Multiple sequence alignment - TraesCS2A01G576400

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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 TraesCS2A01G576400 chr2A 100.000 5002 0 0 1 5002 770362267 770357266 0.000000e+00 9238.0
1 TraesCS2A01G576400 chr2A 84.795 171 24 2 4620 4789 768719737 768719906 2.390000e-38 171.0
2 TraesCS2A01G576400 chr2A 89.286 84 8 1 3100 3182 651599232 651599149 2.460000e-18 104.0
3 TraesCS2A01G576400 chr2D 91.944 1651 89 22 1447 3082 645011946 645010325 0.000000e+00 2272.0
4 TraesCS2A01G576400 chr2D 93.420 1079 55 11 3189 4262 645010319 645009252 0.000000e+00 1585.0
5 TraesCS2A01G576400 chr2D 88.802 1277 57 34 134 1394 645013167 645011961 0.000000e+00 1487.0
6 TraesCS2A01G576400 chr2D 86.842 608 60 14 4400 5002 644987824 644988416 0.000000e+00 662.0
7 TraesCS2A01G576400 chr2D 94.340 106 5 1 4249 4354 644986635 644986739 1.440000e-35 161.0
8 TraesCS2A01G576400 chr2D 87.050 139 18 0 4636 4774 643841556 643841694 1.860000e-34 158.0
9 TraesCS2A01G576400 chr2D 92.045 88 5 2 2621 2706 24916184 24916271 6.800000e-24 122.0
10 TraesCS2A01G576400 chr2D 89.157 83 9 0 3100 3182 506776636 506776554 2.460000e-18 104.0
11 TraesCS2A01G576400 chr3B 92.611 1394 69 17 1700 3082 48888465 48887095 0.000000e+00 1973.0
12 TraesCS2A01G576400 chr3B 95.349 516 23 1 3189 3704 48887089 48886575 0.000000e+00 819.0
13 TraesCS2A01G576400 chr3B 90.409 563 52 2 3107 3668 48803332 48802771 0.000000e+00 739.0
14 TraesCS2A01G576400 chr3B 93.056 504 35 0 4499 5002 48885987 48885484 0.000000e+00 737.0
15 TraesCS2A01G576400 chr3B 92.140 458 30 2 3701 4158 48886473 48886022 4.220000e-180 641.0
16 TraesCS2A01G576400 chr3B 89.375 480 19 6 387 857 48889421 48888965 4.340000e-160 575.0
17 TraesCS2A01G576400 chr3B 89.196 398 30 8 1041 1438 48888848 48888464 7.530000e-133 484.0
18 TraesCS2A01G576400 chr3B 89.394 66 3 3 4169 4232 48886035 48885972 4.150000e-11 80.5
19 TraesCS2A01G576400 chr2B 91.252 1406 89 17 1679 3079 790584685 790586061 0.000000e+00 1884.0
20 TraesCS2A01G576400 chr2B 94.058 690 36 4 3183 3871 790586064 790586749 0.000000e+00 1042.0
21 TraesCS2A01G576400 chr2B 91.261 698 34 8 158 851 790583271 790583945 0.000000e+00 926.0
22 TraesCS2A01G576400 chr2B 89.121 671 45 13 956 1623 790584007 790584652 0.000000e+00 809.0
23 TraesCS2A01G576400 chr2B 89.813 481 45 2 4523 5002 790588236 790588713 9.200000e-172 614.0
24 TraesCS2A01G576400 chr2B 91.262 103 8 1 4065 4167 790587787 790587888 6.750000e-29 139.0
25 TraesCS2A01G576400 chr2B 84.286 140 8 6 4224 4359 790588008 790588137 1.890000e-24 124.0
26 TraesCS2A01G576400 chr2B 87.209 86 9 2 3103 3187 33908929 33908845 4.120000e-16 97.1
27 TraesCS2A01G576400 chr4A 100.000 134 0 0 1 134 615413341 615413208 1.080000e-61 248.0
28 TraesCS2A01G576400 chr6A 99.265 136 1 0 1 136 418614082 418614217 3.870000e-61 246.0
29 TraesCS2A01G576400 chr6A 98.496 133 2 0 1 133 40270494 40270626 8.370000e-58 235.0
30 TraesCS2A01G576400 chr6A 97.101 138 4 0 1 138 209782277 209782414 3.010000e-57 233.0
31 TraesCS2A01G576400 chr1A 99.254 134 1 0 1 134 474203068 474202935 5.000000e-60 243.0
32 TraesCS2A01G576400 chr3A 98.519 135 2 0 1 135 497190375 497190241 6.470000e-59 239.0
33 TraesCS2A01G576400 chr3A 98.507 134 2 0 1 134 691685884 691685751 2.330000e-58 237.0
34 TraesCS2A01G576400 chr3A 97.794 136 3 0 1 136 547264822 547264957 8.370000e-58 235.0
35 TraesCS2A01G576400 chr5A 98.507 134 2 0 1 134 77899871 77900004 2.330000e-58 237.0
36 TraesCS2A01G576400 chr1B 90.588 85 8 0 3098 3182 556993860 556993776 4.090000e-21 113.0
37 TraesCS2A01G576400 chr1B 93.023 43 2 1 1524 1566 34203009 34202968 1.500000e-05 62.1
38 TraesCS2A01G576400 chr7B 89.655 87 7 2 3100 3185 222300201 222300116 5.290000e-20 110.0
39 TraesCS2A01G576400 chr6B 88.372 86 7 2 3100 3182 40456618 40456703 3.190000e-17 100.0
40 TraesCS2A01G576400 chr5D 88.235 85 9 1 3103 3187 521674718 521674801 3.190000e-17 100.0
41 TraesCS2A01G576400 chr5B 88.889 81 8 1 3107 3187 527769965 527769886 1.150000e-16 99.0


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 TraesCS2A01G576400 chr2A 770357266 770362267 5001 True 9238.000000 9238 100.000000 1 5002 1 chr2A.!!$R2 5001
1 TraesCS2A01G576400 chr2D 645009252 645013167 3915 True 1781.333333 2272 91.388667 134 4262 3 chr2D.!!$R2 4128
2 TraesCS2A01G576400 chr2D 644986635 644988416 1781 False 411.500000 662 90.591000 4249 5002 2 chr2D.!!$F3 753
3 TraesCS2A01G576400 chr3B 48885484 48889421 3937 True 758.500000 1973 91.588714 387 5002 7 chr3B.!!$R2 4615
4 TraesCS2A01G576400 chr3B 48802771 48803332 561 True 739.000000 739 90.409000 3107 3668 1 chr3B.!!$R1 561
5 TraesCS2A01G576400 chr2B 790583271 790588713 5442 False 791.142857 1884 90.150429 158 5002 7 chr2B.!!$F1 4844

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
64 65 0.238289 CCAAGATTCGTGCACACACC 59.762 55.000 18.64 2.89 44.40 4.16 F
691 712 0.250295 TTTGCTCTGTCTTGTCCCGG 60.250 55.000 0.00 0.00 0.00 5.73 F
