Multiple sequence alignment - TraesCS3A01G432400

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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 TraesCS3A01G432400 chr3A 100.000 3539 0 0 1 3539 673478809 673475271 0.000000e+00 6536
1 TraesCS3A01G432400 chr3D 88.437 2335 125 53 815 3051 537941660 537939373 0.000000e+00 2682
2 TraesCS3A01G432400 chr3D 78.840 586 52 42 255 803 537942252 537941702 2.630000e-86 329
3 TraesCS3A01G432400 chr3D 86.854 213 14 4 51 257 537942499 537942295 3.550000e-55 226
4 TraesCS3A01G432400 chr3D 79.444 180 21 8 3048 3218 537939089 537938917 2.890000e-21 113
5 TraesCS3A01G432400 chr3B 85.556 2077 113 58 775 2732 712755337 712753329 0.000000e+00 2001
6 TraesCS3A01G432400 chr3B 84.392 551 49 25 255 774 712755919 712755375 1.130000e-139 507
7 TraesCS3A01G432400 chr3B 80.054 742 68 49 2812 3537 712750475 712749798 8.890000e-131 477
8 TraesCS3A01G432400 chr3B 91.827 208 13 2 51 257 712756161 712755957 1.610000e-73 287
9 TraesCS3A01G432400 chr3B 98.507 67 1 0 2623 2689 712753446 712753380 6.210000e-23 119


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 TraesCS3A01G432400 chr3A 673475271 673478809 3538 True 6536.0 6536 100.00000 1 3539 1 chr3A.!!$R1 3538
1 TraesCS3A01G432400 chr3D 537938917 537942499 3582 True 837.5 2682 83.39375 51 3218 4 chr3D.!!$R1 3167
2 TraesCS3A01G432400 chr3B 712749798 712756161 6363 True 678.2 2001 88.06720 51 3537 5 chr3B.!!$R1 3486

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
134 135 0.370273 CGCAAGTTGACCATCGCTAC 59.630 55.0 7.16 0.0 0.0 3.58 F
808 971 0.391597 TCGATCGGTAATTCCTGGGC 59.608 55.0 16.41 0.0 0.0 5.36 F
2278 2542 0.034767 AGGTGTACTGATCCCGACGA 60.035 55.0 0.00 0.0 0.0 4.20 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1032 1252 0.234625 CGAGCGAGCTCAGCTAGTAG 59.765 60.0 25.72 16.38 46.13 2.57 R
2373 2654 0.179156 TAAGCTAGCGAACGAACGGG 60.179 55.0 9.55 0.00 0.00 5.28 R
3082 6546 0.030638 CCACCGTTTTGCTGGTTCTG 59.969 55.0 0.00 0.00 35.96 3.02 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
34 35 8.433421 AGAAAACGATTTTAGTTCAGACAAGA 57.567 30.769 0.00 0.00 31.94 3.02
35 36 8.889717 AGAAAACGATTTTAGTTCAGACAAGAA 58.110 29.630 0.00 0.00 31.94 2.52
36 37 9.159470 GAAAACGATTTTAGTTCAGACAAGAAG 57.841 33.333 0.00 0.00 31.94 2.85
37 38 8.433421 AAACGATTTTAGTTCAGACAAGAAGA 57.567 30.769 0.00 0.00 0.00 2.87
38 39 8.433421 AACGATTTTAGTTCAGACAAGAAGAA 57.567 30.769 0.00 0.00 0.00 2.52
39 40 8.608844 ACGATTTTAGTTCAGACAAGAAGAAT 57.391 30.769 0.00 0.00 0.00 2.40
40 41 9.706691 ACGATTTTAGTTCAGACAAGAAGAATA 57.293 29.630 0.00 0.00 0.00 1.75
63 64 8.833231 ATAATGTATCAGTAGGTGCATTGTAC 57.167 34.615 0.00 0.00 0.00 2.90
64 65 5.932619 TGTATCAGTAGGTGCATTGTACT 57.067 39.130 4.86 0.00 0.00 2.73
134 135 0.370273 CGCAAGTTGACCATCGCTAC 59.630 55.000 7.16 0.00 0.00 3.58
135 136 0.727398 GCAAGTTGACCATCGCTACC 59.273 55.000 7.16 0.00 0.00 3.18
136 137 1.943968 GCAAGTTGACCATCGCTACCA 60.944 52.381 7.16 0.00 0.00 3.25
137 138 2.632377 CAAGTTGACCATCGCTACCAT 58.368 47.619 0.00 0.00 0.00 3.55
138 139 2.604046 AGTTGACCATCGCTACCATC 57.396 50.000 0.00 0.00 0.00 3.51
139 140 1.202417 AGTTGACCATCGCTACCATCG 60.202 52.381 0.00 0.00 0.00 3.84
140 141 1.107945 TTGACCATCGCTACCATCGA 58.892 50.000 0.00 0.00 40.45 3.59
141 142 0.668535 TGACCATCGCTACCATCGAG 59.331 55.000 0.00 0.00 39.47 4.04
222 234 2.510238 GCTTGCTCGTGCCGATCT 60.510 61.111 7.05 0.00 38.71 2.75
267 324 1.012086 CATCTCGCCAGGTCAACATG 58.988 55.000 0.00 0.00 0.00 3.21
306 363 1.901654 TAGGGCACGGCGGTTATGTT 61.902 55.000 13.24 0.00 0.00 2.71
311 368 1.858399 GCACGGCGGTTATGTTATTGC 60.858 52.381 13.24 3.67 0.00 3.56
315 372 2.286184 CGGCGGTTATGTTATTGCAGTC 60.286 50.000 0.00 0.00 0.00 3.51
374 442 2.080286 AGGGAGTTTGACATTCGTCG 57.920 50.000 0.00 0.00 45.80 5.12
378 446 1.126846 GAGTTTGACATTCGTCGCCAG 59.873 52.381 0.00 0.00 45.80 4.85
395 463 3.053896 GGCCAACTCGTTTCCCCG 61.054 66.667 0.00 0.00 0.00 5.73
432 500 3.138283 AGAGACACTTGGGATGGTTTCAA 59.862 43.478 0.00 0.00 0.00 2.69
435 503 2.819608 ACACTTGGGATGGTTTCAATCG 59.180 45.455 0.00 0.00 0.00 3.34
449 517 8.125728 TGGTTTCAATCGTTCTTGAATTTTTC 57.874 30.769 9.97 0.00 42.87 2.29
450 518 7.761704 TGGTTTCAATCGTTCTTGAATTTTTCA 59.238 29.630 9.97 0.00 42.87 2.69
451 519 8.055986 GGTTTCAATCGTTCTTGAATTTTTCAC 58.944 33.333 9.97 5.89 42.87 3.18
