Multiple sequence alignment - TraesCS7D01G434400

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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 TraesCS7D01G434400 chr7D 100.000 3755 0 0 1 3755 554315457 554319211 0.000000e+00 6935.0
1 TraesCS7D01G434400 chr7D 90.226 133 10 3 684 814 1526253 1526122 1.790000e-38 171.0
2 TraesCS7D01G434400 chr7D 100.000 32 0 0 3231 3262 116468472 116468441 4.050000e-05 60.2
3 TraesCS7D01G434400 chr7B 95.096 2080 80 14 965 3037 600597480 600595416 0.000000e+00 3256.0
4 TraesCS7D01G434400 chr7B 93.846 975 52 5 1 968 600598484 600597511 0.000000e+00 1461.0
5 TraesCS7D01G434400 chr7B 87.184 554 54 10 3207 3755 600595428 600594887 6.890000e-172 614.0
6 TraesCS7D01G434400 chr7B 81.395 129 22 2 3621 3748 24062639 24062512 1.840000e-18 104.0
7 TraesCS7D01G434400 chr7B 81.301 123 21 2 3623 3744 706794924 706794803 8.580000e-17 99.0
8 TraesCS7D01G434400 chr3D 84.134 2061 255 47 969 2987 600188929 600186899 0.000000e+00 1929.0
9 TraesCS7D01G434400 chr3D 94.118 153 7 2 3038 3190 15398735 15398585 8.110000e-57 231.0
10 TraesCS7D01G434400 chr3D 89.844 128 12 1 684 811 559476750 559476876 3.000000e-36 163.0
11 TraesCS7D01G434400 chr3D 88.636 132 13 2 684 814 548541611 548541481 3.880000e-35 159.0
12 TraesCS7D01G434400 chr3B 83.639 2072 231 60 984 2980 807374442 807372404 0.000000e+00 1849.0
13 TraesCS7D01G434400 chr3B 84.496 129 16 3 3402 3530 497713569 497713445 1.420000e-24 124.0
14 TraesCS7D01G434400 chr4A 76.679 536 121 4 1128 1661 738815348 738815881 1.020000e-75 294.0
15 TraesCS7D01G434400 chr6A 89.474 152 15 1 3036 3186 23959568 23959719 1.380000e-44 191.0
16 TraesCS7D01G434400 chr6A 89.313 131 13 1 684 814 827132 827003 3.000000e-36 163.0
17 TraesCS7D01G434400 chr6A 79.762 84 15 2 3229 3311 176992702 176992620 4.050000e-05 60.2
18 TraesCS7D01G434400 chr1D 90.152 132 11 2 684 814 37432578 37432448 1.790000e-38 171.0
19 TraesCS7D01G434400 chr1D 95.000 40 1 1 3221 3260 438319046 438319008 1.130000e-05 62.1
20 TraesCS7D01G434400 chr6B 91.803 122 8 2 684 804 718835980 718835860 6.450000e-38 169.0
21 TraesCS7D01G434400 chr6B 78.740 127 19 8 3219 3341 101727598 101727720 1.120000e-10 78.7
22 TraesCS7D01G434400 chr6B 80.000 90 17 1 3460 3549 697465283 697465371 8.710000e-07 65.8
23 TraesCS7D01G434400 chr6B 80.000 90 17 1 3460 3549 697537723 697537811 8.710000e-07 65.8
24 TraesCS7D01G434400 chr4D 89.922 129 11 2 684 811 3304604 3304731 8.340000e-37 165.0
25 TraesCS7D01G434400 chr2D 89.844 128 12 1 684 811 204265660 204265786 3.000000e-36 163.0
26 TraesCS7D01G434400 chr2D 97.059 34 1 0 3229 3262 628612464 628612497 1.460000e-04 58.4
27 TraesCS7D01G434400 chr5B 79.397 199 31 5 3554 3744 490866305 490866109 8.460000e-27 132.0
28 TraesCS7D01G434400 chr5B 77.000 200 36 6 3554 3744 490864265 490864067 5.130000e-19 106.0
29 TraesCS7D01G434400 chr3A 84.921 126 19 0 3622 3747 621236293 621236418 1.090000e-25 128.0
30 TraesCS7D01G434400 chr5D 83.721 129 16 5 3621 3746 408974913 408974787 2.370000e-22 117.0
31 TraesCS7D01G434400 chr5A 83.193 119 16 4 3624 3740 704341556 704341440 5.130000e-19 106.0
32 TraesCS7D01G434400 chr6D 100.000 34 0 0 3229 3262 263045188 263045221 3.130000e-06 63.9
33 TraesCS7D01G434400 chr6D 89.362 47 4 1 3219 3265 25856585 25856540 1.460000e-04 58.4
34 TraesCS7D01G434400 chr2B 80.488 82 12 4 3232 3311 555519878 555519799 4.050000e-05 60.2


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 TraesCS7D01G434400 chr7D 554315457 554319211 3754 False 6935 6935 100.000 1 3755 1 chr7D.!!$F1 3754
1 TraesCS7D01G434400 chr7B 600594887 600598484 3597 True 1777 3256 92.042 1 3755 3 chr7B.!!$R3 3754
2 TraesCS7D01G434400 chr3D 600186899 600188929 2030 True 1929 1929 84.134 969 2987 1 chr3D.!!$R3 2018
3 TraesCS7D01G434400 chr3B 807372404 807374442 2038 True 1849 1849 83.639 984 2980 1 chr3B.!!$R2 1996
4 TraesCS7D01G434400 chr4A 738815348 738815881 533 False 294 294 76.679 1128 1661 1 chr4A.!!$F1 533


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
234 236 0.184211 TGCAGATCCACATCCATGGG 59.816 55.0 13.02 0.00 40.49 4.00 F
238 240 0.250467 GATCCACATCCATGGGACGG 60.250 60.0 13.02 7.95 40.49 4.79 F
338 341 0.444651 CGTTTTAGCGAATTCGGCCA 59.555 50.0 27.78 8.01 40.23 5.36 F
384 387 0.456628 TGCTACACCGCGCTATAACA 59.543 50.0 5.56 0.00 0.00 2.41 F
1725 1810 0.455005 AGGTAGCTAAGTCGAACGGC 59.545 55.0 0.00 0.00 0.00 5.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1706 1791 0.455005 GCCGTTCGACTTAGCTACCT 59.545 55.000 0.00 0.00 0.00 3.08 R
1707 1792 0.455005 AGCCGTTCGACTTAGCTACC 59.545 55.000 0.00 0.00 30.46 3.18 R
1721 1806 1.507140 TCATCATCCCCTTAAGCCGT 58.493 50.000 0.00 0.00 0.00 5.68 R
2364 2472 1.219124 GTCGATCAGCTTCTGGCCA 59.781 57.895 4.71 4.71 43.05 5.36 R
