0.00 0.00 38.11 2.59
3796 3988 4.008330 TGAGTCGTATCCTCTTTTCGAGT 58.992 43.478 0.00 0.00 38.11 4.18
3797 3989 4.496673 CCTGAGTCGTATCCTCTTTTCGAG 60.497 50.000 0.00 0.00 39.57 4.04
3798 3990 3.377485 CCTGAGTCGTATCCTCTTTTCGA 59.623 47.826 0.00 0.00 0.00 3.71
3799 3991 3.696898 CCTGAGTCGTATCCTCTTTTCG 58.303 50.000 0.00 0.00 0.00 3.46
3800 3992 3.449632 GCCTGAGTCGTATCCTCTTTTC 58.550 50.000 0.00 0.00 0.00 2.29
3801 3993 2.168728 GGCCTGAGTCGTATCCTCTTTT 59.831 50.000 0.00 0.00 0.00 2.27
3802 3994 1.757699 GGCCTGAGTCGTATCCTCTTT 59.242 52.381 0.00 0.00 0.00 2.52
3803 3995 1.404843 GGCCTGAGTCGTATCCTCTT 58.595 55.000 0.00 0.00 0.00 2.85
3804 3996 0.820074 CGGCCTGAGTCGTATCCTCT 60.820 60.000 0.00 0.00 36.00 3.69
3805 3997 1.655329 CGGCCTGAGTCGTATCCTC 59.345 63.158 0.00 0.00 36.00 3.71
3806 3998 3.843304 CGGCCTGAGTCGTATCCT 58.157 61.111 0.00 0.00 36.00 3.24


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

AutoCloner maintained by Alex Coulton.