454 522 9.663904 TTCAATCGTTCTTGAATTTTTCACTAG 57.336 29.630 6.51 0.00 39.55 2.57
460 528 7.952637 CGTTCTTGAATTTTTCACTAGAGTAGC 59.047 37.037 0.00 0.00 39.87 3.58
471 539 1.320344 TAGAGTAGCGTGCACCCTGG 61.320 60.000 14.33 0.00 0.00 4.45
473 541 4.016706 GTAGCGTGCACCCTGGGT 62.017 66.667 14.05 14.05 35.62 4.51
524 604 2.126346 GGCCACGCATTGAAGCAC 60.126 61.111 0.00 0.00 0.00 4.40
543 644 4.694233 CCGTGAGCTGCCTGCACT 62.694 66.667 13.49 0.00 45.94 4.40
544 645 3.420606 CGTGAGCTGCCTGCACTG 61.421 66.667 13.49 6.08 45.94 3.66
545 646 2.281345 GTGAGCTGCCTGCACTGT 60.281 61.111 0.00 0.00 45.94 3.55
546 647 2.281276 TGAGCTGCCTGCACTGTG 60.281 61.111 2.76 2.76 45.94 3.66
547 648 3.735029 GAGCTGCCTGCACTGTGC 61.735 66.667 25.15 25.15 45.94 4.57
548 649 4.266543 AGCTGCCTGCACTGTGCT 62.267 61.111 30.43 8.41 45.31 4.40
549 650 4.039357 GCTGCCTGCACTGTGCTG 62.039 66.667 30.43 28.44 45.31 4.41
550 651 4.039357 CTGCCTGCACTGTGCTGC 62.039 66.667 30.43 29.37 45.31 5.25
551 652 4.879528 TGCCTGCACTGTGCTGCA 62.880 61.111 31.77 31.77 45.31 4.41
657 768 2.450160 GATTAATTTTCACCGGCGCAG 58.550 47.619 10.83 4.65 0.00 5.18
804 967 1.341531 CAGGCTCGATCGGTAATTCCT 59.658 52.381 16.41 9.64 0.00 3.36
807 970 1.605712 GCTCGATCGGTAATTCCTGGG 60.606 57.143 16.41 0.00 0.00 4.45
808 971 0.391597 TCGATCGGTAATTCCTGGGC 59.608 55.000 16.41 0.00 0.00 5.36
811 974 2.052047 ATCGGTAATTCCTGGGCGGG 62.052 60.000 0.00 0.00 0.00 6.13
813 976 2.518587 GTAATTCCTGGGCGGGGC 60.519 66.667 0.00 0.00 0.00 5.80
925 1133 5.973158 TGTGATTGATGATAAATACGCGTG 58.027 37.500 24.59 0.00 0.00 5.34
926 1134 5.522097 TGTGATTGATGATAAATACGCGTGT 59.478 36.000 24.59 13.76 0.00 4.49
959 1167 1.448013 CGCCTCCCTTTCTCGTTCC 60.448 63.158 0.00 0.00 0.00 3.62
960 1168 1.448013 GCCTCCCTTTCTCGTTCCG 60.448 63.158 0.00 0.00 0.00 4.30
961 1169 1.448013 CCTCCCTTTCTCGTTCCGC 60.448 63.158 0.00 0.00 0.00 5.54
978 1198 2.703418 CCCCCATCCCCATTCCCA 60.703 66.667 0.00 0.00 0.00 4.37
1022 1242 3.017581 GTCCCTCCCACCCATGCT 61.018 66.667 0.00 0.00 0.00 3.79
1031 1251 2.034687 ACCCATGCTGTCCTGCAC 59.965 61.111 0.72 0.00 46.33 4.57
1032 1252 2.753043 CCCATGCTGTCCTGCACC 60.753 66.667 0.72 0.00 46.33 5.01
1033 1253 2.353958 CCATGCTGTCCTGCACCT 59.646 61.111 0.72 0.00 46.33 4.00
1034 1254 1.603842 CCATGCTGTCCTGCACCTA 59.396 57.895 0.72 0.00 46.33 3.08
1046 1266 1.066908 CTGCACCTACTAGCTGAGCTC 59.933 57.143 11.68 6.82 40.44 4.09
1225 1459 3.961414 GGCAAGAACCCGGGGACA 61.961 66.667 27.92 0.00 0.00 4.02
1285 1519 2.045926 GACGGCATTGTGCTCCCT 60.046 61.111 1.64 0.00 44.28 4.20
1312 1546 4.101077 CTCCAGGCCCCTCCTCCT 62.101 72.222 0.00 0.00 45.52 3.69
1356 1596 3.592070 CGAGGAAGACGCTGAGGA 58.408 61.111 0.00 0.00 0.00 3.71
1357 1597 1.883732 CGAGGAAGACGCTGAGGAA 59.116 57.895 0.00 0.00 0.00 3.36
1374 1614 2.798148 GAAGATGCCGACCCCAACGT 62.798 60.000 0.00 0.00 0.00 3.99
1375 1615 2.798148 AAGATGCCGACCCCAACGTC 62.798 60.000 0.00 0.00 0.00 4.34
1391 1631 4.054085 TCGACGTCAACGACTCCT 57.946 55.556 17.16 0.00 43.02 3.69
1393 1633 1.509370 CGACGTCAACGACTCCTCG 60.509 63.158 17.16 3.94 46.06 4.63
1665 1920 3.437795 CAGCAAGGCCAAGGCGAG 61.438 66.667 5.01 0.00 43.06 5.03
1668 1923 3.741476 CAAGGCCAAGGCGAGCAC 61.741 66.667 5.01 0.00 43.06 4.40
1907 2162 3.715097 GTCAGGGCAGAGCAGGCT 61.715 66.667 0.00 0.00 0.00 4.58
1977 2232 2.616330 GGCGCAACAAGCTACAGCA 61.616 57.895 10.83 0.00 45.16 4.41
1978 2233 1.154338 GCGCAACAAGCTACAGCAG 60.154 57.895 0.30 0.00 45.16 4.24
2050 2311 2.032071 AAGAACAAGGCCGTCCCG 59.968 61.111 0.00 0.00 39.21 5.14
2277 2541 0.815734 AAGGTGTACTGATCCCGACG 59.184 55.000 0.00 0.00 0.00 5.12
2278 2542 0.034767 AGGTGTACTGATCCCGACGA 60.035 55.000 0.00 0.00 0.00 4.20
2279 2543 0.381089 GGTGTACTGATCCCGACGAG 59.619 60.000 0.00 0.00 0.00 4.18
2280 2544 0.248539 GTGTACTGATCCCGACGAGC 60.249 60.000 0.00 0.00 0.00 5.03
2281 2545 1.359475 GTACTGATCCCGACGAGCC 59.641 63.158 0.00 0.00 0.00 4.70
2320 2601 3.318275 TGAATGTACATAGGACTCGAGCC 59.682 47.826 13.61 14.77 0.00 4.70
2352 2633 1.332375 GTCTCTCTCGTCGATCCCTTG 59.668 57.143 0.00 0.00 0.00 3.61
2366 2647 3.322466 CTTGCACGACCCCCTCCT 61.322 66.667 0.00 0.00 0.00 3.69
2408 2689 6.261859 GCTAGCTTAAGCATTCTTTTTCTCC 58.738 40.000 28.39 0.00 45.16 3.71
2410 2691 6.264841 AGCTTAAGCATTCTTTTTCTCCTG 57.735 37.500 28.39 0.00 45.16 3.86
2421 2702 5.181748 TCTTTTTCTCCTGCTTATCTCTGC 58.818 41.667 0.00 0.00 0.00 4.26