1148 1188 0.467290 GAGATCGGTGAGGAGGAGCT 60.467 60.000 0.00 0.00 0.00 4.09 F
2171 2232 0.036765 CCTTTTGGCTGCATGCACAT 60.037 50.000 18.46 0.00 45.15 3.21 F
2172 2233 1.205179 CCTTTTGGCTGCATGCACATA 59.795 47.619 18.46 6.82 45.15 2.29 F
3803 3978 0.245266 TCGATGCGTTCTTACCTGCA 59.755 50.000 0.00 0.00 42.22 4.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1168 1211 0.455815 GGCATTTGGTAAAGCCGGAG 59.544 55.0 5.05 0.00 41.21 4.63 R
2157 2218 1.765230 TCAATATGTGCATGCAGCCA 58.235 45.0 23.41 17.37 44.83 4.75 R
3053 3121 1.303309 GGAGTGCATCACCTACATGC 58.697 55.0 0.00 0.00 45.92 4.06 R
3764 3939 0.734253 CAGCGACCTCCTTGTTCTCG 60.734 60.0 0.00 0.00 0.00 4.04 R
3892 4068 0.756294 ACACCTTCACCGTCATCACA 59.244 50.0 0.00 0.00 0.00 3.58 R
4793 6980 0.669318 TTGTCGATGCGAGGGTGAAC 60.669 55.0 0.00 0.00 36.23 3.18 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
17 18 2.494918 ACACGCGCCTCATCCTAC 59.505 61.111 5.73 0.00 0.00 3.18
18 19 2.655364 CACGCGCCTCATCCTACG 60.655 66.667 5.73 0.00 0.00 3.51
19 20 3.138798 ACGCGCCTCATCCTACGT 61.139 61.111 5.73 0.00 0.00 3.57
20 21 2.655364 CGCGCCTCATCCTACGTG 60.655 66.667 0.00 0.00 0.00 4.49
21 22 2.279517 GCGCCTCATCCTACGTGG 60.280 66.667 0.00 0.00 37.10 4.94
22 23 2.279517 CGCCTCATCCTACGTGGC 60.280 66.667 0.00 0.00 39.19 5.01
23 24 2.900273 GCCTCATCCTACGTGGCA 59.100 61.111 0.00 0.00 41.59 4.92
24 25 1.521681 GCCTCATCCTACGTGGCAC 60.522 63.158 7.79 7.79 41.59 5.01
25 26 1.897423 CCTCATCCTACGTGGCACA 59.103 57.895 19.09 0.00 35.26 4.57
26 27 0.249120 CCTCATCCTACGTGGCACAA 59.751 55.000 19.09 3.85 44.16 3.33
27 28 1.338674 CCTCATCCTACGTGGCACAAA 60.339 52.381 19.09 3.45 44.16 2.83
28 29 2.422597 CTCATCCTACGTGGCACAAAA 58.577 47.619 19.09 0.72 44.16 2.44
29 30 2.811431 CTCATCCTACGTGGCACAAAAA 59.189 45.455 19.09 0.00 44.16 1.94
50 51 2.065899 CCACCTGGTTTGTTCCAAGA 57.934 50.000 0.00 0.00 37.01 3.02
51 52 2.597455 CCACCTGGTTTGTTCCAAGAT 58.403 47.619 0.00 0.00 37.01 2.40
52 53 2.965147 CCACCTGGTTTGTTCCAAGATT 59.035 45.455 0.00 0.00 37.01 2.40
53 54 3.005791 CCACCTGGTTTGTTCCAAGATTC 59.994 47.826 0.00 0.00 37.01 2.52
54 55 2.884639 ACCTGGTTTGTTCCAAGATTCG 59.115 45.455 0.00 0.00 37.01 3.34
55 56 2.884639 CCTGGTTTGTTCCAAGATTCGT 59.115 45.455 0.00 0.00 37.01 3.85
56 57 3.304659 CCTGGTTTGTTCCAAGATTCGTG 60.305 47.826 0.00 0.00 37.01 4.35
57 58 2.034053 TGGTTTGTTCCAAGATTCGTGC 59.966 45.455 0.00 0.00 34.24 5.34
58 59 2.034053 GGTTTGTTCCAAGATTCGTGCA 59.966 45.455 0.00 0.00 0.00 4.57
59 60 3.042887 GTTTGTTCCAAGATTCGTGCAC 58.957 45.455 6.82 6.82 0.00 4.57
60 61 1.960417 TGTTCCAAGATTCGTGCACA 58.040 45.000 18.64 0.00 0.00 4.57
61 62 1.601903 TGTTCCAAGATTCGTGCACAC 59.398 47.619 18.64 3.62 0.00 3.82
62 63 1.601903 GTTCCAAGATTCGTGCACACA 59.398 47.619 18.64 1.99 0.00 3.72
63 64 1.225855 TCCAAGATTCGTGCACACAC 58.774 50.000 18.64 4.98 43.76 3.82
64 65 0.238289 CCAAGATTCGTGCACACACC 59.762 55.000 18.64 2.89 44.40 4.16
65 66 1.229428 CAAGATTCGTGCACACACCT 58.771 50.000 18.64 5.34 44.40 4.00
66 67 1.069703 CAAGATTCGTGCACACACCTG 60.070 52.381 18.64 2.60 44.40 4.00
67 68 1.207593 GATTCGTGCACACACCTGC 59.792 57.895 18.64 0.00 44.40 4.85
68 69 2.187599 GATTCGTGCACACACCTGCC 62.188 60.000 18.64 0.00 44.40 4.85
69 70 2.956799 ATTCGTGCACACACCTGCCA 62.957 55.000 18.64 0.00 44.40 4.92
70 71 3.208383 CGTGCACACACCTGCCAA 61.208 61.111 18.64 0.00 44.40 4.52
71 72 2.412937 GTGCACACACCTGCCAAC 59.587 61.111 13.17 0.00 41.21 3.77
72 73 3.208383 TGCACACACCTGCCAACG 61.208 61.111 0.00 0.00 36.21 4.10
73 74 3.964875 GCACACACCTGCCAACGG 61.965 66.667 0.00 0.00 0.00 4.44
74 75 2.515991 CACACACCTGCCAACGGT 60.516 61.111 0.00 0.00 34.38 4.83
79 80 2.672996 ACCTGCCAACGGTGATGC 60.673 61.111 0.00 0.00 32.41 3.91
80 81 2.360350 CCTGCCAACGGTGATGCT 60.360 61.111 0.00 0.00 0.00 3.79
81 82 1.973281 CCTGCCAACGGTGATGCTT 60.973 57.895 0.00 0.00 0.00 3.91
82 83 1.210931 CTGCCAACGGTGATGCTTG 59.789 57.895 0.00 0.00 0.00 4.01
83 84 2.126346 GCCAACGGTGATGCTTGC 60.126 61.111 0.00 0.00 0.00 4.01
84 85 2.176546 CCAACGGTGATGCTTGCG 59.823 61.111 0.00 0.00 0.00 4.85
85 86 2.616330 CCAACGGTGATGCTTGCGT 61.616 57.895 0.00 0.00 0.00 5.24
86 87 1.440850 CAACGGTGATGCTTGCGTG 60.441 57.895 0.00 0.00 0.00 5.34
87 88 1.891919 AACGGTGATGCTTGCGTGT 60.892 52.632 0.00 0.00 0.00 4.49
88 89 2.116736 AACGGTGATGCTTGCGTGTG 62.117 55.000 0.00 0.00 0.00 3.82
89 90 2.562912 GGTGATGCTTGCGTGTGG 59.437 61.111 0.00 0.00 0.00 4.17
90 91 2.260869 GGTGATGCTTGCGTGTGGT 61.261 57.895 0.00 0.00 0.00 4.16
91 92 1.207593 GTGATGCTTGCGTGTGGTC 59.792 57.895 0.00 0.00 0.00 4.02
92 93 2.316867 TGATGCTTGCGTGTGGTCG 61.317 57.895 0.00 0.00 0.00 4.79
93 94 3.027170 GATGCTTGCGTGTGGTCGG 62.027 63.158 0.00 0.00 0.00 4.79
96 97 4.619227 CTTGCGTGTGGTCGGGGT 62.619 66.667 0.00 0.00 0.00 4.95
97 98 4.920112 TTGCGTGTGGTCGGGGTG 62.920 66.667 0.00 0.00 0.00 4.61
100 101 4.980805 CGTGTGGTCGGGGTGGTG 62.981 72.222 0.00 0.00 0.00 4.17
101 102 3.552384 GTGTGGTCGGGGTGGTGA 61.552 66.667 0.00 0.00 0.00 4.02