3178 3338 0.033920 GACTCACGGGGGTTTTACGT 59.966 55.000 0.00 0.00 42.17 3.57 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
48 49 4.641989 AGATTGTTCTATGGTTGGTGCATC 59.358 41.667 0.00 0.00 0.00 3.91
134 136 2.047830 GGGTCGGAGGGAGTATCAAAT 58.952 52.381 0.00 0.00 36.25 2.32
163 165 3.785982 TGGCGACACCTTAGAGCA 58.214 55.556 0.00 0.00 40.22 4.26
214 216 4.275196 CAGTTGATGGTGAGCATCTTATGG 59.725 45.833 23.14 7.59 34.92 2.74
234 236 0.184211 TGCAGATCCACATCCATGGG 59.816 55.000 13.02 0.00 40.49 4.00
238 240 0.250467 GATCCACATCCATGGGACGG 60.250 60.000 13.02 7.95 40.49 4.79
250 252 4.072131 CCATGGGACGGATTCGATTTTAT 58.928 43.478 2.85 0.00 40.11 1.40
338 341 0.444651 CGTTTTAGCGAATTCGGCCA 59.555 50.000 27.78 8.01 40.23 5.36
384 387 0.456628 TGCTACACCGCGCTATAACA 59.543 50.000 5.56 0.00 0.00 2.41
391 394 2.096909 CACCGCGCTATAACATTGTAGC 60.097 50.000 5.56 9.62 42.34 3.58
392 395 2.131972 CCGCGCTATAACATTGTAGCA 58.868 47.619 17.27 0.00 44.91 3.49
407 410 6.759356 ACATTGTAGCATGTAACGTTATAGCA 59.241 34.615 22.70 13.52 0.00 3.49
414 417 6.226988 CATGTAACGTTATAGCATGCATGA 57.773 37.500 30.64 10.92 34.79 3.07
443 446 4.798574 AGAAACAGAAAATAAGGCAAGCG 58.201 39.130 0.00 0.00 0.00 4.68
446 449 2.095059 ACAGAAAATAAGGCAAGCGCAG 60.095 45.455 11.47 2.01 41.24 5.18
544 547 2.233922 ACCACAACCCTAGTTCTCATCG 59.766 50.000 0.00 0.00 32.45 3.84
564 567 0.598562 TCTATTCCGCCGAGATGAGC 59.401 55.000 0.00 0.00 0.00 4.26
639 642 4.156622 CGCGAGCGACGGTAGTGA 62.157 66.667 12.58 0.00 42.83 3.41
680 683 2.815211 CACCTGGCGGTCACATCG 60.815 66.667 0.00 0.00 43.24 3.84
695 698 7.016466 CGGTCACATCGTCTATTTCTAGATAC 58.984 42.308 0.00 0.00 36.40 2.24
701 704 9.613957 ACATCGTCTATTTCTAGATACATTTCG 57.386 33.333 0.00 0.00 36.40 3.46
814 819 6.007936 TGTAGCGTGCTATGTTTTTCATTT 57.992 33.333 4.68 0.00 37.91 2.32
979 1021 0.611200 TAAGCTGCCGGTTCTAGCAA 59.389 50.000 19.19 8.28 38.82 3.91
1125 1197 6.199393 CCTGATCATGAATTATATGCATGCG 58.801 40.000 14.09 0.00 39.30 4.73
1447 1519 1.225704 GGTGGATGCCCAGAAGGAG 59.774 63.158 0.00 0.00 44.55 3.69
1459 1531 1.743252 GAAGGAGCTCAAGGCCGTG 60.743 63.158 17.19 13.08 43.05 4.94
1513 1585 1.153939 CAAGAGTGGCCTCGAGACG 60.154 63.158 15.71 0.00 42.86 4.18
1574 1646 2.048127 GCGCCAACGTCTTCCTCT 60.048 61.111 0.00 0.00 42.83 3.69
1615 1687 1.497278 CAACGAAGCCACGGATGTG 59.503 57.895 0.00 0.00 46.00 3.21
1633 1705 4.838152 GATCTTGGCAGCGCGGGA 62.838 66.667 8.83 0.00 0.00 5.14
1677 1762 4.054359 AGGACTCAGATCACAAGGTAGT 57.946 45.455 0.00 0.00 0.00 2.73
1684 1769 6.151985 ACTCAGATCACAAGGTAGTTACTCTG 59.848 42.308 0.00 0.00 0.00 3.35
1696 1781 7.379750 AGGTAGTTACTCTGTCTAGCTTTTTG 58.620 38.462 0.00 0.00 38.72 2.44
1697 1782 7.015389 AGGTAGTTACTCTGTCTAGCTTTTTGT 59.985 37.037 0.00 0.00 38.72 2.83
1698 1783 7.656542 GGTAGTTACTCTGTCTAGCTTTTTGTT 59.343 37.037 0.00 0.00 31.93 2.83
1699 1784 7.716768 AGTTACTCTGTCTAGCTTTTTGTTC 57.283 36.000 0.00 0.00 0.00 3.18
1700 1785 6.706716 AGTTACTCTGTCTAGCTTTTTGTTCC 59.293 38.462 0.00 0.00 0.00 3.62
1701 1786 4.058817 ACTCTGTCTAGCTTTTTGTTCCG 58.941 43.478 0.00 0.00 0.00 4.30
1702 1787 4.202223 ACTCTGTCTAGCTTTTTGTTCCGA 60.202 41.667 0.00 0.00 0.00 4.55
1703 1788 4.894784 TCTGTCTAGCTTTTTGTTCCGAT 58.105 39.130 0.00 0.00 0.00 4.18
1704 1789 4.690748 TCTGTCTAGCTTTTTGTTCCGATG 59.309 41.667 0.00 0.00 0.00 3.84
1706 1791 5.060506 TGTCTAGCTTTTTGTTCCGATGAA 58.939 37.500 0.00 0.00 0.00 2.57
1707 1792 5.179368 TGTCTAGCTTTTTGTTCCGATGAAG 59.821 40.000 0.00 0.00 0.00 3.02
1708 1793 3.923017 AGCTTTTTGTTCCGATGAAGG 57.077 42.857 0.00 0.00 0.00 3.46
1719 1804 2.617308 TCCGATGAAGGTAGCTAAGTCG 59.383 50.000 12.86 12.86 0.00 4.18
1721 1806 3.066342 CCGATGAAGGTAGCTAAGTCGAA 59.934 47.826 18.41 0.00 0.00 3.71
1725 1810 0.455005 AGGTAGCTAAGTCGAACGGC 59.545 55.000 0.00 0.00 0.00 5.68
1732 1818 2.537401 CTAAGTCGAACGGCTTAAGGG 58.463 52.381 18.99 7.17 41.09 3.95
1781 1882 0.746923 TGCCATTGCTAGCTGCTCAG 60.747 55.000 17.23 3.60 43.37 3.35
2431 2539 1.379576 AAGCTCATGGCCTCCAAGC 60.380 57.895 3.32 8.10 43.05 4.01
2484 2592 1.908793 CGCCTCCGATACCTCCCAT 60.909 63.158 0.00 0.00 36.29 4.00
2877 3025 6.150809 CGCCCCTAAAATCCTAGTACTAGTAG 59.849 46.154 24.84 18.69 0.00 2.57
2906 3062 7.120873 CCATCCAATATCCATCTGTTTCATCTC 59.879 40.741 0.00 0.00 0.00 2.75
2991 3150 2.597340 CCCCCATGGATGCGTCTT 59.403 61.111 15.22 0.00 35.39 3.01
3008 3168 6.738114 TGCGTCTTCATTCTTTTCTCATTTT 58.262 32.000 0.00 0.00 0.00 1.82
3029 3189 9.039870 CATTTTTGTATTTCAACCAGCTTGTTA 57.960 29.630 2.38 0.00 35.61 2.41
3031 3191 9.606631 TTTTTGTATTTCAACCAGCTTGTTAAT 57.393 25.926 2.38 3.72 35.61 1.40
3037 3197 8.601845 ATTTCAACCAGCTTGTTAATTTTACC 57.398 30.769 2.38 0.00 0.00 2.85
3038 3198 5.764131 TCAACCAGCTTGTTAATTTTACCG 58.236 37.500 2.38 0.00 0.00 4.02
3039 3199 4.776795 ACCAGCTTGTTAATTTTACCGG 57.223 40.909 0.00 0.00 0.00 5.28