2429 2710 3.452474 CTGCTTATCTCTGCACTGTACC 58.548 50.000 0.00 0.00 35.20 3.34
2515 2796 3.118408 TCAATGTCCATGTACCACTAGCC 60.118 47.826 0.00 0.00 0.00 3.93
2598 2886 2.034879 CCTTGCACGGCGAGACATT 61.035 57.895 16.62 0.00 42.27 2.71
2603 2891 1.852067 GCACGGCGAGACATTGGTTT 61.852 55.000 16.62 0.00 0.00 3.27
2667 2985 1.149101 AAGGCTGGAAAAGTCAGGGA 58.851 50.000 0.00 0.00 30.52 4.20
2710 3036 4.758251 TCCATGCACGCACCGGAG 62.758 66.667 9.46 0.00 0.00 4.63
2728 3054 1.734477 GCCGGATCGACGATGGATG 60.734 63.158 16.49 2.15 35.47 3.51
2740 3066 2.026542 ACGATGGATGGATGGATGGATG 60.027 50.000 0.00 0.00 0.00 3.51
2891 6033 1.066858 AGCGGCCTGTATTATCGATGG 60.067 52.381 8.54 0.00 0.00 3.51
2904 6046 1.153597 TCGATGGCGATGCATCACAC 61.154 55.000 25.70 15.01 42.51 3.82
2908 6050 2.039974 GGCGATGCATCACACCACA 61.040 57.895 25.70 0.00 0.00 4.17
2909 6051 1.135315 GCGATGCATCACACCACAC 59.865 57.895 25.70 0.00 0.00 3.82
2910 6052 1.796151 CGATGCATCACACCACACC 59.204 57.895 25.70 0.00 0.00 4.16
2911 6053 1.647545 CGATGCATCACACCACACCC 61.648 60.000 25.70 0.00 0.00 4.61
2912 6054 1.304381 ATGCATCACACCACACCCC 60.304 57.895 0.00 0.00 0.00 4.95
2913 6055 2.079088 ATGCATCACACCACACCCCA 62.079 55.000 0.00 0.00 0.00 4.96
2914 6056 1.973281 GCATCACACCACACCCCAG 60.973 63.158 0.00 0.00 0.00 4.45
2915 6057 1.455849 CATCACACCACACCCCAGT 59.544 57.895 0.00 0.00 0.00 4.00
2916 6058 0.606401 CATCACACCACACCCCAGTC 60.606 60.000 0.00 0.00 0.00 3.51
2917 6059 2.111999 ATCACACCACACCCCAGTCG 62.112 60.000 0.00 0.00 0.00 4.18
2918 6060 2.445085 ACACCACACCCCAGTCGA 60.445 61.111 0.00 0.00 0.00 4.20
2919 6061 2.030562 CACCACACCCCAGTCGAC 59.969 66.667 7.70 7.70 0.00 4.20
2920 6062 3.612681 ACCACACCCCAGTCGACG 61.613 66.667 10.46 5.16 0.00 5.12
2921 6063 4.373116 CCACACCCCAGTCGACGG 62.373 72.222 10.46 14.06 0.00 4.79
2922 6064 3.612681 CACACCCCAGTCGACGGT 61.613 66.667 20.03 14.69 0.00 4.83
2923 6065 2.841044 ACACCCCAGTCGACGGTT 60.841 61.111 20.03 8.23 0.00 4.44
2924 6066 2.048503 CACCCCAGTCGACGGTTC 60.049 66.667 20.03 0.00 0.00 3.62
2925 6067 2.522436 ACCCCAGTCGACGGTTCA 60.522 61.111 20.03 0.00 0.00 3.18
2926 6068 2.261671 CCCCAGTCGACGGTTCAG 59.738 66.667 20.03 8.70 0.00 3.02
2927 6069 2.261671 CCCAGTCGACGGTTCAGG 59.738 66.667 20.03 9.32 0.00 3.86
2928 6070 2.273179 CCCAGTCGACGGTTCAGGA 61.273 63.158 20.03 0.00 0.00 3.86
2929 6071 1.080705 CCAGTCGACGGTTCAGGAC 60.081 63.158 14.64 0.00 0.00 3.85
2939 6081 1.573108 GGTTCAGGACTCCTCCATCA 58.427 55.000 0.00 0.00 39.39 3.07
2976 6125 2.434185 CTTGTTCTAGGCCGCGCA 60.434 61.111 8.75 0.00 0.00 6.09
2979 6128 2.202878 GTTCTAGGCCGCGCATGA 60.203 61.111 8.75 0.00 0.00 3.07
2980 6129 2.202878 TTCTAGGCCGCGCATGAC 60.203 61.111 8.75 0.00 0.00 3.06
2981 6130 2.721167 TTCTAGGCCGCGCATGACT 61.721 57.895 8.75 8.04 0.00 3.41
2982 6131 2.629050 TTCTAGGCCGCGCATGACTC 62.629 60.000 8.75 0.00 0.00 3.36
2990 6139 2.512286 CGCATGACTCGTGGCCAT 60.512 61.111 9.72 0.00 0.00 4.40
3100 6564 0.738389 ACAGAACCAGCAAAACGGTG 59.262 50.000 0.00 0.00 43.02 4.94
3119 6591 2.742589 GTGGTAAAACTGGTCTGCTAGC 59.257 50.000 8.10 8.10 0.00 3.42
3174 6652 1.083489 CAGATGGCGGCGTTAAAGAA 58.917 50.000 9.37 0.00 0.00 2.52
3175 6653 1.466950 CAGATGGCGGCGTTAAAGAAA 59.533 47.619 9.37 0.00 0.00 2.52
3177 6655 1.735571 GATGGCGGCGTTAAAGAAAGA 59.264 47.619 9.37 0.00 0.00 2.52
3178 6656 1.153353 TGGCGGCGTTAAAGAAAGAG 58.847 50.000 9.37 0.00 0.00 2.85
3179 6657 0.179197 GGCGGCGTTAAAGAAAGAGC 60.179 55.000 9.37 0.00 0.00 4.09
3180 6658 0.179197 GCGGCGTTAAAGAAAGAGCC 60.179 55.000 9.37 0.00 38.23 4.70
3208 6686 4.948621 TCTCCTCCTTAACTGTACAGCTAC 59.051 45.833 22.90 0.00 0.00 3.58
3225 6703 2.299521 CTACCGAAGCTAGCTAGTGGT 58.700 52.381 28.14 28.14 0.00 4.16
3226 6704 0.818296 ACCGAAGCTAGCTAGTGGTG 59.182 55.000 26.03 12.67 0.00 4.17
3227 6705 0.103208 CCGAAGCTAGCTAGTGGTGG 59.897 60.000 19.70 14.54 0.00 4.61
3228 6706 0.528684 CGAAGCTAGCTAGTGGTGGC 60.529 60.000 19.70 7.43 46.33 5.01
3230 6708 3.207354 GCTAGCTAGTGGTGGCGA 58.793 61.111 21.62 0.00 38.31 5.54
3231 6709 1.066587 GCTAGCTAGTGGTGGCGAG 59.933 63.158 21.62 0.00 38.31 5.03
3232 6710 1.066587 CTAGCTAGTGGTGGCGAGC 59.933 63.158 12.92 0.00 37.37 5.03
3233 6711 2.356818 CTAGCTAGTGGTGGCGAGCC 62.357 65.000 12.92 7.26 37.75 4.70
3235 6713 4.514577 CTAGTGGTGGCGAGCCGG 62.515 72.222 9.78 0.00 39.42 6.13
3237 6715 3.942377 TAGTGGTGGCGAGCCGGTA 62.942 63.158 9.78 0.00 39.42 4.02