102 103 2.768769 TGTGGTCGGGGTGGTGAA 60.769 61.111 0.00 0.00 0.00 3.18
103 104 2.281276 GTGGTCGGGGTGGTGAAC 60.281 66.667 0.00 0.00 0.00 3.18
104 105 3.931247 TGGTCGGGGTGGTGAACG 61.931 66.667 0.00 0.00 0.00 3.95
124 125 3.720531 CACACGTGTGGGCGTTAA 58.279 55.556 35.65 0.00 43.83 2.01
125 126 1.277440 CACACGTGTGGGCGTTAAC 59.723 57.895 35.65 0.00 43.83 2.01
126 127 1.153409 ACACGTGTGGGCGTTAACA 60.153 52.632 22.71 0.00 43.83 2.41
127 128 0.533308 ACACGTGTGGGCGTTAACAT 60.533 50.000 22.71 0.00 43.83 2.71
128 129 0.589223 CACGTGTGGGCGTTAACATT 59.411 50.000 7.58 0.00 43.83 2.71
129 130 1.002251 CACGTGTGGGCGTTAACATTT 60.002 47.619 7.58 0.00 43.83 2.32
130 131 1.264826 ACGTGTGGGCGTTAACATTTC 59.735 47.619 6.39 0.00 43.04 2.17
131 132 1.400500 CGTGTGGGCGTTAACATTTCC 60.400 52.381 6.39 1.91 0.00 3.13
132 133 0.875728 TGTGGGCGTTAACATTTCCG 59.124 50.000 6.39 0.00 0.00 4.30
154 157 1.555967 AATTAATGGGTGTGCGCCTT 58.444 45.000 4.18 0.00 0.00 4.35
313 320 6.263344 TGAGTGACACACGAGTATTAATAGC 58.737 40.000 8.59 0.00 39.64 2.97
382 391 3.693085 TGGTTACTCGTTAGGCTAGACTG 59.307 47.826 8.90 0.00 0.00 3.51
533 546 0.684805 CTACTCTTCCTCCCACCGCT 60.685 60.000 0.00 0.00 0.00 5.52
603 616 3.775654 CGCAGGTGACCCCTCCTC 61.776 72.222 0.00 0.00 43.86 3.71
604 617 3.403558 GCAGGTGACCCCTCCTCC 61.404 72.222 0.00 0.00 43.86 4.30
605 618 3.077556 CAGGTGACCCCTCCTCCG 61.078 72.222 0.00 0.00 43.86 4.63
608 621 3.462678 GTGACCCCTCCTCCGCTC 61.463 72.222 0.00 0.00 0.00 5.03
609 622 4.779733 TGACCCCTCCTCCGCTCC 62.780 72.222 0.00 0.00 0.00 4.70
630 643 3.550030 CCCAAAAGCGTCTTTTCAATCGT 60.550 43.478 12.60 0.00 0.00 3.73
691 712 0.250295 TTTGCTCTGTCTTGTCCCGG 60.250 55.000 0.00 0.00 0.00 5.73
764 785 0.669318 TGTTCATGTTCCTCGCGGAC 60.669 55.000 6.13 0.78 39.60 4.79
822 843 1.065345 GGGTCAAAAGGGGCTACTCTC 60.065 57.143 0.00 0.00 0.00 3.20
898 924 5.033522 AGCAGGGAAAGAAACTATCTACCT 58.966 41.667 0.00 0.00 37.42 3.08
903 929 7.883311 CAGGGAAAGAAACTATCTACCTTGAAA 59.117 37.037 0.00 0.00 40.70 2.69
912 938 6.252995 ACTATCTACCTTGAAATTTTGGCCA 58.747 36.000 0.00 0.00 0.00 5.36
918 944 4.533311 ACCTTGAAATTTTGGCCAGATGAT 59.467 37.500 5.11 0.00 0.00 2.45
962 988 2.173519 CTGTAAGGGGACGTGTTCCTA 58.826 52.381 0.00 0.00 45.09 2.94
993 1024 3.197766 TCTGATTCGTGGCTTATCTTGGT 59.802 43.478 0.00 0.00 0.00 3.67
1068 1102 2.187946 CCCGCTCCGAAGCTCAAT 59.812 61.111 0.00 0.00 46.91 2.57
1148 1188 0.467290 GAGATCGGTGAGGAGGAGCT 60.467 60.000 0.00 0.00 0.00 4.09
1163 1206 2.174360 GGAGCTGCCTTTTCTCCATTT 58.826 47.619 0.00 0.00 44.38 2.32
1167 1210 2.560105 GCTGCCTTTTCTCCATTTCTGT 59.440 45.455 0.00 0.00 0.00 3.41
1168 1211 3.366781 GCTGCCTTTTCTCCATTTCTGTC 60.367 47.826 0.00 0.00 0.00 3.51
1169 1212 4.077822 CTGCCTTTTCTCCATTTCTGTCT 58.922 43.478 0.00 0.00 0.00 3.41
1170 1213 4.074970 TGCCTTTTCTCCATTTCTGTCTC 58.925 43.478 0.00 0.00 0.00 3.36
1171 1214 3.441922 GCCTTTTCTCCATTTCTGTCTCC 59.558 47.826 0.00 0.00 0.00 3.71
1172 1215 3.686726 CCTTTTCTCCATTTCTGTCTCCG 59.313 47.826 0.00 0.00 0.00 4.63
1173 1216 3.334583 TTTCTCCATTTCTGTCTCCGG 57.665 47.619 0.00 0.00 0.00 5.14
1174 1217 0.537188 TCTCCATTTCTGTCTCCGGC 59.463 55.000 0.00 0.00 0.00 6.13
1175 1218 0.539051 CTCCATTTCTGTCTCCGGCT 59.461 55.000 0.00 0.00 0.00 5.52
1176 1219 0.984230 TCCATTTCTGTCTCCGGCTT 59.016 50.000 0.00 0.00 0.00 4.35
1177 1220 1.351017 TCCATTTCTGTCTCCGGCTTT 59.649 47.619 0.00 0.00 0.00 3.51
1178 1221 2.569853 TCCATTTCTGTCTCCGGCTTTA 59.430 45.455 0.00 0.00 0.00 1.85
1179 1222 2.678336 CCATTTCTGTCTCCGGCTTTAC 59.322 50.000 0.00 0.00 0.00 2.01
1180 1223 2.467566 TTTCTGTCTCCGGCTTTACC 57.532 50.000 0.00 0.00 0.00 2.85
1181 1224 1.344065 TTCTGTCTCCGGCTTTACCA 58.656 50.000 0.00 0.00 39.03 3.25
1197 1240 7.294676 GCTTTACCAAATGCCTTGATAAAAG 57.705 36.000 0.00 5.55 33.41 2.27
1198 1241 6.873605 GCTTTACCAAATGCCTTGATAAAAGT 59.126 34.615 0.00 0.00 33.41 2.66
1199 1242 7.387673 GCTTTACCAAATGCCTTGATAAAAGTT 59.612 33.333 0.00 0.00 33.41 2.66
1211 1254 7.644157 GCCTTGATAAAAGTTAAATAAGCTCGG 59.356 37.037 0.00 0.00 0.00 4.63
1212 1255 7.644157 CCTTGATAAAAGTTAAATAAGCTCGGC 59.356 37.037 0.00 0.00 0.00 5.54
1229 1272 0.532115 GGCGAATTGCTGATTGGGTT 59.468 50.000 0.00 0.00 45.43 4.11
1276 1319 2.031157 AGCGGTGTTCAATGTTGTAAGC 60.031 45.455 0.00 0.00 0.00 3.09
1356 1399 8.958119 TCTGTTATCGCAAAGTAAATTAGGAT 57.042 30.769 0.00 0.00 0.00 3.24
1438 1481 4.269183 TGTTGACCTCATTGTTGTCTGTT 58.731 39.130 8.86 0.00 0.00 3.16
1559 1602 6.814043 TCAGTGAGATCTCGATGAAATTCAT 58.186 36.000 21.22 8.39 40.34 2.57
1628 1671 9.952030 TGGTACACATGACTTCAAATAATTCTA 57.048 29.630 0.00 0.00 0.00 2.10
1667 1710 1.202952 TGAATGTTACGGCCCTTTGGT 60.203 47.619 0.00 0.00 0.00 3.67
1669 1712 0.610785 ATGTTACGGCCCTTTGGTGG 60.611 55.000 0.00 0.00 0.00 4.61
1796 1848 3.440228 GTTGCGCTTGTTAAAAGGTGAA 58.560 40.909 9.73 0.00 0.00 3.18
1976 2037 5.373222 GCACATAAATCTACCCACCATACA 58.627 41.667 0.00 0.00 0.00 2.29