3040 3200 4.146564 ACCAGCTTGTTAATTTTACCGGT 58.853 39.130 13.98 13.98 0.00 5.28
3041 3201 5.315348 ACCAGCTTGTTAATTTTACCGGTA 58.685 37.500 11.16 11.16 0.00 4.02
3042 3202 5.769162 ACCAGCTTGTTAATTTTACCGGTAA 59.231 36.000 23.17 23.17 0.00 2.85
3043 3203 6.434965 ACCAGCTTGTTAATTTTACCGGTAAT 59.565 34.615 27.03 15.29 0.00 1.89
3044 3204 6.750039 CCAGCTTGTTAATTTTACCGGTAATG 59.250 38.462 27.03 16.54 0.00 1.90
3045 3205 6.252655 CAGCTTGTTAATTTTACCGGTAATGC 59.747 38.462 27.03 16.17 0.00 3.56
3046 3206 6.152154 AGCTTGTTAATTTTACCGGTAATGCT 59.848 34.615 27.03 17.96 0.00 3.79
3047 3207 7.337436 AGCTTGTTAATTTTACCGGTAATGCTA 59.663 33.333 27.03 14.99 0.00 3.49
3048 3208 7.642586 GCTTGTTAATTTTACCGGTAATGCTAG 59.357 37.037 27.03 17.66 0.00 3.42
3049 3209 8.789825 TTGTTAATTTTACCGGTAATGCTAGA 57.210 30.769 27.03 8.96 0.00 2.43
3050 3210 8.967664 TGTTAATTTTACCGGTAATGCTAGAT 57.032 30.769 27.03 11.65 0.00 1.98
3051 3211 8.832521 TGTTAATTTTACCGGTAATGCTAGATG 58.167 33.333 27.03 0.00 0.00 2.90
3052 3212 5.941948 ATTTTACCGGTAATGCTAGATGC 57.058 39.130 27.03 0.00 43.25 3.91
3061 3221 2.279517 GCTAGATGCACGGACGGG 60.280 66.667 0.00 0.00 42.31 5.28
3062 3222 2.279517 CTAGATGCACGGACGGGC 60.280 66.667 12.67 12.67 46.35 6.13
3063 3223 3.792053 CTAGATGCACGGACGGGCC 62.792 68.421 16.99 0.00 45.41 5.80
3065 3225 2.914756 TAGATGCACGGACGGGCCTA 62.915 60.000 16.99 8.55 45.41 3.93
3066 3226 3.161450 ATGCACGGACGGGCCTAT 61.161 61.111 16.99 0.85 45.41 2.57
3067 3227 2.660258 GATGCACGGACGGGCCTATT 62.660 60.000 16.99 0.00 45.41 1.73
3068 3228 1.404479 ATGCACGGACGGGCCTATTA 61.404 55.000 16.99 0.00 45.41 0.98
3069 3229 1.593479 GCACGGACGGGCCTATTAC 60.593 63.158 7.89 0.00 38.90 1.89
3070 3230 1.817881 CACGGACGGGCCTATTACA 59.182 57.895 0.84 0.00 0.00 2.41
3071 3231 0.249322 CACGGACGGGCCTATTACAG 60.249 60.000 0.84 0.00 0.00 2.74
3090 3250 8.773404 ATTACAGGATTTACGGAATAGCATAC 57.227 34.615 0.00 0.00 0.00 2.39
3091 3251 5.227908 ACAGGATTTACGGAATAGCATACG 58.772 41.667 0.00 0.00 0.00 3.06
3092 3252 5.221382 ACAGGATTTACGGAATAGCATACGT 60.221 40.000 0.00 0.00 42.71 3.57
3093 3253 5.118664 CAGGATTTACGGAATAGCATACGTG 59.881 44.000 0.00 0.00 40.12 4.49
3094 3254 4.387862 GGATTTACGGAATAGCATACGTGG 59.612 45.833 0.00 0.00 40.12 4.94
3095 3255 3.374220 TTACGGAATAGCATACGTGGG 57.626 47.619 0.00 0.00 40.12 4.61
3096 3256 0.249741 ACGGAATAGCATACGTGGGC 60.250 55.000 0.00 0.86 38.24 5.36
3097 3257 0.249699 CGGAATAGCATACGTGGGCA 60.250 55.000 14.46 2.87 0.00 5.36
3098 3258 1.808512 CGGAATAGCATACGTGGGCAA 60.809 52.381 14.46 0.00 0.00 4.52
3099 3259 2.504367 GGAATAGCATACGTGGGCAAT 58.496 47.619 14.46 1.64 0.00 3.56
3100 3260 2.484264 GGAATAGCATACGTGGGCAATC 59.516 50.000 14.46 9.25 0.00 2.67
3101 3261 1.795768 ATAGCATACGTGGGCAATCG 58.204 50.000 14.46 0.00 0.00 3.34
3102 3262 0.249699 TAGCATACGTGGGCAATCGG 60.250 55.000 14.46 0.00 0.00 4.18
3103 3263 2.542907 GCATACGTGGGCAATCGGG 61.543 63.158 0.00 0.00 0.00 5.14
3104 3264 1.145156 CATACGTGGGCAATCGGGA 59.855 57.895 0.00 0.00 0.00 5.14
3105 3265 0.250295 CATACGTGGGCAATCGGGAT 60.250 55.000 0.00 0.00 0.00 3.85
3106 3266 0.472471 ATACGTGGGCAATCGGGATT 59.528 50.000 0.00 0.00 0.00 3.01
3108 3268 2.480610 CGTGGGCAATCGGGATTGG 61.481 63.158 19.75 5.37 46.14 3.16
3109 3269 2.127232 GTGGGCAATCGGGATTGGG 61.127 63.158 19.75 0.00 46.14 4.12
3110 3270 2.521708 GGGCAATCGGGATTGGGG 60.522 66.667 19.75 0.00 46.14 4.96
3111 3271 2.600731 GGCAATCGGGATTGGGGA 59.399 61.111 19.75 0.00 46.14 4.81
3112 3272 1.076339 GGCAATCGGGATTGGGGAA 60.076 57.895 19.75 0.00 46.14 3.97
3113 3273 1.109323 GGCAATCGGGATTGGGGAAG 61.109 60.000 19.75 0.00 46.14 3.46
3114 3274 0.106719 GCAATCGGGATTGGGGAAGA 60.107 55.000 19.75 0.00 46.14 2.87
3115 3275 1.972872 CAATCGGGATTGGGGAAGAG 58.027 55.000 12.51 0.00 43.25 2.85
3116 3276 0.846693 AATCGGGATTGGGGAAGAGG 59.153 55.000 0.00 0.00 0.00 3.69
3117 3277 1.062488 ATCGGGATTGGGGAAGAGGG 61.062 60.000 0.00 0.00 0.00 4.30
3118 3278 1.692749 CGGGATTGGGGAAGAGGGA 60.693 63.158 0.00 0.00 0.00 4.20
3119 3279 1.700042 CGGGATTGGGGAAGAGGGAG 61.700 65.000 0.00 0.00 0.00 4.30
3120 3280 1.534203 GGATTGGGGAAGAGGGAGC 59.466 63.158 0.00 0.00 0.00 4.70
3121 3281 1.281925 GGATTGGGGAAGAGGGAGCA 61.282 60.000 0.00 0.00 0.00 4.26
3122 3282 0.849417 GATTGGGGAAGAGGGAGCAT 59.151 55.000 0.00 0.00 0.00 3.79
3123 3283 0.554792 ATTGGGGAAGAGGGAGCATG 59.445 55.000 0.00 0.00 0.00 4.06
3124 3284 1.574526 TTGGGGAAGAGGGAGCATGG 61.575 60.000 0.00 0.00 0.00 3.66
3125 3285 2.761465 GGGGAAGAGGGAGCATGGG 61.761 68.421 0.00 0.00 0.00 4.00
3126 3286 2.194326 GGAAGAGGGAGCATGGGC 59.806 66.667 0.00 0.00 41.61 5.36
3127 3287 2.194326 GAAGAGGGAGCATGGGCC 59.806 66.667 0.00 0.00 42.56 5.80
3128 3288 3.424105 AAGAGGGAGCATGGGCCC 61.424 66.667 17.59 17.59 45.04 5.80
3144 3304 4.751820 CCCACCCCCGCCGAAAAT 62.752 66.667 0.00 0.00 0.00 1.82