3240 6718 4.814294 GGTGGCGAGCCGGTACTG 62.814 72.222 9.78 0.00 39.42 2.74
3246 6724 3.755628 GAGCCGGTACTGCGGTGA 61.756 66.667 8.92 0.00 45.33 4.02
3247 6725 3.701604 GAGCCGGTACTGCGGTGAG 62.702 68.421 8.92 0.00 45.33 3.51
3248 6726 4.814294 GCCGGTACTGCGGTGAGG 62.814 72.222 8.92 9.85 0.00 3.86
3249 6727 3.379445 CCGGTACTGCGGTGAGGT 61.379 66.667 8.92 0.00 0.00 3.85
3250 6728 2.654877 CGGTACTGCGGTGAGGTT 59.345 61.111 8.92 0.00 0.00 3.50
3251 6729 1.445582 CGGTACTGCGGTGAGGTTC 60.446 63.158 8.92 0.00 0.00 3.62
3252 6730 1.669440 GGTACTGCGGTGAGGTTCA 59.331 57.895 8.92 0.00 0.00 3.18
3253 6731 0.249398 GGTACTGCGGTGAGGTTCAT 59.751 55.000 8.92 0.00 0.00 2.57
3254 6732 1.338769 GGTACTGCGGTGAGGTTCATT 60.339 52.381 8.92 0.00 0.00 2.57
3255 6733 1.732259 GTACTGCGGTGAGGTTCATTG 59.268 52.381 8.92 0.00 0.00 2.82
3256 6734 1.237285 ACTGCGGTGAGGTTCATTGC 61.237 55.000 0.00 0.38 32.35 3.56
3257 6735 0.957395 CTGCGGTGAGGTTCATTGCT 60.957 55.000 6.92 0.00 32.75 3.91
3258 6736 0.955428 TGCGGTGAGGTTCATTGCTC 60.955 55.000 6.92 0.00 32.75 4.26
3259 6737 1.648467 GCGGTGAGGTTCATTGCTCC 61.648 60.000 0.00 0.00 0.00 4.70
3260 6738 0.036010 CGGTGAGGTTCATTGCTCCT 60.036 55.000 0.31 0.31 0.00 3.69
3267 6745 1.078214 TTCATTGCTCCTGCGAGGG 60.078 57.895 2.86 0.00 43.34 4.30
3268 6746 1.552799 TTCATTGCTCCTGCGAGGGA 61.553 55.000 2.86 0.00 43.34 4.20
3269 6747 1.078214 CATTGCTCCTGCGAGGGAA 60.078 57.895 2.86 0.00 43.34 3.97
3277 6755 1.439644 CTGCGAGGGAAGTAGCCTC 59.560 63.158 0.00 0.00 0.00 4.70
3285 6763 1.279271 GGGAAGTAGCCTCTTGCAGAA 59.721 52.381 10.89 0.00 44.83 3.02
3300 6778 0.463620 CAGAAGGCAGAGGGACTAGC 59.536 60.000 0.00 0.00 41.55 3.42
3301 6779 0.041833 AGAAGGCAGAGGGACTAGCA 59.958 55.000 0.00 0.00 41.55 3.49
3302 6780 0.905357 GAAGGCAGAGGGACTAGCAA 59.095 55.000 0.00 0.00 41.55 3.91
3303 6781 0.908198 AAGGCAGAGGGACTAGCAAG 59.092 55.000 0.00 0.00 41.55 4.01
3304 6782 0.252467 AGGCAGAGGGACTAGCAAGT 60.252 55.000 0.00 0.00 41.55 3.16
3305 6783 0.107945 GGCAGAGGGACTAGCAAGTG 60.108 60.000 0.00 0.00 41.55 3.16
3307 6785 0.107945 CAGAGGGACTAGCAAGTGGC 60.108 60.000 0.00 0.00 41.55 5.01
3363 6852 2.005451 CCAGATCAACCTTGCTTCGAG 58.995 52.381 0.00 0.00 0.00 4.04
3372 6861 5.408604 TCAACCTTGCTTCGAGTTAAAGATC 59.591 40.000 0.00 0.00 0.00 2.75
3376 6865 3.250744 TGCTTCGAGTTAAAGATCGGTG 58.749 45.455 6.25 2.36 39.38 4.94
3377 6866 3.057104 TGCTTCGAGTTAAAGATCGGTGA 60.057 43.478 6.25 0.00 39.38 4.02
3385 6874 5.178797 AGTTAAAGATCGGTGATGGTTGAG 58.821 41.667 0.00 0.00 0.00 3.02
3386 6875 2.029838 AAGATCGGTGATGGTTGAGC 57.970 50.000 0.00 0.00 0.00 4.26
3387 6876 0.179000 AGATCGGTGATGGTTGAGCC 59.821 55.000 0.00 0.00 37.90 4.70
3388 6877 0.179000 GATCGGTGATGGTTGAGCCT 59.821 55.000 0.00 0.00 38.35 4.58
3389 6878 0.620556 ATCGGTGATGGTTGAGCCTT 59.379 50.000 0.00 0.00 38.35 4.35
3390 6879 0.321564 TCGGTGATGGTTGAGCCTTG 60.322 55.000 0.00 0.00 38.35 3.61
3391 6880 0.321564 CGGTGATGGTTGAGCCTTGA 60.322 55.000 0.00 0.00 38.35 3.02
3392 6881 1.457346 GGTGATGGTTGAGCCTTGAG 58.543 55.000 0.00 0.00 38.35 3.02
3457 6946 7.479291 GTGCTAATCGTAATCTAATCTCTCGAC 59.521 40.741 0.00 0.00 0.00 4.20
3476 6965 2.663566 TCAGAGTGAGACAGGCAGG 58.336 57.895 0.00 0.00 0.00 4.85
3477 6966 1.079266 CAGAGTGAGACAGGCAGGC 60.079 63.158 0.00 0.00 0.00 4.85
3478 6967 1.534959 AGAGTGAGACAGGCAGGCA 60.535 57.895 0.00 0.00 0.00 4.75
3479 6968 1.079266 GAGTGAGACAGGCAGGCAG 60.079 63.158 0.00 0.00 0.00 4.85
3480 6969 1.825281 GAGTGAGACAGGCAGGCAGT 61.825 60.000 0.00 0.00 0.00 4.40
3481 6970 1.670406 GTGAGACAGGCAGGCAGTG 60.670 63.158 0.00 0.00 0.00 3.66
3493 6982 1.741706 CAGGCAGTGCTGATTAGTTGG 59.258 52.381 16.11 0.00 0.00 3.77
3494 6983 1.352352 AGGCAGTGCTGATTAGTTGGT 59.648 47.619 16.11 0.00 0.00 3.67
3495 6984 2.162681 GGCAGTGCTGATTAGTTGGTT 58.837 47.619 16.11 0.00 0.00 3.67
3496 6985 2.095059 GGCAGTGCTGATTAGTTGGTTG 60.095 50.000 16.11 0.00 0.00 3.77
3497 6986 2.813754 GCAGTGCTGATTAGTTGGTTGA 59.186 45.455 8.18 0.00 0.00 3.18
3498 6987 3.120060 GCAGTGCTGATTAGTTGGTTGAG 60.120 47.826 8.18 0.00 0.00 3.02
3512 7001 9.634163 TTAGTTGGTTGAGAAGAAAAGAAAAAC 57.366 29.630 0.00 0.00 0.00 2.43
3515 7004 4.503007 GGTTGAGAAGAAAAGAAAAACGGC 59.497 41.667 0.00 0.00 0.00 5.68
3518 7007 4.210832 AGAAGAAAAGAAAAACGGCGAG 57.789 40.909 16.62 0.00 0.00 5.03
3524 7013 1.082104 GAAAAACGGCGAGGCAGTG 60.082 57.895 16.62 0.00 37.01 3.66