2132 2193 5.584649 TGTGCACTATCTGTTAATAACCTGC 59.415 40.000 19.41 0.00 0.00 4.85
2157 2218 3.042560 GCCTTCAGCACGCCTTTT 58.957 55.556 0.00 0.00 42.97 2.27
2158 2219 1.372128 GCCTTCAGCACGCCTTTTG 60.372 57.895 0.00 0.00 42.97 2.44
2159 2220 1.286880 CCTTCAGCACGCCTTTTGG 59.713 57.895 0.00 0.00 44.18 3.28
2169 2230 4.272100 CCTTTTGGCTGCATGCAC 57.728 55.556 18.46 13.69 45.15 4.57
2170 2231 1.368209 CCTTTTGGCTGCATGCACA 59.632 52.632 18.46 11.97 45.15 4.57
2171 2232 0.036765 CCTTTTGGCTGCATGCACAT 60.037 50.000 18.46 0.00 45.15 3.21
2172 2233 1.205179 CCTTTTGGCTGCATGCACATA 59.795 47.619 18.46 6.82 45.15 2.29
2232 2293 6.855763 TTTGCTGAATTGGGTCTATGATTT 57.144 33.333 0.00 0.00 0.00 2.17
2269 2330 7.823745 AATTGTCACTGTGATTTTAGACCTT 57.176 32.000 14.37 0.00 0.00 3.50
2271 2332 7.639113 TTGTCACTGTGATTTTAGACCTTTT 57.361 32.000 14.37 0.00 0.00 2.27
2284 2345 2.302157 AGACCTTTTGTTACCTCCGGAG 59.698 50.000 25.36 25.36 0.00 4.63
2296 2357 1.626825 CCTCCGGAGTTTTGTCCCTTA 59.373 52.381 29.25 0.00 32.26 2.69
2338 2399 7.654520 TGACTTACGAATTGTAGCACTAGTTTT 59.345 33.333 0.00 0.00 33.75 2.43
2342 2403 6.828672 ACGAATTGTAGCACTAGTTTTTAGC 58.171 36.000 0.00 0.00 0.00 3.09
2360 2421 8.972349 GTTTTTAGCCTTGAAATTGAAAGAGAG 58.028 33.333 2.66 0.00 0.00 3.20
2389 2450 9.278978 GCTTTTAATCTAACCATTTTTCCCAAA 57.721 29.630 0.00 0.00 0.00 3.28
2461 2527 5.763088 TGTGCAACATTAAGATGCGTTTAA 58.237 33.333 0.00 0.00 45.67 1.52
2462 2528 6.209361 TGTGCAACATTAAGATGCGTTTAAA 58.791 32.000 0.00 0.00 45.67 1.52
2528 2594 8.567948 CACAAGTATATTGAGTGGTCTTTGTTT 58.432 33.333 0.00 0.00 0.00 2.83
2574 2640 4.650972 TTATGTAAAGTTGGTCCTGGCT 57.349 40.909 0.00 0.00 0.00 4.75
2593 2660 3.303406 GCTGTGCTTTGAACTCATGAAC 58.697 45.455 0.00 0.00 0.00 3.18
2681 2748 4.464008 TGAGCTTGACAAGAAAACTGGAT 58.536 39.130 19.51 0.00 0.00 3.41
2697 2764 6.976934 AACTGGATTGATTAAGGTGTGTTT 57.023 33.333 0.00 0.00 0.00 2.83
2853 2921 6.587608 GCTGTGCTTGCTAAATTGATTTAGTT 59.412 34.615 19.29 0.00 46.78 2.24
2869 2937 8.763049 TGATTTAGTTCTGTACTCATGAGTTG 57.237 34.615 32.14 21.37 42.54 3.16
2908 2976 8.722342 TTTTTCGTCAAAGCATAATGTACTTC 57.278 30.769 0.00 0.00 0.00 3.01
2913 2981 6.738200 CGTCAAAGCATAATGTACTTCTGTTG 59.262 38.462 0.00 0.00 0.00 3.33
3012 3080 3.809832 CGAGGACACTTTGTGAAGACAAT 59.190 43.478 4.61 0.00 41.77 2.71
3059 3127 5.128663 TGATGCAGGTTAGTCTTAGCATGTA 59.871 40.000 2.12 0.00 42.18 2.29
3060 3128 5.011090 TGCAGGTTAGTCTTAGCATGTAG 57.989 43.478 0.00 0.00 0.00 2.74
3061 3129 4.141937 TGCAGGTTAGTCTTAGCATGTAGG 60.142 45.833 0.00 0.00 0.00 3.18
3062 3130 4.141914 GCAGGTTAGTCTTAGCATGTAGGT 60.142 45.833 0.00 0.00 0.00 3.08
3063 3131 5.352284 CAGGTTAGTCTTAGCATGTAGGTG 58.648 45.833 0.00 0.00 0.00 4.00
3074 3142 2.747467 GCATGTAGGTGATGCACTCCAT 60.747 50.000 0.00 0.00 44.74 3.41
3117 3185 6.786967 TTATCTACTACCACCTCTGTTTCC 57.213 41.667 0.00 0.00 0.00 3.13
3128 3196 5.048713 CCACCTCTGTTTCCAAATGTAAGAC 60.049 44.000 0.00 0.00 0.00 3.01
3129 3197 5.530915 CACCTCTGTTTCCAAATGTAAGACA 59.469 40.000 0.00 0.00 0.00 3.41
3164 3232 2.325583 TTGAACTGCCAGAACGTCTT 57.674 45.000 0.00 0.00 0.00 3.01
3178 3246 6.425721 CCAGAACGTCTTACATTTAGGAACAA 59.574 38.462 0.00 0.00 0.00 2.83
3181 3249 6.796705 ACGTCTTACATTTAGGAACAAAGG 57.203 37.500 0.00 0.00 0.00 3.11
3185 3253 7.360361 GTCTTACATTTAGGAACAAAGGTGTG 58.640 38.462 0.00 0.00 38.27 3.82
3187 3255 5.514274 ACATTTAGGAACAAAGGTGTGTG 57.486 39.130 0.00 0.00 38.27 3.82
3210 3278 6.531594 GTGTCCTTTTCATTTTATAAGGCTGC 59.468 38.462 0.00 0.00 37.62 5.25
3297 3366 7.509141 TTGACTTGAGACAAATTATGCAGAA 57.491 32.000 0.00 0.00 0.00 3.02
3298 3367 7.137490 TGACTTGAGACAAATTATGCAGAAG 57.863 36.000 0.00 0.00 0.00 2.85
3327 3396 1.975680 TGAAACAGAGGGGGTAGTGAC 59.024 52.381 0.00 0.00 0.00 3.67
3341 3410 5.148651 GGTAGTGACCATTGTGTTACTCT 57.851 43.478 6.15 0.00 46.12 3.24
3441 3510 7.405292 TGATCAGGTATTCCTTGTTCATTCTT 58.595 34.615 0.00 0.00 43.07 2.52
3473 3543 4.487714 TGGGAGATGAACGAAAATAGCT 57.512 40.909 0.00 0.00 0.00 3.32
3655 3725 5.482908 ACTGTATCCTGCATAATCCGATTC 58.517 41.667 0.00 0.00 0.00 2.52
3803 3978 0.245266 TCGATGCGTTCTTACCTGCA 59.755 50.000 0.00 0.00 42.22 4.41
3880 4055 4.635765 TCTCTGCCAAGATGTATTTTTCCG 59.364 41.667 0.00 0.00 0.00 4.30
3884 4059 4.764823 TGCCAAGATGTATTTTTCCGTTCT 59.235 37.500 0.00 0.00 0.00 3.01
3885 4060 5.242838 TGCCAAGATGTATTTTTCCGTTCTT 59.757 36.000 0.00 0.00 0.00 2.52
3886 4061 5.800438 GCCAAGATGTATTTTTCCGTTCTTC 59.200 40.000 0.00 0.00 0.00 2.87
3892 4068 6.671614 TGTATTTTTCCGTTCTTCGCATAT 57.328 33.333 0.00 0.00 38.35 1.78
3917 4093 5.048991 GTGATGACGGTGAAGGTGTATTTTT 60.049 40.000 0.00 0.00 0.00 1.94
3939 4115 8.912787 TTTTGTTTACATTGACGCTTCTTTTA 57.087 26.923 0.00 0.00 0.00 1.52
4014 4190 0.174845 GCAGTAGCATGTCGGTGGTA 59.825 55.000 0.00 0.00 41.58 3.25
4054 4230 9.628500 AATCTTCTATTAATAACAAGTGGGGAC 57.372 33.333 11.19 0.00 0.00 4.46
4292 5437 0.178947 TTTAACAGGCCTGGGGTTGG 60.179 55.000 35.42 10.23 34.19 3.77
4299 5444 1.076549 GCCTGGGGTTGGATGTGAA 59.923 57.895 0.00 0.00 0.00 3.18