3145 3305 2.272797 CCACCCCCGCCGAAAATA 59.727 61.111 0.00 0.00 0.00 1.40
3146 3306 1.378778 CCACCCCCGCCGAAAATAA 60.379 57.895 0.00 0.00 0.00 1.40
3147 3307 1.381165 CCACCCCCGCCGAAAATAAG 61.381 60.000 0.00 0.00 0.00 1.73
3148 3308 1.077285 ACCCCCGCCGAAAATAAGG 60.077 57.895 0.00 0.00 0.00 2.69
3149 3309 1.826487 CCCCCGCCGAAAATAAGGG 60.826 63.158 0.00 0.00 41.68 3.95
3150 3310 3.836151 CCCGCCGAAAATAAGGGG 58.164 61.111 0.00 0.00 38.44 4.79
3171 3331 6.413783 GGGGGAGAGAGATTAGTTTAGAAG 57.586 45.833 0.00 0.00 0.00 2.85
3172 3332 6.137559 GGGGGAGAGAGATTAGTTTAGAAGA 58.862 44.000 0.00 0.00 0.00 2.87
3173 3333 6.612049 GGGGGAGAGAGATTAGTTTAGAAGAA 59.388 42.308 0.00 0.00 0.00 2.52
3174 3334 7.125963 GGGGGAGAGAGATTAGTTTAGAAGAAA 59.874 40.741 0.00 0.00 0.00 2.52
3175 3335 8.541234 GGGGAGAGAGATTAGTTTAGAAGAAAA 58.459 37.037 0.00 0.00 0.00 2.29
3181 3341 9.930693 AGAGATTAGTTTAGAAGAAAATCACGT 57.069 29.630 0.00 0.00 0.00 4.49
3188 3348 8.347771 AGTTTAGAAGAAAATCACGTAAAACCC 58.652 33.333 0.00 0.00 0.00 4.11
3189 3349 5.700722 AGAAGAAAATCACGTAAAACCCC 57.299 39.130 0.00 0.00 0.00 4.95
3190 3350 4.521639 AGAAGAAAATCACGTAAAACCCCC 59.478 41.667 0.00 0.00 0.00 5.40
3191 3351 2.815503 AGAAAATCACGTAAAACCCCCG 59.184 45.455 0.00 0.00 0.00 5.73
3192 3352 2.275134 AAATCACGTAAAACCCCCGT 57.725 45.000 0.00 0.00 34.71 5.28
3196 3356 2.135890 ACGTAAAACCCCCGTGAGT 58.864 52.632 0.00 0.00 32.86 3.41
3197 3357 0.033920 ACGTAAAACCCCCGTGAGTC 59.966 55.000 0.00 0.00 32.86 3.36
3198 3358 0.319405 CGTAAAACCCCCGTGAGTCT 59.681 55.000 0.00 0.00 0.00 3.24
3199 3359 1.545582 CGTAAAACCCCCGTGAGTCTA 59.454 52.381 0.00 0.00 0.00 2.59
3200 3360 2.416431 CGTAAAACCCCCGTGAGTCTAG 60.416 54.545 0.00 0.00 0.00 2.43
3201 3361 0.981943 AAAACCCCCGTGAGTCTAGG 59.018 55.000 0.00 0.00 0.00 3.02
3202 3362 0.115745 AAACCCCCGTGAGTCTAGGA 59.884 55.000 6.10 0.00 0.00 2.94
3203 3363 0.338814 AACCCCCGTGAGTCTAGGAT 59.661 55.000 6.10 0.00 0.00 3.24
3204 3364 0.338814 ACCCCCGTGAGTCTAGGATT 59.661 55.000 6.10 0.00 0.00 3.01
3205 3365 1.572415 ACCCCCGTGAGTCTAGGATTA 59.428 52.381 6.10 0.00 0.00 1.75
3206 3366 2.179424 ACCCCCGTGAGTCTAGGATTAT 59.821 50.000 6.10 0.00 0.00 1.28
3207 3367 3.240302 CCCCCGTGAGTCTAGGATTATT 58.760 50.000 6.10 0.00 0.00 1.40
3208 3368 3.006967 CCCCCGTGAGTCTAGGATTATTG 59.993 52.174 6.10 0.00 0.00 1.90
3209 3369 3.641906 CCCCGTGAGTCTAGGATTATTGT 59.358 47.826 6.10 0.00 0.00 2.71
3210 3370 4.101119 CCCCGTGAGTCTAGGATTATTGTT 59.899 45.833 6.10 0.00 0.00 2.83
3211 3371 5.303589 CCCCGTGAGTCTAGGATTATTGTTA 59.696 44.000 6.10 0.00 0.00 2.41
3212 3372 6.014499 CCCCGTGAGTCTAGGATTATTGTTAT 60.014 42.308 6.10 0.00 0.00 1.89
3213 3373 7.442656 CCCGTGAGTCTAGGATTATTGTTATT 58.557 38.462 6.10 0.00 0.00 1.40
3214 3374 7.931948 CCCGTGAGTCTAGGATTATTGTTATTT 59.068 37.037 6.10 0.00 0.00 1.40
3215 3375 9.326413 CCGTGAGTCTAGGATTATTGTTATTTT 57.674 33.333 0.00 0.00 0.00 1.82
3256 3416 3.636300 TCATGCTTGCCAACTAAACTTGT 59.364 39.130 0.00 0.00 0.00 3.16
3265 3425 3.813166 CCAACTAAACTTGTCATCCACGT 59.187 43.478 0.00 0.00 0.00 4.49
3266 3426 4.319477 CCAACTAAACTTGTCATCCACGTG 60.319 45.833 9.08 9.08 0.00 4.49
3273 3433 3.245797 CTTGTCATCCACGTGTCACTAG 58.754 50.000 15.65 7.49 0.00 2.57
3276 3436 3.509967 TGTCATCCACGTGTCACTAGAAT 59.490 43.478 15.65 0.00 0.00 2.40
3283 3443 1.732259 CGTGTCACTAGAATTGCCACC 59.268 52.381 0.00 0.00 0.00 4.61
3289 3449 4.220602 GTCACTAGAATTGCCACCCAAAAT 59.779 41.667 0.00 0.00 36.92 1.82
3290 3450 4.220382 TCACTAGAATTGCCACCCAAAATG 59.780 41.667 0.00 0.00 36.92 2.32
3298 3462 3.737850 TGCCACCCAAAATGTTTGATTC 58.262 40.909 2.30 0.00 0.00 2.52
3305 3469 3.371591 CCAAAATGTTTGATTCGCCATGG 59.628 43.478 7.63 7.63 0.00 3.66
3314 3478 1.002468 GATTCGCCATGGTCAAATCCG 60.002 52.381 14.67 6.47 0.00 4.18
3315 3479 0.035915 TTCGCCATGGTCAAATCCGA 60.036 50.000 14.67 8.96 0.00 4.55
3318 3482 1.467374 CGCCATGGTCAAATCCGAAAC 60.467 52.381 14.67 0.00 0.00 2.78
3339 3503 0.760572 TTCGGGATTTATCGGGGTCC 59.239 55.000 0.00 0.00 0.00 4.46
3352 3516 1.539827 CGGGGTCCTTGTTGAAATCAC 59.460 52.381 0.00 0.00 0.00 3.06
3354 3518 3.558321 CGGGGTCCTTGTTGAAATCACTA 60.558 47.826 0.00 0.00 0.00 2.74
3394 3558 1.665735 CGGTGTTCATTTCGGCCAAAG 60.666 52.381 2.24 0.00 0.00 2.77
3396 3560 1.611491 GTGTTCATTTCGGCCAAAGGA 59.389 47.619 2.24 7.23 32.93 3.36
3397 3561 2.231235 GTGTTCATTTCGGCCAAAGGAT 59.769 45.455 13.27 0.00 34.80 3.24
3398 3562 2.230992 TGTTCATTTCGGCCAAAGGATG 59.769 45.455 13.27 5.79 34.80 3.51
3400 3564 2.091541 TCATTTCGGCCAAAGGATGAC 58.908 47.619 2.24 0.00 29.75 3.06
3401 3565 1.134946 CATTTCGGCCAAAGGATGACC 59.865 52.381 2.24 0.00 0.00 4.02
3402 3566 0.111446 TTTCGGCCAAAGGATGACCA 59.889 50.000 2.24 0.00 38.94 4.02
3403 3567 0.111446 TTCGGCCAAAGGATGACCAA 59.889 50.000 2.24 0.00 38.94 3.67