3537 7026 2.809601 CAGTGGTACGGCTGCGTC 60.810 66.667 0.00 0.00 0.00 5.19
3538 7027 4.415332 AGTGGTACGGCTGCGTCG 62.415 66.667 0.00 1.18 36.42 5.12
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 9.537192 TCTTGTCTGAACTAAAATCGTTTTCTA 57.463 29.630 0.00 0.00 34.19 2.10
9 10 8.433421 TCTTGTCTGAACTAAAATCGTTTTCT 57.567 30.769 0.00 0.00 34.19 2.52
10 11 9.159470 CTTCTTGTCTGAACTAAAATCGTTTTC 57.841 33.333 0.00 0.00 34.19 2.29
11 12 8.889717 TCTTCTTGTCTGAACTAAAATCGTTTT 58.110 29.630 2.23 2.23 36.67 2.43
12 13 8.433421 TCTTCTTGTCTGAACTAAAATCGTTT 57.567 30.769 0.00 0.00 0.00 3.60
13 14 8.433421 TTCTTCTTGTCTGAACTAAAATCGTT 57.567 30.769 0.00 0.00 0.00 3.85
14 15 8.608844 ATTCTTCTTGTCTGAACTAAAATCGT 57.391 30.769 0.00 0.00 0.00 3.73
29 30 9.823647 CACCTACTGATACATTATTCTTCTTGT 57.176 33.333 0.00 0.00 0.00 3.16
30 31 8.768955 GCACCTACTGATACATTATTCTTCTTG 58.231 37.037 0.00 0.00 0.00 3.02
31 32 8.486210 TGCACCTACTGATACATTATTCTTCTT 58.514 33.333 0.00 0.00 0.00 2.52
32 33 8.023021 TGCACCTACTGATACATTATTCTTCT 57.977 34.615 0.00 0.00 0.00 2.85
33 34 8.839310 ATGCACCTACTGATACATTATTCTTC 57.161 34.615 0.00 0.00 0.00 2.87
34 35 9.060347 CAATGCACCTACTGATACATTATTCTT 57.940 33.333 0.00 0.00 0.00 2.52
35 36 8.213679 ACAATGCACCTACTGATACATTATTCT 58.786 33.333 0.00 0.00 0.00 2.40
36 37 8.383318 ACAATGCACCTACTGATACATTATTC 57.617 34.615 0.00 0.00 0.00 1.75
37 38 9.273016 GTACAATGCACCTACTGATACATTATT 57.727 33.333 0.00 0.00 0.00 1.40
38 39 8.651389 AGTACAATGCACCTACTGATACATTAT 58.349 33.333 0.00 0.00 0.00 1.28
39 40 8.018537 AGTACAATGCACCTACTGATACATTA 57.981 34.615 0.00 0.00 0.00 1.90
40 41 6.889198 AGTACAATGCACCTACTGATACATT 58.111 36.000 0.00 0.00 0.00 2.71
41 42 6.485830 AGTACAATGCACCTACTGATACAT 57.514 37.500 0.00 0.00 0.00 2.29
42 43 5.932619 AGTACAATGCACCTACTGATACA 57.067 39.130 0.00 0.00 0.00 2.29
43 44 7.040473 AGTAGTACAATGCACCTACTGATAC 57.960 40.000 2.52 2.11 38.85 2.24
44 45 7.040617 GCTAGTAGTACAATGCACCTACTGATA 60.041 40.741 16.12 7.21 40.13 2.15
45 46 6.239064 GCTAGTAGTACAATGCACCTACTGAT 60.239 42.308 16.12 6.66 40.13 2.90
46 47 5.067413 GCTAGTAGTACAATGCACCTACTGA 59.933 44.000 16.12 5.80 40.13 3.41
47 48 5.163550 TGCTAGTAGTACAATGCACCTACTG 60.164 44.000 16.12 10.36 40.13 2.74
48 49 4.954202 TGCTAGTAGTACAATGCACCTACT 59.046 41.667 2.52 13.16 42.02 2.57
49 50 5.258456 TGCTAGTAGTACAATGCACCTAC 57.742 43.478 2.52 0.00 0.00 3.18
63 64 2.035632 AGCTGCCCTAGTTGCTAGTAG 58.964 52.381 0.00 3.30 32.62 2.57
64 65 2.160721 AGCTGCCCTAGTTGCTAGTA 57.839 50.000 0.00 0.00 32.62 1.82
126 127 0.037882 ATGGCTCGATGGTAGCGATG 60.038 55.000 0.00 0.00 41.03 3.84
129 130 4.251760 GATGGCTCGATGGTAGCG 57.748 61.111 0.00 0.00 41.03 4.26
222 234 2.238646 AGCATGGGAGAAACGGTAATGA 59.761 45.455 0.00 0.00 0.00 2.57
267 324 0.237498 GGCTAGTTTTGCGTGTGTCC 59.763 55.000 0.00 0.00 0.00 4.02
269 326 2.413837 CTAGGCTAGTTTTGCGTGTGT 58.586 47.619 13.53 0.00 0.00 3.72
293 350 1.668751 CTGCAATAACATAACCGCCGT 59.331 47.619 0.00 0.00 0.00 5.68
306 363 3.438781 GGTGGAAACAATCGACTGCAATA 59.561 43.478 0.00 0.00 46.06 1.90
311 368 0.165944 GCGGTGGAAACAATCGACTG 59.834 55.000 0.00 0.00 46.06 3.51
315 372 1.501741 CTGGCGGTGGAAACAATCG 59.498 57.895 0.00 0.00 46.06 3.34
374 442 2.626780 GGAAACGAGTTGGCCTGGC 61.627 63.158 11.05 11.05 0.00 4.85
378 446 3.053896 CGGGGAAACGAGTTGGCC 61.054 66.667 0.00 0.00 35.47 5.36
395 463 3.119709 CTCTCTCGAGGAGTGCGCC 62.120 68.421 13.56 0.00 42.40 6.53
399 467 2.107950 AGTGTCTCTCTCGAGGAGTG 57.892 55.000 22.36 15.01 42.40 3.51
409 477 3.244561 TGAAACCATCCCAAGTGTCTCTC 60.245 47.826 0.00 0.00 0.00 3.20
417 485 3.758554 AGAACGATTGAAACCATCCCAAG 59.241 43.478 0.00 0.00 0.00 3.61
432 500 8.608844 ACTCTAGTGAAAAATTCAAGAACGAT 57.391 30.769 0.00 0.00 42.15 3.73
435 503 7.952637 CGCTACTCTAGTGAAAAATTCAAGAAC 59.047 37.037 0.00 0.00 42.15 3.01
449 517 0.179134 GGGTGCACGCTACTCTAGTG 60.179 60.000 25.28 0.00 41.90 2.74
450 518 0.323542 AGGGTGCACGCTACTCTAGT 60.324 55.000 32.60 8.40 37.38 2.57
451 519 0.101399 CAGGGTGCACGCTACTCTAG 59.899 60.000 32.91 17.58 37.38 2.43
453 521 2.650116 CCAGGGTGCACGCTACTCT 61.650 63.158 32.91 11.33 37.38 3.24
454 522 2.125512 CCAGGGTGCACGCTACTC 60.126 66.667 32.91 8.05 37.38 2.59
547 648 0.790207 ATCAGTTAACGTGCGTGCAG 59.210 50.000 0.00 0.00 0.00 4.41
548 649 0.787787 GATCAGTTAACGTGCGTGCA 59.212 50.000 0.00 0.00 0.00 4.57
549 650 0.094730 GGATCAGTTAACGTGCGTGC 59.905 55.000 0.00 0.00 0.00 5.34