4357 5502 3.859061 ACTAATTAGTAAGCCTGGGGC 57.141 47.619 16.60 0.00 41.30 5.80
4359 5504 5.077534 ACTAATTAGTAAGCCTGGGGCGG 62.078 52.174 16.60 0.00 43.93 6.13
4376 5521 4.284550 GGTGCCAGACCTTGCCCA 62.285 66.667 0.00 0.00 42.25 5.36
4377 5522 2.203480 GTGCCAGACCTTGCCCAA 60.203 61.111 0.00 0.00 0.00 4.12
4384 5823 0.398318 AGACCTTGCCCAACTCTGTC 59.602 55.000 0.00 0.00 0.00 3.51
4416 6600 2.430367 GAACGGGCCCAACTCTGT 59.570 61.111 24.92 7.35 0.00 3.41
4420 6604 1.746615 CGGGCCCAACTCTGTCATG 60.747 63.158 24.92 0.00 0.00 3.07
4427 6611 1.446907 CAACTCTGTCATGTCCAGGC 58.553 55.000 12.91 0.00 0.00 4.85
4428 6612 1.002888 CAACTCTGTCATGTCCAGGCT 59.997 52.381 12.91 0.00 0.00 4.58
4429 6613 1.356124 ACTCTGTCATGTCCAGGCTT 58.644 50.000 12.91 0.00 0.00 4.35
4452 6636 5.838531 TTTTTAACTCCACGATGTTGGTT 57.161 34.783 0.00 0.00 37.93 3.67
4453 6637 5.427036 TTTTAACTCCACGATGTTGGTTC 57.573 39.130 0.00 0.00 37.93 3.62
4454 6638 2.930826 AACTCCACGATGTTGGTTCT 57.069 45.000 0.00 0.00 37.93 3.01
4455 6639 2.457366 ACTCCACGATGTTGGTTCTC 57.543 50.000 0.00 0.00 37.93 2.87
4457 6641 1.001974 CTCCACGATGTTGGTTCTCCA 59.998 52.381 0.00 0.00 42.66 3.86
4488 6672 8.826293 AAAATAAATAGAAAATCCACGGGGTA 57.174 30.769 2.12 0.00 34.93 3.69
4497 6681 6.546034 AGAAAATCCACGGGGTAAGAATATTG 59.454 38.462 2.12 0.00 34.93 1.90
4582 6768 1.133253 CATTGTTGCACTCGGCTCG 59.867 57.895 0.00 0.00 45.15 5.03
4615 6801 1.638529 CACAGTGGTCTTCTCTCCCT 58.361 55.000 0.00 0.00 0.00 4.20
4838 7025 1.393883 GTTTTCTGAATCTCGCGACCC 59.606 52.381 3.71 0.00 0.00 4.46
4896 7083 0.669318 TGTCGTGTCCTTGATTCGGC 60.669 55.000 0.00 0.00 0.00 5.54
4997 7184 1.728490 GCCGCTCATGAAATCCCACC 61.728 60.000 0.00 0.00 0.00 4.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.494918 GTAGGATGAGGCGCGTGT 59.505 61.111 7.63 0.00 0.00 4.49
1 2 2.655364 CGTAGGATGAGGCGCGTG 60.655 66.667 7.63 0.00 0.00 5.34
2 3 3.138798 ACGTAGGATGAGGCGCGT 61.139 61.111 8.43 0.27 0.00 6.01
3 4 2.655364 CACGTAGGATGAGGCGCG 60.655 66.667 0.00 0.00 0.00 6.86
4 5 2.279517 CCACGTAGGATGAGGCGC 60.280 66.667 0.00 0.00 41.22 6.53
5 6 2.279517 GCCACGTAGGATGAGGCG 60.280 66.667 8.04 0.00 41.22 5.52
6 7 1.521681 GTGCCACGTAGGATGAGGC 60.522 63.158 8.04 6.09 45.41 4.70
7 8 0.249120 TTGTGCCACGTAGGATGAGG 59.751 55.000 8.04 0.00 41.22 3.86
8 9 2.093306 TTTGTGCCACGTAGGATGAG 57.907 50.000 8.04 0.00 41.22 2.90
9 10 2.552599 TTTTGTGCCACGTAGGATGA 57.447 45.000 8.04 0.00 41.22 2.92
39 40 7.877950 GTGTGTGCACGAATCTTGGAACAAA 62.878 44.000 13.13 0.00 38.80 2.83
40 41 6.495892 GTGTGTGCACGAATCTTGGAACAA 62.496 45.833 13.13 0.00 38.80 2.83
41 42 1.601903 GTGTGCACGAATCTTGGAACA 59.398 47.619 13.13 0.00 0.00 3.18
42 43 1.601903 TGTGTGCACGAATCTTGGAAC 59.398 47.619 13.13 0.83 0.00 3.62
43 44 1.601903 GTGTGTGCACGAATCTTGGAA 59.398 47.619 13.13 0.00 35.75 3.53
44 45 1.225855 GTGTGTGCACGAATCTTGGA 58.774 50.000 13.13 0.00 35.75 3.53
45 46 0.238289 GGTGTGTGCACGAATCTTGG 59.762 55.000 13.13 0.00 46.13 3.61
46 47 1.069703 CAGGTGTGTGCACGAATCTTG 60.070 52.381 13.13 5.71 46.13 3.02
47 48 1.229428 CAGGTGTGTGCACGAATCTT 58.771 50.000 13.13 0.00 46.13 2.40
48 49 1.230635 GCAGGTGTGTGCACGAATCT 61.231 55.000 13.13 5.39 46.13 2.40
49 50 1.207593 GCAGGTGTGTGCACGAATC 59.792 57.895 13.13 2.78 46.13 2.52
50 51 2.260869 GGCAGGTGTGTGCACGAAT 61.261 57.895 13.13 0.00 45.93 3.34
51 52 2.899838 GGCAGGTGTGTGCACGAA 60.900 61.111 13.13 0.00 45.93 3.85
52 53 3.689002 TTGGCAGGTGTGTGCACGA 62.689 57.895 13.13 0.00 45.93 4.35
53 54 3.208383 TTGGCAGGTGTGTGCACG 61.208 61.111 13.13 0.00 45.93 5.34
54 55 2.412937 GTTGGCAGGTGTGTGCAC 59.587 61.111 10.75 10.75 45.93 4.57
55 56 3.208383 CGTTGGCAGGTGTGTGCA 61.208 61.111 0.00 0.00 45.93 4.57
56 57 3.964875 CCGTTGGCAGGTGTGTGC 61.965 66.667 0.00 0.00 43.19 4.57
57 58 2.515991 ACCGTTGGCAGGTGTGTG 60.516 61.111 0.00 0.00 41.10 3.82
62 63 2.672996 GCATCACCGTTGGCAGGT 60.673 61.111 0.00 0.00 43.97 4.00
63 64 1.973281 AAGCATCACCGTTGGCAGG 60.973 57.895 0.00 0.00 0.00 4.85
64 65 1.210931 CAAGCATCACCGTTGGCAG 59.789 57.895 0.00 0.00 0.00 4.85
65 66 2.918345 GCAAGCATCACCGTTGGCA 61.918 57.895 0.00 0.00 0.00 4.92
66 67 2.126346 GCAAGCATCACCGTTGGC 60.126 61.111 0.00 0.00 0.00 4.52
67 68 2.176546 CGCAAGCATCACCGTTGG 59.823 61.111 0.00 0.00 0.00 3.77
68 69 1.440850 CACGCAAGCATCACCGTTG 60.441 57.895 0.00 0.00 45.62 4.10
69 70 1.891919 ACACGCAAGCATCACCGTT 60.892 52.632 0.00 0.00 45.62 4.44
70 71 2.280797 ACACGCAAGCATCACCGT 60.281 55.556 0.00 0.00 45.62 4.83
71 72 2.174107 CACACGCAAGCATCACCG 59.826 61.111 0.00 0.00 45.62 4.94
72 73 2.187599 GACCACACGCAAGCATCACC 62.188 60.000 0.00 0.00 45.62 4.02
73 74 1.207593 GACCACACGCAAGCATCAC 59.792 57.895 0.00 0.00 45.62 3.06
74 75 2.316867 CGACCACACGCAAGCATCA 61.317 57.895 0.00 0.00 45.62 3.07
75 76 2.476051 CGACCACACGCAAGCATC 59.524 61.111 0.00 0.00 45.62 3.91
76 77 3.049674 CCGACCACACGCAAGCAT 61.050 61.111 0.00 0.00 45.62 3.79
80 81 4.920112 CACCCCGACCACACGCAA 62.920 66.667 0.00 0.00 0.00 4.85