3404 3568 0.111446 TCGGCCAAAGGATGACCAAA 59.889 50.000 2.24 0.00 38.94 3.28
3405 3569 0.527565 CGGCCAAAGGATGACCAAAG 59.472 55.000 2.24 0.00 38.94 2.77
3406 3570 0.897621 GGCCAAAGGATGACCAAAGG 59.102 55.000 0.00 0.00 38.94 3.11
3407 3571 1.549950 GGCCAAAGGATGACCAAAGGA 60.550 52.381 0.00 0.00 38.94 3.36
3408 3572 1.546029 GCCAAAGGATGACCAAAGGAC 59.454 52.381 0.00 0.00 38.94 3.85
3409 3573 2.171003 CCAAAGGATGACCAAAGGACC 58.829 52.381 0.00 0.00 38.94 4.46
3410 3574 1.812571 CAAAGGATGACCAAAGGACCG 59.187 52.381 0.00 0.00 38.94 4.79
3413 3577 1.702957 AGGATGACCAAAGGACCGAAA 59.297 47.619 0.00 0.00 38.94 3.46
3418 3582 2.888414 TGACCAAAGGACCGAAATTTCC 59.112 45.455 12.54 0.00 0.00 3.13
3425 3589 3.146847 AGGACCGAAATTTCCACTTGAC 58.853 45.455 12.54 0.00 33.92 3.18
3448 3612 8.085909 TGACTTTGACTGAGATACAACGATTTA 58.914 33.333 0.00 0.00 0.00 1.40
3450 3614 9.088512 ACTTTGACTGAGATACAACGATTTATC 57.911 33.333 0.00 0.00 0.00 1.75
3502 3666 9.632807 GAATTTATGTGTACTACCAAAATTGCA 57.367 29.630 14.84 0.00 34.97 4.08
3503 3667 9.988815 AATTTATGTGTACTACCAAAATTGCAA 57.011 25.926 0.00 0.00 34.23 4.08
3508 3672 9.988815 ATGTGTACTACCAAAATTGCAAAAATA 57.011 25.926 1.71 0.00 0.00 1.40
3540 3704 8.407064 ACCGAAACAAAATTATTTCAGTGTGTA 58.593 29.630 9.27 0.00 35.02 2.90
3553 3717 3.985279 TCAGTGTGTACCGAAATTTCTCG 59.015 43.478 15.92 8.34 38.58 4.04
3570 3734 0.178767 TCGGATTCCTGGACTGCATG 59.821 55.000 6.39 0.00 0.00 4.06
3601 3765 4.090761 TGGAAGGATTGTCCATATGCTC 57.909 45.455 0.00 0.00 40.33 4.26
3603 3767 4.079844 TGGAAGGATTGTCCATATGCTCAA 60.080 41.667 11.30 11.30 40.33 3.02
3606 3770 5.057843 AGGATTGTCCATATGCTCAACAT 57.942 39.130 11.18 0.00 39.61 2.71
3607 3771 5.452255 AGGATTGTCCATATGCTCAACATT 58.548 37.500 11.18 4.02 39.61 2.71
3629 3793 4.773323 GCCAATACTAAGGCCATCATTC 57.227 45.455 5.01 0.00 45.18 2.67
3651 3815 5.730550 TCTTGAAGTAGTTGTGTCACAAGT 58.269 37.500 25.38 25.38 43.55 3.16
3652 3816 6.869695 TCTTGAAGTAGTTGTGTCACAAGTA 58.130 36.000 23.56 23.56 41.57 2.24
3679 3843 4.639135 AACTTGACACTCTTTCTTTGGC 57.361 40.909 0.00 0.00 0.00 4.52
3683 3847 0.663153 ACACTCTTTCTTTGGCGTGC 59.337 50.000 0.00 0.00 0.00 5.34
3698 3862 0.514255 CGTGCCAGTGTCTCACAATG 59.486 55.000 2.80 0.00 43.12 2.82
3706 3870 4.083643 CCAGTGTCTCACAATGACATCAAC 60.084 45.833 5.69 0.00 46.01 3.18
3715 3879 2.975193 CAATGACATCAACGTGTTGCAG 59.025 45.455 7.85 5.48 40.24 4.41
3719 3883 1.891919 ATCAACGTGTTGCAGCGGT 60.892 52.632 7.85 2.77 40.24 5.68
3723 3887 2.356313 CGTGTTGCAGCGGTCTCT 60.356 61.111 0.00 0.00 0.00 3.10
3736 3900 1.927174 CGGTCTCTATTGTTTGCGAGG 59.073 52.381 0.00 0.00 0.00 4.63
3747 3911 1.380403 TTTGCGAGGTTGTGTGTGGG 61.380 55.000 0.00 0.00 0.00 4.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 6.594159 ACCAACCATAGAACAATCTTTCTACG 59.406 38.462 0.00 0.00 40.18 3.51
26 27 4.398988 TGATGCACCAACCATAGAACAATC 59.601 41.667 0.00 0.00 0.00 2.67
30 31 4.782019 TTTGATGCACCAACCATAGAAC 57.218 40.909 0.00 0.00 0.00 3.01
134 136 3.611674 TCGCCACGCCTGTCTTCA 61.612 61.111 0.00 0.00 0.00 3.02
163 165 6.328672 ACTGATAGCCTGATACTCAATTTCCT 59.671 38.462 0.00 0.00 0.00 3.36
214 216 1.315690 CCATGGATGTGGATCTGCAC 58.684 55.000 5.56 0.00 42.02 4.57
322 325 2.676632 TAGTGGCCGAATTCGCTAAA 57.323 45.000 22.36 4.60 38.18 1.85
364 367 0.850856 GTTATAGCGCGGTGTAGCAC 59.149 55.000 23.02 10.97 36.85 4.40
367 370 3.120792 ACAATGTTATAGCGCGGTGTAG 58.879 45.455 23.02 8.81 0.00 2.74
384 387 7.796838 CATGCTATAACGTTACATGCTACAAT 58.203 34.615 18.69 8.26 32.54 2.71
391 394 6.226988 TCATGCATGCTATAACGTTACATG 57.773 37.500 22.25 23.16 40.80 3.21
392 395 6.650390 TCATCATGCATGCTATAACGTTACAT 59.350 34.615 22.25 7.10 31.70 2.29
407 410 8.665643 TTTTCTGTTTCTTTTTCATCATGCAT 57.334 26.923 0.00 0.00 0.00 3.96
414 417 9.612066 TTGCCTTATTTTCTGTTTCTTTTTCAT 57.388 25.926 0.00 0.00 0.00 2.57
459 462 2.445155 GGGTGGATTTGGGCCTGT 59.555 61.111 4.53 0.00 0.00 4.00
465 468 3.131478 GCCGACGGGTGGATTTGG 61.131 66.667 17.22 0.00 34.97 3.28
544 547 1.667467 GCTCATCTCGGCGGAATAGAC 60.667 57.143 7.21 0.00 0.00 2.59
634 637 1.053424 ACGGCCAGGTCTTTTCACTA 58.947 50.000 2.24 0.00 0.00 2.74
639 642 1.600916 GCTCACGGCCAGGTCTTTT 60.601 57.895 2.24 0.00 34.27 2.27
770 775 3.686916 AAATATAGCGAGGCCCTTCTC 57.313 47.619 0.00 0.00 0.00 2.87
979 1021 0.179089 CTGAGCTTGCGATGGCTAGT 60.179 55.000 12.19 0.49 42.87 2.57
1431 1503 1.617536 AGCTCCTTCTGGGCATCCA 60.618 57.895 0.00 0.00 41.58 3.41
1447 1519 4.373116 TCGACCACGGCCTTGAGC 62.373 66.667 11.54 0.95 40.21 4.26
1533 1605 1.064952 GGGATTTTACGATGTTGCGGG 59.935 52.381 0.00 0.00 35.12 6.13
1574 1646 4.680237 CTGCTGGCCGTCGGACAA 62.680 66.667 22.76 6.26 41.95 3.18
1633 1705 0.795085 CGAGACCGAACGTGTAGACT 59.205 55.000 0.00 0.00 38.22 3.24
1677 1762 5.694910 CGGAACAAAAAGCTAGACAGAGTAA 59.305 40.000 0.00 0.00 0.00 2.24
1684 1769 5.390991 CCTTCATCGGAACAAAAAGCTAGAC 60.391 44.000 0.00 0.00 0.00 2.59