550 651 0.365523 CGGATCAGTTAACGTGCGTG 59.634 55.000 12.02 1.13 0.00 5.34
551 652 0.734942 CCGGATCAGTTAACGTGCGT 60.735 55.000 16.42 0.00 0.00 5.24
609 720 3.426568 GAAGCCCACAGTGCGAGC 61.427 66.667 0.00 0.00 0.00 5.03
657 768 2.087009 GGCAGTCAGTCACGTACGC 61.087 63.158 16.72 0.00 0.00 4.42
741 867 0.948678 TAAACAACTGCTTCGTGCCC 59.051 50.000 1.30 0.00 42.00 5.36
768 894 0.532862 CCTGCACGGTGAAAGTCACT 60.533 55.000 13.29 0.00 46.19 3.41
925 1133 1.671880 GGCGTACGAAGCGACTTGAC 61.672 60.000 21.65 0.00 34.02 3.18
926 1134 1.443194 GGCGTACGAAGCGACTTGA 60.443 57.895 21.65 0.00 34.02 3.02
938 1146 0.245813 AACGAGAAAGGGAGGCGTAC 59.754 55.000 0.00 0.00 34.46 3.67
959 1167 4.603535 GGAATGGGGATGGGGGCG 62.604 72.222 0.00 0.00 0.00 6.13
960 1168 4.239568 GGGAATGGGGATGGGGGC 62.240 72.222 0.00 0.00 0.00 5.80
961 1169 2.097978 GATGGGAATGGGGATGGGGG 62.098 65.000 0.00 0.00 0.00 5.40
1006 1226 3.016971 CAGCATGGGTGGGAGGGA 61.017 66.667 0.00 0.00 0.00 4.20
1007 1227 3.341629 ACAGCATGGGTGGGAGGG 61.342 66.667 0.00 0.00 43.62 4.30
1008 1228 2.273449 GACAGCATGGGTGGGAGG 59.727 66.667 0.00 0.00 43.62 4.30
1009 1229 2.273449 GGACAGCATGGGTGGGAG 59.727 66.667 0.00 0.00 43.62 4.30
1022 1242 1.186200 CAGCTAGTAGGTGCAGGACA 58.814 55.000 15.96 0.00 36.88 4.02
1031 1251 0.591170 GAGCGAGCTCAGCTAGTAGG 59.409 60.000 25.72 4.39 46.13 3.18
1032 1252 0.234625 CGAGCGAGCTCAGCTAGTAG 59.765 60.000 25.72 16.38 46.13 2.57
1033 1253 0.462225 ACGAGCGAGCTCAGCTAGTA 60.462 55.000 29.49 0.00 46.01 1.82
1034 1254 1.747367 ACGAGCGAGCTCAGCTAGT 60.747 57.895 27.14 27.14 46.13 2.57
1222 1456 4.191015 GCGGGGGAGGGGAATGTC 62.191 72.222 0.00 0.00 0.00 3.06
1285 1519 2.607750 GCCTGGAGGGTGTGGAGA 60.608 66.667 0.00 0.00 37.43 3.71
1341 1581 1.480137 CATCTTCCTCAGCGTCTTCCT 59.520 52.381 0.00 0.00 0.00 3.36
1356 1596 2.046314 CGTTGGGGTCGGCATCTT 60.046 61.111 0.00 0.00 0.00 2.40
1357 1597 3.310860 GACGTTGGGGTCGGCATCT 62.311 63.158 0.00 0.00 36.24 2.90
1374 1614 1.864862 GAGGAGTCGTTGACGTCGA 59.135 57.895 11.62 6.16 40.80 4.20
1375 1615 1.509370 CGAGGAGTCGTTGACGTCG 60.509 63.158 11.62 0.00 41.57 5.12
1376 1616 1.154263 CCGAGGAGTCGTTGACGTC 60.154 63.158 9.11 9.11 45.30 4.34
1907 2162 3.487202 GATGCCGTTCGCGCTCAA 61.487 61.111 5.56 0.00 42.08 3.02
1933 2188 3.076092 CAGACTGGGCTGGCTCTT 58.924 61.111 0.00 0.00 32.26 2.85
1945 2200 4.079850 CGCCTCAGCTGCCAGACT 62.080 66.667 9.47 0.00 36.60 3.24
2240 2504 2.568623 TTCTTGGAGAAGAAGGTGCC 57.431 50.000 0.00 0.00 42.23 5.01
2296 2577 4.541779 CTCGAGTCCTATGTACATTCAGC 58.458 47.826 14.77 3.11 0.00 4.26
2320 2601 0.745128 AGAGAGACGAGCCTGTACCG 60.745 60.000 0.00 0.00 0.00 4.02
2366 2647 4.668118 GAACGAACGGGTGGCGGA 62.668 66.667 0.00 0.00 0.00 5.54
2372 2653 2.126189 GCTAGCGAACGAACGGGT 60.126 61.111 0.00 0.00 0.00 5.28
2373 2654 0.179156 TAAGCTAGCGAACGAACGGG 60.179 55.000 9.55 0.00 0.00 5.28
2374 2655 1.582502 CTTAAGCTAGCGAACGAACGG 59.417 52.381 9.55 0.00 0.00 4.44
2408 2689 3.118992 TGGTACAGTGCAGAGATAAGCAG 60.119 47.826 0.00 0.00 42.14 4.24
2410 2691 3.190874 GTGGTACAGTGCAGAGATAAGC 58.809 50.000 0.00 0.00 41.80 3.09
2421 2702 2.452813 GGCGATGCGTGGTACAGTG 61.453 63.158 0.00 0.00 41.80 3.66
2429 2710 0.589708 ATCATTCATGGCGATGCGTG 59.410 50.000 3.45 5.46 0.00 5.34
2471 2752 0.541392 TGGACGGTTCATGATGGAGG 59.459 55.000 0.00 0.00 0.00 4.30
2515 2796 3.735240 TGCGTGTTACGGTTTTACTACTG 59.265 43.478 3.41 0.00 42.82 2.74
2545 2833 1.337354 TGTTACACGCCACATCGATGT 60.337 47.619 25.18 25.18 42.84 3.06
2568 2856 4.097361 GCAAGGGACCCGGGAGTC 62.097 72.222 32.02 16.07 35.95 3.36
2598 2886 1.503784 TCAACCAACCCCCATAAACCA 59.496 47.619 0.00 0.00 0.00 3.67
2603 2891 0.701731 CCACTCAACCAACCCCCATA 59.298 55.000 0.00 0.00 0.00 2.74
2710 3036 1.734477 CATCCATCGTCGATCCGGC 60.734 63.158 4.34 0.00 0.00 6.13
2728 3054 0.254178 CCCGATCCATCCATCCATCC 59.746 60.000 0.00 0.00 0.00 3.51
2891 6033 1.135315 GTGTGGTGTGATGCATCGC 59.865 57.895 29.23 29.23 39.09 4.58
2898 6040 1.761174 GACTGGGGTGTGGTGTGAT 59.239 57.895 0.00 0.00 0.00 3.06
2899 6041 2.802724 CGACTGGGGTGTGGTGTGA 61.803 63.158 0.00 0.00 0.00 3.58
2904 6046 4.373116 CCGTCGACTGGGGTGTGG 62.373 72.222 14.70 0.36 0.00 4.17
2908 6050 2.522436 TGAACCGTCGACTGGGGT 60.522 61.111 23.77 16.87 34.99 4.95
2909 6051 2.261671 CTGAACCGTCGACTGGGG 59.738 66.667 23.77 16.30 0.00 4.96
2910 6052 2.261671 CCTGAACCGTCGACTGGG 59.738 66.667 23.77 16.92 0.00 4.45