83 84 4.980805 CACCACCCCGACCACACG 62.981 72.222 0.00 0.00 0.00 4.49
84 85 3.109592 TTCACCACCCCGACCACAC 62.110 63.158 0.00 0.00 0.00 3.82
85 86 2.768769 TTCACCACCCCGACCACA 60.769 61.111 0.00 0.00 0.00 4.17
86 87 2.281276 GTTCACCACCCCGACCAC 60.281 66.667 0.00 0.00 0.00 4.16
87 88 3.931247 CGTTCACCACCCCGACCA 61.931 66.667 0.00 0.00 0.00 4.02
96 97 4.164087 ACGTGTGGGCGTTCACCA 62.164 61.111 7.58 0.00 43.04 4.17
97 98 3.645975 CACGTGTGGGCGTTCACC 61.646 66.667 7.58 0.00 43.83 4.02
98 99 2.893404 ACACGTGTGGGCGTTCAC 60.893 61.111 22.71 3.83 43.83 3.18
99 100 2.892914 CACACGTGTGGGCGTTCA 60.893 61.111 35.65 0.00 43.83 3.18
111 112 1.400500 GGAAATGTTAACGCCCACACG 60.400 52.381 0.26 0.00 39.50 4.49
112 113 1.400500 CGGAAATGTTAACGCCCACAC 60.400 52.381 0.26 0.00 0.00 3.82
113 114 0.875728 CGGAAATGTTAACGCCCACA 59.124 50.000 0.26 0.00 0.00 4.17
114 115 0.876399 ACGGAAATGTTAACGCCCAC 59.124 50.000 0.26 0.00 0.00 4.61
115 116 2.469274 TACGGAAATGTTAACGCCCA 57.531 45.000 0.26 0.00 0.00 5.36
116 117 3.828060 TTTACGGAAATGTTAACGCCC 57.172 42.857 0.26 0.00 0.00 6.13
117 118 7.043920 CCATTAATTTACGGAAATGTTAACGCC 60.044 37.037 6.32 0.00 35.38 5.68
118 119 7.043920 CCCATTAATTTACGGAAATGTTAACGC 60.044 37.037 6.32 0.00 35.38 4.84
119 120 7.969508 ACCCATTAATTTACGGAAATGTTAACG 59.030 33.333 6.32 0.00 35.38 3.18
120 121 9.078753 CACCCATTAATTTACGGAAATGTTAAC 57.921 33.333 6.32 0.00 35.38 2.01
121 122 8.804204 ACACCCATTAATTTACGGAAATGTTAA 58.196 29.630 6.32 3.91 35.38 2.01
122 123 8.244802 CACACCCATTAATTTACGGAAATGTTA 58.755 33.333 6.32 0.00 35.38 2.41
123 124 7.093992 CACACCCATTAATTTACGGAAATGTT 58.906 34.615 6.32 0.00 35.38 2.71
124 125 6.626302 CACACCCATTAATTTACGGAAATGT 58.374 36.000 6.32 0.00 35.38 2.71
125 126 5.518487 GCACACCCATTAATTTACGGAAATG 59.482 40.000 6.32 0.00 35.38 2.32
126 127 5.656480 GCACACCCATTAATTTACGGAAAT 58.344 37.500 0.00 0.00 36.82 2.17
127 128 4.379603 CGCACACCCATTAATTTACGGAAA 60.380 41.667 0.00 0.00 0.00 3.13
128 129 3.127203 CGCACACCCATTAATTTACGGAA 59.873 43.478 0.00 0.00 0.00 4.30
129 130 2.678836 CGCACACCCATTAATTTACGGA 59.321 45.455 0.00 0.00 0.00 4.69
130 131 2.793237 GCGCACACCCATTAATTTACGG 60.793 50.000 0.30 0.00 0.00 4.02
131 132 2.446282 GCGCACACCCATTAATTTACG 58.554 47.619 0.30 0.00 0.00 3.18
132 133 2.425668 AGGCGCACACCCATTAATTTAC 59.574 45.455 10.83 0.00 0.00 2.01
186 189 6.722328 TGTCTCTCTCAAGGAACATACTAGA 58.278 40.000 0.00 0.00 0.00 2.43
187 190 7.424803 CATGTCTCTCTCAAGGAACATACTAG 58.575 42.308 0.00 0.00 31.21 2.57
189 192 5.395103 GCATGTCTCTCTCAAGGAACATACT 60.395 44.000 0.00 0.00 31.21 2.12
190 193 4.808364 GCATGTCTCTCTCAAGGAACATAC 59.192 45.833 0.00 0.00 31.21 2.39
229 236 2.845363 AAAGCAAAAGATGGCCAAGG 57.155 45.000 10.96 0.00 0.00 3.61
230 237 4.452114 GGTTAAAAGCAAAAGATGGCCAAG 59.548 41.667 10.96 0.00 0.00 3.61
313 320 9.507280 CTTTGTATGTATTTTTATGCTGTCCAG 57.493 33.333 0.00 0.00 0.00 3.86
355 364 3.694926 AGCCTAACGAGTAACCACTACT 58.305 45.455 0.00 0.00 43.95 2.57
356 365 4.878397 TCTAGCCTAACGAGTAACCACTAC 59.122 45.833 0.00 0.00 34.21 2.73
357 366 4.878397 GTCTAGCCTAACGAGTAACCACTA 59.122 45.833 0.00 0.00 34.21 2.74
382 391 1.757699 GACAGATCAGTCCCTGGGTAC 59.242 57.143 13.56 9.74 34.85 3.34
598 611 1.746991 GCTTTTGGGAGCGGAGGAG 60.747 63.158 0.00 0.00 32.23 3.69
599 612 2.351276 GCTTTTGGGAGCGGAGGA 59.649 61.111 0.00 0.00 32.23 3.71
605 618 1.336755 TGAAAAGACGCTTTTGGGAGC 59.663 47.619 18.08 7.59 39.29 4.70
606 619 3.708563 TTGAAAAGACGCTTTTGGGAG 57.291 42.857 18.08 0.00 36.14 4.30
607 620 3.304391 CGATTGAAAAGACGCTTTTGGGA 60.304 43.478 18.08 7.67 36.14 4.37
608 621 2.979813 CGATTGAAAAGACGCTTTTGGG 59.020 45.455 18.08 3.98 38.45 4.12
609 622 3.421888 CACGATTGAAAAGACGCTTTTGG 59.578 43.478 18.08 7.94 34.00 3.28
610 623 4.035017 ACACGATTGAAAAGACGCTTTTG 58.965 39.130 18.08 8.96 34.00 2.44
617 630 3.241678 CGGATCGACACGATTGAAAAGAC 60.242 47.826 8.01 0.00 47.00 3.01
630 643 1.407618 CCACCTTGTATCGGATCGACA 59.592 52.381 0.00 0.00 39.18 4.35
764 785 1.299468 GCCACGCCTAGATCGAGTG 60.299 63.158 10.57 3.46 0.00 3.51
898 924 5.483231 TGGTATCATCTGGCCAAAATTTCAA 59.517 36.000 7.01 0.00 0.00 2.69
903 929 4.352009 TGTTGGTATCATCTGGCCAAAAT 58.648 39.130 7.01 0.00 41.89 1.82
908 934 1.610522 GCATGTTGGTATCATCTGGCC 59.389 52.381 0.00 0.00 0.00 5.36
912 938 1.942657 GCACGCATGTTGGTATCATCT 59.057 47.619 0.00 0.00 0.00 2.90
918 944 1.265635 GAAACAGCACGCATGTTGGTA 59.734 47.619 0.83 0.00 35.65 3.25
962 988 1.137086 CCACGAATCAGACCTCGGAAT 59.863 52.381 8.28 0.00 39.38 3.01
993 1024 1.035923 CCTCTTCGCTCATCCTGCTA 58.964 55.000 0.00 0.00 0.00 3.49
1068 1102 1.377366 GCGACGACAGGATCCTCTCA 61.377 60.000 12.69 0.00 0.00 3.27
1148 1188 4.074970 GAGACAGAAATGGAGAAAAGGCA 58.925 43.478 0.00 0.00 0.00 4.75
1163 1206 1.344065 TTGGTAAAGCCGGAGACAGA 58.656 50.000 5.05 0.00 41.21 3.41
1167 1210 1.459450 GCATTTGGTAAAGCCGGAGA 58.541 50.000 5.05 0.00 41.21 3.71
1168 1211 0.455815 GGCATTTGGTAAAGCCGGAG 59.544 55.000 5.05 0.00 41.21 4.63