1696 1781 4.361420 GACTTAGCTACCTTCATCGGAAC 58.639 47.826 0.00 0.00 0.00 3.62
1697 1782 3.066342 CGACTTAGCTACCTTCATCGGAA 59.934 47.826 0.00 0.00 0.00 4.30
1698 1783 2.617308 CGACTTAGCTACCTTCATCGGA 59.383 50.000 0.00 0.00 0.00 4.55
1699 1784 2.617308 TCGACTTAGCTACCTTCATCGG 59.383 50.000 0.00 0.00 0.00 4.18
1700 1785 3.965292 TCGACTTAGCTACCTTCATCG 57.035 47.619 0.00 0.00 0.00 3.84
1701 1786 4.036352 CGTTCGACTTAGCTACCTTCATC 58.964 47.826 0.00 0.00 0.00 2.92
1702 1787 3.181489 CCGTTCGACTTAGCTACCTTCAT 60.181 47.826 0.00 0.00 0.00 2.57
1703 1788 2.163010 CCGTTCGACTTAGCTACCTTCA 59.837 50.000 0.00 0.00 0.00 3.02
1704 1789 2.795117 CCGTTCGACTTAGCTACCTTC 58.205 52.381 0.00 0.00 0.00 3.46
1706 1791 0.455005 GCCGTTCGACTTAGCTACCT 59.545 55.000 0.00 0.00 0.00 3.08
1707 1792 0.455005 AGCCGTTCGACTTAGCTACC 59.545 55.000 0.00 0.00 30.46 3.18
1708 1793 2.274920 AAGCCGTTCGACTTAGCTAC 57.725 50.000 0.00 0.00 32.39 3.58
1719 1804 2.158813 TCATCATCCCCTTAAGCCGTTC 60.159 50.000 0.00 0.00 0.00 3.95
1721 1806 1.507140 TCATCATCCCCTTAAGCCGT 58.493 50.000 0.00 0.00 0.00 5.68
1725 1810 4.362470 TCAGCATCATCATCCCCTTAAG 57.638 45.455 0.00 0.00 0.00 1.85
1732 1818 8.959705 TTAAGATATCATCAGCATCATCATCC 57.040 34.615 5.32 0.00 0.00 3.51
2115 2223 3.596066 CTGGGCGCTGTAGCTGTGT 62.596 63.158 7.64 0.00 39.32 3.72
2364 2472 1.219124 GTCGATCAGCTTCTGGCCA 59.781 57.895 4.71 4.71 43.05 5.36
2559 2667 1.153549 CTTGGCCTGCTCGAGGTAC 60.154 63.158 15.58 0.00 44.97 3.34
2836 2966 4.027755 CGTCCGCGCTTATTGGAT 57.972 55.556 5.56 0.00 33.63 3.41
2877 3025 6.998074 TGAAACAGATGGATATTGGATGGTAC 59.002 38.462 0.00 0.00 0.00 3.34
2906 3062 2.364970 TGAAGCAAATGGGTTGACAAGG 59.635 45.455 0.00 0.00 39.87 3.61
2980 3139 4.326826 AGAAAAGAATGAAGACGCATCCA 58.673 39.130 0.00 0.00 0.00 3.41
3008 3168 9.606631 AAAATTAACAAGCTGGTTGAAATACAA 57.393 25.926 24.71 1.06 38.60 2.41
3016 3176 4.920927 CCGGTAAAATTAACAAGCTGGTTG 59.079 41.667 17.16 17.29 42.48 3.77
3029 3189 6.313744 GCATCTAGCATTACCGGTAAAATT 57.686 37.500 29.74 19.10 44.79 1.82
3044 3204 2.279517 CCCGTCCGTGCATCTAGC 60.280 66.667 0.00 0.00 45.96 3.42
3045 3205 2.279517 GCCCGTCCGTGCATCTAG 60.280 66.667 0.00 0.00 0.00 2.43
3046 3206 2.914756 TAGGCCCGTCCGTGCATCTA 62.915 60.000 0.00 0.00 40.77 1.98
3048 3208 2.660258 AATAGGCCCGTCCGTGCATC 62.660 60.000 0.00 0.00 40.77 3.91
3049 3209 1.404479 TAATAGGCCCGTCCGTGCAT 61.404 55.000 0.00 0.00 40.77 3.96
3050 3210 2.059190 TAATAGGCCCGTCCGTGCA 61.059 57.895 0.00 0.00 40.77 4.57
3051 3211 1.593479 GTAATAGGCCCGTCCGTGC 60.593 63.158 0.00 0.00 40.77 5.34
3052 3212 0.249322 CTGTAATAGGCCCGTCCGTG 60.249 60.000 0.00 0.00 40.77 4.94
3053 3213 1.397390 CCTGTAATAGGCCCGTCCGT 61.397 60.000 0.00 0.00 40.38 4.69
3054 3214 1.111116 TCCTGTAATAGGCCCGTCCG 61.111 60.000 0.00 0.00 46.87 4.79
3055 3215 1.349067 ATCCTGTAATAGGCCCGTCC 58.651 55.000 0.00 0.00 46.87 4.79
3056 3216 3.487120 AAATCCTGTAATAGGCCCGTC 57.513 47.619 0.00 0.00 46.87 4.79
3057 3217 3.243975 CGTAAATCCTGTAATAGGCCCGT 60.244 47.826 0.00 0.00 46.87 5.28
3058 3218 3.323243 CGTAAATCCTGTAATAGGCCCG 58.677 50.000 0.00 0.00 46.87 6.13
3059 3219 3.325716 TCCGTAAATCCTGTAATAGGCCC 59.674 47.826 0.00 0.00 46.87 5.80
3060 3220 4.612264 TCCGTAAATCCTGTAATAGGCC 57.388 45.455 0.00 0.00 46.87 5.19
3061 3221 6.313164 GCTATTCCGTAAATCCTGTAATAGGC 59.687 42.308 0.00 0.00 46.87 3.93
3064 3224 9.865321 GTATGCTATTCCGTAAATCCTGTAATA 57.135 33.333 0.00 0.00 0.00 0.98
3065 3225 7.544566 CGTATGCTATTCCGTAAATCCTGTAAT 59.455 37.037 0.00 0.00 0.00 1.89
3066 3226 6.864685 CGTATGCTATTCCGTAAATCCTGTAA 59.135 38.462 0.00 0.00 0.00 2.41
3067 3227 6.016024 ACGTATGCTATTCCGTAAATCCTGTA 60.016 38.462 0.00 0.00 0.00 2.74
3068 3228 5.221382 ACGTATGCTATTCCGTAAATCCTGT 60.221 40.000 0.00 0.00 0.00 4.00
3069 3229 5.118664 CACGTATGCTATTCCGTAAATCCTG 59.881 44.000 0.00 0.00 31.42 3.86
3070 3230 5.227908 CACGTATGCTATTCCGTAAATCCT 58.772 41.667 0.00 0.00 31.42 3.24
3071 3231 4.387862 CCACGTATGCTATTCCGTAAATCC 59.612 45.833 0.00 0.00 31.42 3.01
3072 3232 4.387862 CCCACGTATGCTATTCCGTAAATC 59.612 45.833 0.00 0.00 31.42 2.17
3073 3233 4.312443 CCCACGTATGCTATTCCGTAAAT 58.688 43.478 0.00 0.00 31.42 1.40
3074 3234 3.719924 CCCACGTATGCTATTCCGTAAA 58.280 45.455 0.00 0.00 31.42 2.01
3075 3235 2.546373 GCCCACGTATGCTATTCCGTAA 60.546 50.000 0.00 0.00 31.42 3.18
3076 3236 1.000060 GCCCACGTATGCTATTCCGTA 60.000 52.381 0.00 0.00 31.42 4.02
3077 3237 0.249741 GCCCACGTATGCTATTCCGT 60.250 55.000 0.00 0.00 0.00 4.69
3078 3238 0.249699 TGCCCACGTATGCTATTCCG 60.250 55.000 9.54 0.00 0.00 4.30
3079 3239 1.961793 TTGCCCACGTATGCTATTCC 58.038 50.000 9.54 0.00 0.00 3.01
3080 3240 2.157668 CGATTGCCCACGTATGCTATTC 59.842 50.000 9.54 3.89 0.00 1.75
3081 3241 2.143122 CGATTGCCCACGTATGCTATT 58.857 47.619 9.54 0.00 0.00 1.73