2911 6053 1.080705 GTCCTGAACCGTCGACTGG 60.081 63.158 20.16 20.16 0.00 4.00
2912 6054 0.109689 GAGTCCTGAACCGTCGACTG 60.110 60.000 14.70 9.99 0.00 3.51
2913 6055 1.242665 GGAGTCCTGAACCGTCGACT 61.243 60.000 14.70 0.00 0.00 4.18
2914 6056 1.212229 GGAGTCCTGAACCGTCGAC 59.788 63.158 5.18 5.18 0.00 4.20
2915 6057 0.959372 GAGGAGTCCTGAACCGTCGA 60.959 60.000 18.90 0.00 31.76 4.20
2916 6058 1.507174 GAGGAGTCCTGAACCGTCG 59.493 63.158 18.90 0.00 31.76 5.12
2917 6059 0.898789 TGGAGGAGTCCTGAACCGTC 60.899 60.000 18.90 0.00 44.30 4.79
2918 6060 0.252284 ATGGAGGAGTCCTGAACCGT 60.252 55.000 18.90 10.49 44.30 4.83
2919 6061 0.461961 GATGGAGGAGTCCTGAACCG 59.538 60.000 18.90 0.00 44.30 4.44
2920 6062 1.484240 CTGATGGAGGAGTCCTGAACC 59.516 57.143 18.90 12.64 44.30 3.62
2921 6063 1.134551 GCTGATGGAGGAGTCCTGAAC 60.135 57.143 18.90 7.31 44.30 3.18
2922 6064 1.198713 GCTGATGGAGGAGTCCTGAA 58.801 55.000 18.90 4.41 44.30 3.02
2923 6065 0.689080 GGCTGATGGAGGAGTCCTGA 60.689 60.000 18.90 2.73 44.30 3.86
2924 6066 1.694133 GGGCTGATGGAGGAGTCCTG 61.694 65.000 18.90 1.40 44.30 3.86
2925 6067 1.383803 GGGCTGATGGAGGAGTCCT 60.384 63.158 12.85 12.85 44.30 3.85
2926 6068 2.447714 GGGGCTGATGGAGGAGTCC 61.448 68.421 0.00 0.00 44.24 3.85
2927 6069 2.801631 CGGGGCTGATGGAGGAGTC 61.802 68.421 0.00 0.00 0.00 3.36
2928 6070 2.765807 CGGGGCTGATGGAGGAGT 60.766 66.667 0.00 0.00 0.00 3.85
2929 6071 2.765807 ACGGGGCTGATGGAGGAG 60.766 66.667 0.00 0.00 0.00 3.69
2955 6104 1.671054 GCGGCCTAGAACAAGCACA 60.671 57.895 0.00 0.00 0.00 4.57
2976 6125 2.124570 GCCATGGCCACGAGTCAT 60.125 61.111 27.24 0.00 34.56 3.06
2986 6135 3.807631 CTGCATGCATGGCCATGGC 62.808 63.158 39.72 33.72 42.18 4.40
2987 6136 2.131067 TCTGCATGCATGGCCATGG 61.131 57.895 39.72 27.01 42.18 3.66
2989 6138 0.759060 ATGTCTGCATGCATGGCCAT 60.759 50.000 27.34 14.09 33.37 4.40
2990 6139 1.380650 ATGTCTGCATGCATGGCCA 60.381 52.632 27.34 8.56 33.37 5.36
3071 6535 1.748591 GCTGGTTCTGTCCATCCATCC 60.749 57.143 0.00 0.00 36.84 3.51
3075 6539 1.909700 TTTGCTGGTTCTGTCCATCC 58.090 50.000 0.00 0.00 36.84 3.51
3076 6540 2.350772 CGTTTTGCTGGTTCTGTCCATC 60.351 50.000 0.00 0.00 36.84 3.51
3077 6541 1.608590 CGTTTTGCTGGTTCTGTCCAT 59.391 47.619 0.00 0.00 36.84 3.41
3078 6542 1.021202 CGTTTTGCTGGTTCTGTCCA 58.979 50.000 0.00 0.00 36.00 4.02
3079 6543 0.310854 CCGTTTTGCTGGTTCTGTCC 59.689 55.000 0.00 0.00 0.00 4.02
3080 6544 1.021968 ACCGTTTTGCTGGTTCTGTC 58.978 50.000 0.00 0.00 33.81 3.51
3081 6545 0.738389 CACCGTTTTGCTGGTTCTGT 59.262 50.000 0.00 0.00 35.96 3.41
3082 6546 0.030638 CCACCGTTTTGCTGGTTCTG 59.969 55.000 0.00 0.00 35.96 3.02
3100 6564 2.000447 CGCTAGCAGACCAGTTTTACC 59.000 52.381 16.45 0.00 0.00 2.85
3177 6655 2.091555 AGTTAAGGAGGAGAGATCGGCT 60.092 50.000 0.00 0.00 0.00 5.52
3178 6656 2.035321 CAGTTAAGGAGGAGAGATCGGC 59.965 54.545 0.00 0.00 0.00 5.54
3179 6657 3.292460 ACAGTTAAGGAGGAGAGATCGG 58.708 50.000 0.00 0.00 0.00 4.18
3180 6658 4.882427 TGTACAGTTAAGGAGGAGAGATCG 59.118 45.833 0.00 0.00 0.00 3.69
3208 6686 0.103208 CCACCACTAGCTAGCTTCGG 59.897 60.000 24.88 21.70 0.00 4.30
3218 6696 4.514577 CCGGCTCGCCACCACTAG 62.515 72.222 8.87 0.00 35.37 2.57
3219 6697 3.942377 TACCGGCTCGCCACCACTA 62.942 63.158 0.00 0.00 35.37 2.74
3223 6701 4.814294 CAGTACCGGCTCGCCACC 62.814 72.222 0.00 0.00 35.37 4.61
3233 6711 1.445582 GAACCTCACCGCAGTACCG 60.446 63.158 0.00 0.00 0.00 4.02
3234 6712 0.249398 ATGAACCTCACCGCAGTACC 59.751 55.000 0.00 0.00 0.00 3.34
3235 6713 1.732259 CAATGAACCTCACCGCAGTAC 59.268 52.381 0.00 0.00 0.00 2.73
3236 6714 1.943968 GCAATGAACCTCACCGCAGTA 60.944 52.381 0.00 0.00 29.98 2.74
3237 6715 1.237285 GCAATGAACCTCACCGCAGT 61.237 55.000 0.00 0.00 29.98 4.40
3238 6716 0.957395 AGCAATGAACCTCACCGCAG 60.957 55.000 0.00 0.00 31.44 5.18
3239 6717 0.955428 GAGCAATGAACCTCACCGCA 60.955 55.000 0.00 0.00 31.44 5.69
3240 6718 1.648467 GGAGCAATGAACCTCACCGC 61.648 60.000 0.00 0.00 0.00 5.68
3241 6719 0.036010 AGGAGCAATGAACCTCACCG 60.036 55.000 0.00 0.00 0.00 4.94
3242 6720 1.457346 CAGGAGCAATGAACCTCACC 58.543 55.000 0.00 0.00 31.06 4.02
3243 6721 0.807496 GCAGGAGCAATGAACCTCAC 59.193 55.000 0.00 0.00 41.58 3.51
3244 6722 0.674581 CGCAGGAGCAATGAACCTCA 60.675 55.000 0.00 0.00 42.27 3.86
3245 6723 0.391661 TCGCAGGAGCAATGAACCTC 60.392 55.000 0.00 0.00 42.27 3.85
3246 6724 0.392193 CTCGCAGGAGCAATGAACCT 60.392 55.000 0.00 0.00 42.27 3.50