1169 1212 2.573920 GGCATTTGGTAAAGCCGGA 58.426 52.632 5.05 0.00 41.21 5.14
1172 1215 5.729510 TTTATCAAGGCATTTGGTAAAGCC 58.270 37.500 12.14 0.00 43.82 4.35
1190 1233 6.940714 TCGCCGAGCTTATTTAACTTTTATC 58.059 36.000 0.00 0.00 0.00 1.75
1197 1240 3.724257 GCAATTCGCCGAGCTTATTTAAC 59.276 43.478 0.00 0.00 32.94 2.01
1198 1241 3.625764 AGCAATTCGCCGAGCTTATTTAA 59.374 39.130 0.00 0.00 44.04 1.52
1199 1242 3.002246 CAGCAATTCGCCGAGCTTATTTA 59.998 43.478 0.00 0.00 44.04 1.40
1208 1251 1.375853 CCCAATCAGCAATTCGCCGA 61.376 55.000 0.00 0.00 44.04 5.54
1209 1252 1.064621 CCCAATCAGCAATTCGCCG 59.935 57.895 0.00 0.00 44.04 6.46
1211 1254 2.368655 AAACCCAATCAGCAATTCGC 57.631 45.000 0.00 0.00 42.91 4.70
1212 1255 3.432933 CCAAAAACCCAATCAGCAATTCG 59.567 43.478 0.00 0.00 0.00 3.34
1226 1269 1.227527 GGCCTGTGCACCAAAAACC 60.228 57.895 15.69 3.53 40.13 3.27
1229 1272 2.132996 CAGGGCCTGTGCACCAAAA 61.133 57.895 25.74 0.00 44.14 2.44
1276 1319 1.070445 TGGCAAGGCAAAAAGATGGTG 59.930 47.619 0.00 0.00 0.00 4.17
1337 1380 6.601613 TCCAACATCCTAATTTACTTTGCGAT 59.398 34.615 0.00 0.00 0.00 4.58
1356 1399 1.619654 CACTTGCCCAAGATCCAACA 58.380 50.000 14.46 0.00 40.79 3.33
1438 1481 2.039480 GCATCCTGCAGAGATCCCATAA 59.961 50.000 17.39 0.00 44.26 1.90
1492 1535 4.336993 CCTACTTCCTAGTACAGAGTGCAG 59.663 50.000 0.00 0.00 35.78 4.41
1559 1602 7.670009 TTTGAACGAAAGGTAAATATTCCGA 57.330 32.000 0.00 0.00 0.00 4.55
1560 1603 8.905103 ATTTTGAACGAAAGGTAAATATTCCG 57.095 30.769 0.00 0.00 0.00 4.30
1592 1635 7.882791 TGAAGTCATGTGTACCACTGAAATTAT 59.117 33.333 0.00 0.00 35.11 1.28
1633 1676 8.756864 GCCGTAACATTCACTTGAATTTAAAAA 58.243 29.630 1.52 0.00 42.41 1.94
1634 1677 7.382759 GGCCGTAACATTCACTTGAATTTAAAA 59.617 33.333 1.52 0.00 42.41 1.52
1635 1678 6.864165 GGCCGTAACATTCACTTGAATTTAAA 59.136 34.615 1.52 0.00 42.41 1.52
1636 1679 6.383415 GGCCGTAACATTCACTTGAATTTAA 58.617 36.000 1.52 0.00 42.41 1.52
1637 1680 5.106078 GGGCCGTAACATTCACTTGAATTTA 60.106 40.000 1.52 3.14 42.41 1.40
1638 1681 4.321675 GGGCCGTAACATTCACTTGAATTT 60.322 41.667 1.52 3.94 42.41 1.82
1796 1848 8.416329 GTTATTTTGATTCAGACATAGCCCAAT 58.584 33.333 0.00 0.00 0.00 3.16
1929 1983 8.259411 TGCCATTTAATACTGATTGCTTCATTT 58.741 29.630 0.00 0.00 32.72 2.32
2053 2114 6.345298 TCATTAGCCTCAACATTGACGATAA 58.655 36.000 0.00 4.55 31.98 1.75
2123 2184 4.080356 TGAAGGCAGTGATAGCAGGTTATT 60.080 41.667 0.00 0.00 0.00 1.40
2150 2211 2.812178 GCATGCAGCCAAAAGGCG 60.812 61.111 14.21 0.00 40.23 5.52
2155 2216 2.496470 TCAATATGTGCATGCAGCCAAA 59.504 40.909 23.41 5.58 44.83 3.28
2157 2218 1.765230 TCAATATGTGCATGCAGCCA 58.235 45.000 23.41 17.37 44.83 4.75
2158 2219 3.380479 AATCAATATGTGCATGCAGCC 57.620 42.857 23.41 11.34 44.83 4.85
2159 2220 4.116961 ACAAATCAATATGTGCATGCAGC 58.883 39.130 23.41 16.34 45.96 5.25
2160 2221 5.808030 TCAACAAATCAATATGTGCATGCAG 59.192 36.000 23.41 8.47 0.00 4.41
2161 2222 5.721232 TCAACAAATCAATATGTGCATGCA 58.279 33.333 18.46 18.46 0.00 3.96
2162 2223 6.838198 ATCAACAAATCAATATGTGCATGC 57.162 33.333 11.82 11.82 0.00 4.06
2163 2224 8.539674 CAGAATCAACAAATCAATATGTGCATG 58.460 33.333 0.00 0.00 0.00 4.06
2164 2225 8.255206 ACAGAATCAACAAATCAATATGTGCAT 58.745 29.630 0.00 0.00 0.00 3.96
2165 2226 7.604549 ACAGAATCAACAAATCAATATGTGCA 58.395 30.769 0.00 0.00 0.00 4.57
2166 2227 9.571810 TTACAGAATCAACAAATCAATATGTGC 57.428 29.630 0.00 0.00 0.00 4.57
2210 2271 6.436847 TCAAAATCATAGACCCAATTCAGCAA 59.563 34.615 0.00 0.00 0.00 3.91
2211 2272 5.951148 TCAAAATCATAGACCCAATTCAGCA 59.049 36.000 0.00 0.00 0.00 4.41
2216 2277 9.479549 ACTTGTATCAAAATCATAGACCCAATT 57.520 29.630 0.00 0.00 0.00 2.32
2232 2293 9.114952 TCACAGTGACAATTTTACTTGTATCAA 57.885 29.630 0.00 0.00 39.40 2.57
2338 2399 5.183904 GCCTCTCTTTCAATTTCAAGGCTAA 59.816 40.000 2.90 0.00 43.67 3.09
2342 2403 3.671702 GCGCCTCTCTTTCAATTTCAAGG 60.672 47.826 0.00 0.00 0.00 3.61
2360 2421 6.035650 GGAAAAATGGTTAGATTAAAAGCGCC 59.964 38.462 2.29 0.00 0.00 6.53
2481 2547 6.862209 TGTGTGTTACTGAGAAGCAATTTTT 58.138 32.000 0.00 0.00 0.00 1.94
2528 2594 6.688578 AGAGTCTAGCATCGTTAACAGAAAA 58.311 36.000 6.39 0.00 0.00 2.29
2574 2640 6.318648 AGTTAAGTTCATGAGTTCAAAGCACA 59.681 34.615 0.00 0.00 0.00 4.57
2797 2865 2.288030 GCATTATGCTGGTGGATGCTTC 60.288 50.000 10.27 0.00 40.96 3.86
2853 2921 9.208022 CAAAATAAGTCAACTCATGAGTACAGA 57.792 33.333 28.10 21.61 40.94 3.41
3053 3121 1.303309 GGAGTGCATCACCTACATGC 58.697 55.000 0.00 0.00 45.92 4.06
3088 3156 9.435570 AACAGAGGTGGTAGTAGATAATAACAT 57.564 33.333 0.00 0.00 0.00 2.71
3089 3157 8.834004 AACAGAGGTGGTAGTAGATAATAACA 57.166 34.615 0.00 0.00 0.00 2.41
3090 3158 9.747293 GAAACAGAGGTGGTAGTAGATAATAAC 57.253 37.037 0.00 0.00 0.00 1.89
3091 3159 8.921205 GGAAACAGAGGTGGTAGTAGATAATAA 58.079 37.037 0.00 0.00 0.00 1.40
3092 3160 8.063153 TGGAAACAGAGGTGGTAGTAGATAATA 58.937 37.037 0.00 0.00 35.01 0.98
3093 3161 6.901300 TGGAAACAGAGGTGGTAGTAGATAAT 59.099 38.462 0.00 0.00 35.01 1.28
3094 3162 6.258354 TGGAAACAGAGGTGGTAGTAGATAA 58.742 40.000 0.00 0.00 35.01 1.75