3082 3242 1.608025 CCGATTGCCCACGTATGCTAT 60.608 52.381 9.54 7.42 0.00 2.97
3083 3243 0.249699 CCGATTGCCCACGTATGCTA 60.250 55.000 9.54 3.01 0.00 3.49
3084 3244 1.523711 CCGATTGCCCACGTATGCT 60.524 57.895 9.54 0.00 0.00 3.79
3085 3245 2.542907 CCCGATTGCCCACGTATGC 61.543 63.158 1.73 1.73 0.00 3.14
3086 3246 0.250295 ATCCCGATTGCCCACGTATG 60.250 55.000 0.00 0.00 0.00 2.39
3087 3247 0.472471 AATCCCGATTGCCCACGTAT 59.528 50.000 0.00 0.00 0.00 3.06
3088 3248 0.462937 CAATCCCGATTGCCCACGTA 60.463 55.000 4.57 0.00 41.27 3.57
3089 3249 1.748879 CAATCCCGATTGCCCACGT 60.749 57.895 4.57 0.00 41.27 4.49
3090 3250 2.480610 CCAATCCCGATTGCCCACG 61.481 63.158 11.24 0.00 45.06 4.94
3091 3251 2.127232 CCCAATCCCGATTGCCCAC 61.127 63.158 11.24 0.00 45.06 4.61
3092 3252 2.278404 CCCAATCCCGATTGCCCA 59.722 61.111 11.24 0.00 45.06 5.36
3093 3253 2.521708 CCCCAATCCCGATTGCCC 60.522 66.667 11.24 0.00 45.06 5.36
3094 3254 1.076339 TTCCCCAATCCCGATTGCC 60.076 57.895 11.24 0.00 45.06 4.52
3095 3255 0.106719 TCTTCCCCAATCCCGATTGC 60.107 55.000 11.24 0.00 45.06 3.56
3096 3256 1.477558 CCTCTTCCCCAATCCCGATTG 60.478 57.143 9.97 9.97 45.77 2.67
3097 3257 0.846693 CCTCTTCCCCAATCCCGATT 59.153 55.000 0.00 0.00 0.00 3.34
3098 3258 1.062488 CCCTCTTCCCCAATCCCGAT 61.062 60.000 0.00 0.00 0.00 4.18
3099 3259 1.692749 CCCTCTTCCCCAATCCCGA 60.693 63.158 0.00 0.00 0.00 5.14
3100 3260 1.692749 TCCCTCTTCCCCAATCCCG 60.693 63.158 0.00 0.00 0.00 5.14
3101 3261 2.000825 GCTCCCTCTTCCCCAATCCC 62.001 65.000 0.00 0.00 0.00 3.85
3102 3262 1.281925 TGCTCCCTCTTCCCCAATCC 61.282 60.000 0.00 0.00 0.00 3.01
3103 3263 0.849417 ATGCTCCCTCTTCCCCAATC 59.151 55.000 0.00 0.00 0.00 2.67
3104 3264 0.554792 CATGCTCCCTCTTCCCCAAT 59.445 55.000 0.00 0.00 0.00 3.16
3105 3265 1.574526 CCATGCTCCCTCTTCCCCAA 61.575 60.000 0.00 0.00 0.00 4.12
3106 3266 2.002977 CCATGCTCCCTCTTCCCCA 61.003 63.158 0.00 0.00 0.00 4.96
3107 3267 2.761465 CCCATGCTCCCTCTTCCCC 61.761 68.421 0.00 0.00 0.00 4.81
3108 3268 2.922234 CCCATGCTCCCTCTTCCC 59.078 66.667 0.00 0.00 0.00 3.97
3109 3269 2.194326 GCCCATGCTCCCTCTTCC 59.806 66.667 0.00 0.00 33.53 3.46
3110 3270 2.194326 GGCCCATGCTCCCTCTTC 59.806 66.667 0.00 0.00 37.74 2.87
3111 3271 3.424105 GGGCCCATGCTCCCTCTT 61.424 66.667 19.95 0.00 39.46 2.85
3127 3287 2.840467 TTATTTTCGGCGGGGGTGGG 62.840 60.000 7.21 0.00 0.00 4.61
3128 3288 1.378778 TTATTTTCGGCGGGGGTGG 60.379 57.895 7.21 0.00 0.00 4.61
3129 3289 1.381165 CCTTATTTTCGGCGGGGGTG 61.381 60.000 7.21 0.00 0.00 4.61
3130 3290 1.077285 CCTTATTTTCGGCGGGGGT 60.077 57.895 7.21 0.00 0.00 4.95
3131 3291 1.826487 CCCTTATTTTCGGCGGGGG 60.826 63.158 7.21 4.06 0.00 5.40
3132 3292 3.836151 CCCTTATTTTCGGCGGGG 58.164 61.111 7.21 3.50 0.00 5.73
3133 3293 1.826487 CCCCCTTATTTTCGGCGGG 60.826 63.158 7.21 0.00 34.62 6.13
3134 3294 3.836151 CCCCCTTATTTTCGGCGG 58.164 61.111 7.21 0.00 0.00 6.13
3148 3308 6.137559 TCTTCTAAACTAATCTCTCTCCCCC 58.862 44.000 0.00 0.00 0.00 5.40
3149 3309 7.663043 TTCTTCTAAACTAATCTCTCTCCCC 57.337 40.000 0.00 0.00 0.00 4.81
3155 3315 9.930693 ACGTGATTTTCTTCTAAACTAATCTCT 57.069 29.630 0.00 0.00 0.00 3.10
3162 3322 8.347771 GGGTTTTACGTGATTTTCTTCTAAACT 58.652 33.333 0.00 0.00 0.00 2.66
3163 3323 7.592533 GGGGTTTTACGTGATTTTCTTCTAAAC 59.407 37.037 0.00 0.00 0.00 2.01
3164 3324 7.255555 GGGGGTTTTACGTGATTTTCTTCTAAA 60.256 37.037 0.00 0.00 0.00 1.85
3165 3325 6.207221 GGGGGTTTTACGTGATTTTCTTCTAA 59.793 38.462 0.00 0.00 0.00 2.10
3166 3326 5.706833 GGGGGTTTTACGTGATTTTCTTCTA 59.293 40.000 0.00 0.00 0.00 2.10
3167 3327 4.521639 GGGGGTTTTACGTGATTTTCTTCT 59.478 41.667 0.00 0.00 0.00 2.85
3168 3328 4.614306 CGGGGGTTTTACGTGATTTTCTTC 60.614 45.833 0.00 0.00 0.00 2.87
3169 3329 3.253921 CGGGGGTTTTACGTGATTTTCTT 59.746 43.478 0.00 0.00 0.00 2.52
3170 3330 2.815503 CGGGGGTTTTACGTGATTTTCT 59.184 45.455 0.00 0.00 0.00 2.52
3171 3331 2.553602 ACGGGGGTTTTACGTGATTTTC 59.446 45.455 0.00 0.00 39.64 2.29
3172 3332 2.585330 ACGGGGGTTTTACGTGATTTT 58.415 42.857 0.00 0.00 39.64 1.82
3173 3333 2.275134 ACGGGGGTTTTACGTGATTT 57.725 45.000 0.00 0.00 39.64 2.17
3178 3338 0.033920 GACTCACGGGGGTTTTACGT 59.966 55.000 0.00 0.00 42.17 3.57
3179 3339 0.319405 AGACTCACGGGGGTTTTACG 59.681 55.000 0.00 0.00 0.00 3.18
3180 3340 2.093816 CCTAGACTCACGGGGGTTTTAC 60.094 54.545 0.00 0.00 0.00 2.01
3181 3341 2.181975 CCTAGACTCACGGGGGTTTTA 58.818 52.381 0.00 0.00 0.00 1.52
3182 3342 0.981943 CCTAGACTCACGGGGGTTTT 59.018 55.000 0.00 0.00 0.00 2.43
3183 3343 0.115745 TCCTAGACTCACGGGGGTTT 59.884 55.000 0.00 0.00 0.00 3.27
3184 3344 0.338814 ATCCTAGACTCACGGGGGTT 59.661 55.000 0.00 0.00 0.00 4.11
3185 3345 0.338814 AATCCTAGACTCACGGGGGT 59.661 55.000 0.00 0.00 0.00 4.95
3186 3346 2.376695 TAATCCTAGACTCACGGGGG 57.623 55.000 0.00 0.00 0.00 5.40
3187 3347 3.641906 ACAATAATCCTAGACTCACGGGG 59.358 47.826 0.00 0.00 0.00 5.73