3247 6725 1.372087 CCTCGCAGGAGCAATGAACC 61.372 60.000 0.00 0.00 42.27 3.62
3248 6726 1.372087 CCCTCGCAGGAGCAATGAAC 61.372 60.000 4.00 0.00 42.27 3.18
3249 6727 1.078214 CCCTCGCAGGAGCAATGAA 60.078 57.895 4.00 0.00 42.27 2.57
3250 6728 1.552799 TTCCCTCGCAGGAGCAATGA 61.553 55.000 4.00 0.00 42.27 2.57
3251 6729 1.078214 TTCCCTCGCAGGAGCAATG 60.078 57.895 4.00 0.00 42.27 2.82
3252 6730 1.222936 CTTCCCTCGCAGGAGCAAT 59.777 57.895 4.00 0.00 42.27 3.56
3253 6731 0.902984 TACTTCCCTCGCAGGAGCAA 60.903 55.000 4.00 0.00 42.27 3.91
3254 6732 1.304962 TACTTCCCTCGCAGGAGCA 60.305 57.895 4.00 0.00 42.27 4.26
3255 6733 1.439644 CTACTTCCCTCGCAGGAGC 59.560 63.158 4.00 0.00 37.67 4.70
3256 6734 1.439644 GCTACTTCCCTCGCAGGAG 59.560 63.158 4.00 0.00 37.67 3.69
3257 6735 2.058595 GGCTACTTCCCTCGCAGGA 61.059 63.158 4.00 0.00 37.67 3.86
3258 6736 2.022240 GAGGCTACTTCCCTCGCAGG 62.022 65.000 0.00 0.00 39.50 4.85
3259 6737 1.439644 GAGGCTACTTCCCTCGCAG 59.560 63.158 0.00 0.00 39.50 5.18
3260 6738 3.617368 GAGGCTACTTCCCTCGCA 58.383 61.111 0.00 0.00 39.50 5.10
3285 6763 0.252467 ACTTGCTAGTCCCTCTGCCT 60.252 55.000 0.00 0.00 0.00 4.75
3315 6804 0.813184 TAGTACTACGCCAGCACCAC 59.187 55.000 0.00 0.00 0.00 4.16
3342 6831 1.623311 TCGAAGCAAGGTTGATCTGGA 59.377 47.619 0.00 0.00 0.00 3.86
3343 6832 2.005451 CTCGAAGCAAGGTTGATCTGG 58.995 52.381 0.00 0.00 0.00 3.86
3344 6833 2.693069 ACTCGAAGCAAGGTTGATCTG 58.307 47.619 0.00 0.00 0.00 2.90
3363 6852 4.201822 GCTCAACCATCACCGATCTTTAAC 60.202 45.833 0.00 0.00 0.00 2.01
3372 6861 0.321564 TCAAGGCTCAACCATCACCG 60.322 55.000 0.00 0.00 43.14 4.94
3376 6865 2.419851 CCTCTCTCAAGGCTCAACCATC 60.420 54.545 0.00 0.00 43.14 3.51
3377 6866 1.558756 CCTCTCTCAAGGCTCAACCAT 59.441 52.381 0.00 0.00 43.14 3.55
3385 6874 2.003301 CGCTTTAACCTCTCTCAAGGC 58.997 52.381 0.00 0.00 40.34 4.35
3386 6875 2.003301 GCGCTTTAACCTCTCTCAAGG 58.997 52.381 0.00 0.00 42.55 3.61
3387 6876 1.656095 CGCGCTTTAACCTCTCTCAAG 59.344 52.381 5.56 0.00 0.00 3.02
3388 6877 1.710013 CGCGCTTTAACCTCTCTCAA 58.290 50.000 5.56 0.00 0.00 3.02
3389 6878 0.736325 GCGCGCTTTAACCTCTCTCA 60.736 55.000 26.67 0.00 0.00 3.27
3390 6879 0.736325 TGCGCGCTTTAACCTCTCTC 60.736 55.000 33.29 0.00 0.00 3.20
3391 6880 0.737715 CTGCGCGCTTTAACCTCTCT 60.738 55.000 33.29 0.00 0.00 3.10
3392 6881 1.710339 CTGCGCGCTTTAACCTCTC 59.290 57.895 33.29 0.00 0.00 3.20
3416 6905 3.289834 CACCACACCAGCAGCACC 61.290 66.667 0.00 0.00 0.00 5.01
3419 6908 0.962356 ATTAGCACCACACCAGCAGC 60.962 55.000 0.00 0.00 0.00 5.25
3420 6909 1.089920 GATTAGCACCACACCAGCAG 58.910 55.000 0.00 0.00 0.00 4.24
3421 6910 0.673333 CGATTAGCACCACACCAGCA 60.673 55.000 0.00 0.00 0.00 4.41
3422 6911 0.673644 ACGATTAGCACCACACCAGC 60.674 55.000 0.00 0.00 0.00 4.85
3457 6946 0.531657 CCTGCCTGTCTCACTCTGAG 59.468 60.000 2.45 2.45 45.59 3.35
3476 6965 2.813754 TCAACCAACTAATCAGCACTGC 59.186 45.455 0.00 0.00 0.00 4.40
3477 6966 4.318332 TCTCAACCAACTAATCAGCACTG 58.682 43.478 0.00 0.00 0.00 3.66
3478 6967 4.623932 TCTCAACCAACTAATCAGCACT 57.376 40.909 0.00 0.00 0.00 4.40
3479 6968 4.997395 TCTTCTCAACCAACTAATCAGCAC 59.003 41.667 0.00 0.00 0.00 4.40
3480 6969 5.227569 TCTTCTCAACCAACTAATCAGCA 57.772 39.130 0.00 0.00 0.00 4.41
3481 6970 6.560253 TTTCTTCTCAACCAACTAATCAGC 57.440 37.500 0.00 0.00 0.00 4.26
3482 6971 8.383318 TCTTTTCTTCTCAACCAACTAATCAG 57.617 34.615 0.00 0.00 0.00 2.90
3486 6975 9.634163 GTTTTTCTTTTCTTCTCAACCAACTAA 57.366 29.630 0.00 0.00 0.00 2.24
3488 6977 6.806739 CGTTTTTCTTTTCTTCTCAACCAACT 59.193 34.615 0.00 0.00 0.00 3.16
3490 6979 6.096695 CCGTTTTTCTTTTCTTCTCAACCAA 58.903 36.000 0.00 0.00 0.00 3.67
3492 6981 4.503007 GCCGTTTTTCTTTTCTTCTCAACC 59.497 41.667 0.00 0.00 0.00 3.77
3493 6982 4.204370 CGCCGTTTTTCTTTTCTTCTCAAC 59.796 41.667 0.00 0.00 0.00 3.18
3494 6983 4.095185 TCGCCGTTTTTCTTTTCTTCTCAA 59.905 37.500 0.00 0.00 0.00 3.02
3495 6984 3.623960 TCGCCGTTTTTCTTTTCTTCTCA 59.376 39.130 0.00 0.00 0.00 3.27
3496 6985 4.205323 TCGCCGTTTTTCTTTTCTTCTC 57.795 40.909 0.00 0.00 0.00 2.87
3497 6986 3.003378 CCTCGCCGTTTTTCTTTTCTTCT 59.997 43.478 0.00 0.00 0.00 2.85
3498 6987 3.297472 CCTCGCCGTTTTTCTTTTCTTC 58.703 45.455 0.00 0.00 0.00 2.87
3515 7004 3.760035 AGCCGTACCACTGCCTCG 61.760 66.667 0.00 0.00 0.00 4.63


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

AutoCloner maintained by Alex Coulton.