3095 3163 5.834460 TGGAAACAGAGGTGGTAGTAGATA 58.166 41.667 0.00 0.00 35.01 1.98
3096 3164 4.684724 TGGAAACAGAGGTGGTAGTAGAT 58.315 43.478 0.00 0.00 35.01 1.98
3097 3165 4.122337 TGGAAACAGAGGTGGTAGTAGA 57.878 45.455 0.00 0.00 35.01 2.59
3098 3166 4.884668 TTGGAAACAGAGGTGGTAGTAG 57.115 45.455 0.00 0.00 44.54 2.57
3099 3167 5.072600 ACATTTGGAAACAGAGGTGGTAGTA 59.927 40.000 0.00 0.00 38.11 1.82
3100 3168 4.141251 ACATTTGGAAACAGAGGTGGTAGT 60.141 41.667 0.00 0.00 38.11 2.73
3101 3169 4.398319 ACATTTGGAAACAGAGGTGGTAG 58.602 43.478 0.00 0.00 38.11 3.18
3102 3170 4.447138 ACATTTGGAAACAGAGGTGGTA 57.553 40.909 0.00 0.00 38.11 3.25
3103 3171 3.312736 ACATTTGGAAACAGAGGTGGT 57.687 42.857 0.00 0.00 38.11 4.16
3104 3172 5.048713 GTCTTACATTTGGAAACAGAGGTGG 60.049 44.000 0.00 0.00 39.94 4.61
3105 3173 5.530915 TGTCTTACATTTGGAAACAGAGGTG 59.469 40.000 0.00 0.00 39.94 4.00
3139 3207 5.298276 AGACGTTCTGGCAGTTCAATTTAAA 59.702 36.000 15.27 0.00 0.00 1.52
3156 3224 7.041576 ACCTTTGTTCCTAAATGTAAGACGTTC 60.042 37.037 0.00 0.00 0.00 3.95
3157 3225 6.769341 ACCTTTGTTCCTAAATGTAAGACGTT 59.231 34.615 0.00 0.00 0.00 3.99
3164 3232 6.123651 ACACACACCTTTGTTCCTAAATGTA 58.876 36.000 0.00 0.00 31.66 2.29
3181 3249 7.328493 GCCTTATAAAATGAAAAGGACACACAC 59.672 37.037 4.19 0.00 40.85 3.82
3185 3253 6.531594 GCAGCCTTATAAAATGAAAAGGACAC 59.468 38.462 4.19 0.00 40.85 3.67
3187 3255 6.867550 AGCAGCCTTATAAAATGAAAAGGAC 58.132 36.000 4.19 0.00 40.85 3.85
3210 3278 6.926272 AGTGCTTGACTTAAGACAAACTAGAG 59.074 38.462 18.57 9.06 38.76 2.43
3297 3366 5.312443 ACCCCCTCTGTTTCAGTTTATAACT 59.688 40.000 0.00 0.00 44.06 2.24
3298 3367 5.567430 ACCCCCTCTGTTTCAGTTTATAAC 58.433 41.667 0.00 0.00 32.61 1.89
3327 3396 9.219603 TGAGAGATAAAAAGAGTAACACAATGG 57.780 33.333 0.00 0.00 0.00 3.16
3341 3410 4.836825 CAGGCTCCTGTGAGAGATAAAAA 58.163 43.478 7.75 0.00 41.42 1.94
3441 3510 1.013596 CATCTCCCATTAACGCGCAA 58.986 50.000 5.73 0.00 0.00 4.85
3473 3543 6.488683 CACCATCCTCAGTAAAACAAGGTAAA 59.511 38.462 0.00 0.00 0.00 2.01
3655 3725 6.479660 ACTGCATGTAACAAGGAAAACAAATG 59.520 34.615 0.00 0.00 0.00 2.32
3750 3925 5.402867 CCTTGTTCTCGTTCTTCTTGTCTAC 59.597 44.000 0.00 0.00 0.00 2.59
3764 3939 0.734253 CAGCGACCTCCTTGTTCTCG 60.734 60.000 0.00 0.00 0.00 4.04
3850 4025 4.025040 ACATCTTGGCAGAGATCAACAA 57.975 40.909 8.57 0.00 34.20 2.83
3880 4055 3.060272 CCGTCATCACATATGCGAAGAAC 60.060 47.826 1.58 0.00 0.00 3.01
3884 4059 2.159170 TCACCGTCATCACATATGCGAA 60.159 45.455 1.58 0.00 0.00 4.70
3885 4060 1.407258 TCACCGTCATCACATATGCGA 59.593 47.619 1.58 0.00 0.00 5.10
3886 4061 1.851658 TCACCGTCATCACATATGCG 58.148 50.000 1.58 0.00 0.00 4.73
3892 4068 0.756294 ACACCTTCACCGTCATCACA 59.244 50.000 0.00 0.00 0.00 3.58
3917 4093 9.522804 AAAATAAAAGAAGCGTCAATGTAAACA 57.477 25.926 1.61 0.00 0.00 2.83
4054 4230 1.858091 ACACACAAAGTCTCAGCTCG 58.142 50.000 0.00 0.00 0.00 5.03
4180 5251 8.526667 TTCAAAATGGATATACGAATTGGGAA 57.473 30.769 0.00 0.00 0.00 3.97
4181 5252 8.704849 ATTCAAAATGGATATACGAATTGGGA 57.295 30.769 0.00 0.00 0.00 4.37
4190 5261 8.143835 CCAAACCAGGATTCAAAATGGATATAC 58.856 37.037 0.00 0.00 36.62 1.47
4292 5437 1.379044 CCCAGGCCCAGTTCACATC 60.379 63.158 0.00 0.00 0.00 3.06
4364 5509 0.109342 ACAGAGTTGGGCAAGGTCTG 59.891 55.000 0.00 0.00 38.02 3.51
4366 5511 0.398318 AGACAGAGTTGGGCAAGGTC 59.602 55.000 0.00 0.00 0.00 3.85
4367 5512 0.846693 AAGACAGAGTTGGGCAAGGT 59.153 50.000 0.00 0.00 0.00 3.50
4368 5513 1.986882 AAAGACAGAGTTGGGCAAGG 58.013 50.000 0.00 0.00 0.00 3.61
4391 5830 2.087857 TTGGGCCCGTTCCCTCAAAT 62.088 55.000 19.37 0.00 46.67 2.32
4395 5834 3.623703 GAGTTGGGCCCGTTCCCTC 62.624 68.421 19.37 13.28 46.67 4.30
4396 5835 3.647771 GAGTTGGGCCCGTTCCCT 61.648 66.667 19.37 7.80 46.67 4.20
4397 5836 3.647771 AGAGTTGGGCCCGTTCCC 61.648 66.667 19.37 5.01 46.73 3.97
4401 6585 2.224159 ATGACAGAGTTGGGCCCGT 61.224 57.895 19.37 7.50 0.00 5.28
4458 6642 9.816354 CCGTGGATTTTCTATTTATTTTTGGAT 57.184 29.630 0.00 0.00 0.00 3.41
4460 6644 7.494298 CCCCGTGGATTTTCTATTTATTTTTGG 59.506 37.037 0.00 0.00 0.00 3.28
4462 6646 8.141298 ACCCCGTGGATTTTCTATTTATTTTT 57.859 30.769 0.00 0.00 34.81 1.94
4467 6651 7.197901 TCTTACCCCGTGGATTTTCTATTTA 57.802 36.000 0.00 0.00 34.81 1.40
4473 6657 6.320418 ACAATATTCTTACCCCGTGGATTTTC 59.680 38.462 0.00 0.00 34.81 2.29
4475 6659 5.592688 CACAATATTCTTACCCCGTGGATTT 59.407 40.000 0.00 0.00 34.81 2.17
4582 6768 2.016704 CTGTGCAGTCACGTCGTCC 61.017 63.158 0.00 0.00 46.01 4.79
4786 6973 2.819595 CGAGGGTGAACGCCATGG 60.820 66.667 7.63 7.63 0.00 3.66
4793 6980 0.669318 TTGTCGATGCGAGGGTGAAC 60.669 55.000 0.00 0.00 36.23 3.18
4838 7025 1.136884 CGAGACACAAGCGAAAACTCG 60.137 52.381 0.00 0.00 39.32 4.18
4896 7083 4.452733 GGACAAGGAGGCCGTCGG 62.453 72.222 6.99 6.99 34.00 4.79
4923 7110 1.523758 GATCAAGGTCTTGGCGTTGT 58.476 50.000 10.39 0.00 40.78 3.32


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

AutoCloner maintained by Alex Coulton.