3188 3348 4.939052 ACAATAATCCTAGACTCACGGG 57.061 45.455 0.00 0.00 0.00 5.28
3189 3349 8.888579 AAATAACAATAATCCTAGACTCACGG 57.111 34.615 0.00 0.00 0.00 4.94
3207 3367 9.891828 CAAATCTGTGCTTAGTGTAAAATAACA 57.108 29.630 0.00 0.00 0.00 2.41
3208 3368 9.893305 ACAAATCTGTGCTTAGTGTAAAATAAC 57.107 29.630 0.00 0.00 33.30 1.89
3210 3370 9.278978 TGACAAATCTGTGCTTAGTGTAAAATA 57.721 29.630 0.00 0.00 35.30 1.40
3211 3371 8.165239 TGACAAATCTGTGCTTAGTGTAAAAT 57.835 30.769 0.00 0.00 35.30 1.82
3212 3372 7.561021 TGACAAATCTGTGCTTAGTGTAAAA 57.439 32.000 0.00 0.00 35.30 1.52
3213 3373 7.584108 CATGACAAATCTGTGCTTAGTGTAAA 58.416 34.615 0.00 0.00 35.30 2.01
3214 3374 6.348458 GCATGACAAATCTGTGCTTAGTGTAA 60.348 38.462 0.00 0.00 35.30 2.41
3215 3375 5.122239 GCATGACAAATCTGTGCTTAGTGTA 59.878 40.000 0.00 0.00 35.30 2.90
3216 3376 4.083110 GCATGACAAATCTGTGCTTAGTGT 60.083 41.667 0.00 0.00 35.30 3.55
3217 3377 4.155462 AGCATGACAAATCTGTGCTTAGTG 59.845 41.667 0.00 0.00 41.61 2.74
3218 3378 4.330250 AGCATGACAAATCTGTGCTTAGT 58.670 39.130 0.00 0.00 41.61 2.24
3219 3379 4.959596 AGCATGACAAATCTGTGCTTAG 57.040 40.909 0.00 0.00 41.61 2.18
3256 3416 4.494484 CAATTCTAGTGACACGTGGATGA 58.506 43.478 21.57 6.21 0.00 2.92
3265 3425 1.702401 TGGGTGGCAATTCTAGTGACA 59.298 47.619 0.00 0.00 0.00 3.58
3266 3426 2.489938 TGGGTGGCAATTCTAGTGAC 57.510 50.000 0.00 0.00 0.00 3.67
3273 3433 4.133078 TCAAACATTTTGGGTGGCAATTC 58.867 39.130 0.00 0.00 0.00 2.17
3276 3436 3.853355 ATCAAACATTTTGGGTGGCAA 57.147 38.095 0.00 0.00 0.00 4.52
3283 3443 3.371591 CCATGGCGAATCAAACATTTTGG 59.628 43.478 0.00 0.00 0.00 3.28
3289 3449 1.902938 TGACCATGGCGAATCAAACA 58.097 45.000 13.04 0.00 0.00 2.83
3290 3450 3.296322 TTTGACCATGGCGAATCAAAC 57.704 42.857 19.19 0.65 36.42 2.93
3298 3462 0.808125 TTTCGGATTTGACCATGGCG 59.192 50.000 13.04 5.41 0.00 5.69
3314 3478 2.286025 CCCGATAAATCCCGAACGTTTC 59.714 50.000 0.46 0.00 0.00 2.78
3315 3479 2.282407 CCCGATAAATCCCGAACGTTT 58.718 47.619 0.46 0.00 0.00 3.60
3318 3482 0.105408 ACCCCGATAAATCCCGAACG 59.895 55.000 0.00 0.00 0.00 3.95
3332 3496 1.539827 GTGATTTCAACAAGGACCCCG 59.460 52.381 0.00 0.00 0.00 5.73
3361 3525 7.537306 CGAAATGAACACCGAAATAACTGAATT 59.463 33.333 0.00 0.00 0.00 2.17
3394 3558 2.194201 TTTCGGTCCTTTGGTCATCC 57.806 50.000 0.00 0.00 0.00 3.51
3396 3560 3.509967 GGAAATTTCGGTCCTTTGGTCAT 59.490 43.478 11.95 0.00 0.00 3.06
3397 3561 2.888414 GGAAATTTCGGTCCTTTGGTCA 59.112 45.455 11.95 0.00 0.00 4.02
3398 3562 2.888414 TGGAAATTTCGGTCCTTTGGTC 59.112 45.455 11.95 0.00 34.77 4.02
3400 3564 2.890945 AGTGGAAATTTCGGTCCTTTGG 59.109 45.455 11.95 0.00 34.77 3.28
3401 3565 4.037446 TCAAGTGGAAATTTCGGTCCTTTG 59.963 41.667 11.95 9.98 34.77 2.77
3402 3566 4.037565 GTCAAGTGGAAATTTCGGTCCTTT 59.962 41.667 11.95 0.00 34.77 3.11
3403 3567 3.568430 GTCAAGTGGAAATTTCGGTCCTT 59.432 43.478 11.95 7.95 34.77 3.36
3404 3568 3.146847 GTCAAGTGGAAATTTCGGTCCT 58.853 45.455 11.95 2.50 34.77 3.85
3405 3569 3.146847 AGTCAAGTGGAAATTTCGGTCC 58.853 45.455 11.95 0.00 0.00 4.46
3406 3570 4.830826 AAGTCAAGTGGAAATTTCGGTC 57.169 40.909 11.95 5.19 0.00 4.79
3407 3571 4.642885 TCAAAGTCAAGTGGAAATTTCGGT 59.357 37.500 11.95 0.00 0.00 4.69
3408 3572 4.976116 GTCAAAGTCAAGTGGAAATTTCGG 59.024 41.667 11.95 0.05 0.00 4.30
3409 3573 5.682862 CAGTCAAAGTCAAGTGGAAATTTCG 59.317 40.000 11.95 0.00 0.00 3.46
3410 3574 6.795399 TCAGTCAAAGTCAAGTGGAAATTTC 58.205 36.000 9.83 9.83 0.00 2.17
3413 3577 5.684704 TCTCAGTCAAAGTCAAGTGGAAAT 58.315 37.500 0.00 0.00 0.00 2.17
3418 3582 6.346120 CGTTGTATCTCAGTCAAAGTCAAGTG 60.346 42.308 0.00 0.00 0.00 3.16
3425 3589 9.307121 AGATAAATCGTTGTATCTCAGTCAAAG 57.693 33.333 0.98 0.00 32.72 2.77
3553 3717 0.394762 TGCATGCAGTCCAGGAATCC 60.395 55.000 18.46 0.00 0.00 3.01
3629 3793 6.757010 AGTACTTGTGACACAACTACTTCAAG 59.243 38.462 23.86 13.06 35.59 3.02
3651 3815 9.314321 CAAAGAAAGAGTGTCAAGTTTAGAGTA 57.686 33.333 0.00 0.00 0.00 2.59
3652 3816 7.281100 CCAAAGAAAGAGTGTCAAGTTTAGAGT 59.719 37.037 0.00 0.00 0.00 3.24
3657 3821 4.438744 CGCCAAAGAAAGAGTGTCAAGTTT 60.439 41.667 0.00 0.00 0.00 2.66
3660 3824 2.614057 ACGCCAAAGAAAGAGTGTCAAG 59.386 45.455 0.00 0.00 0.00 3.02
3679 3843 0.514255 CATTGTGAGACACTGGCACG 59.486 55.000 0.00 0.00 35.11 5.34
3698 3862 0.722469 CGCTGCAACACGTTGATGTC 60.722 55.000 13.97 0.00 42.93 3.06
3706 3870 0.458543 ATAGAGACCGCTGCAACACG 60.459 55.000 0.00 0.00 0.00 4.49
3715 3879 1.324736 CTCGCAAACAATAGAGACCGC 59.675 52.381 0.00 0.00 32.84 5.68
3719 3883 3.745975 CACAACCTCGCAAACAATAGAGA 59.254 43.478 0.00 0.00 32.84 3.10
3723 3887 2.946329 ACACACAACCTCGCAAACAATA 59.054 40.909 0.00 0.00 0.00 1.90
3736 3900 2.732289 ATCTTGGCCCACACACAAC 58.268 52.632 0.00 0.00 0.00 3.32



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

AutoCloner maintained by Alex Coulton.