Multiple sequence alignment - TraesCS2D01G085300

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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 TraesCS2D01G085300 chr2D 100.000 4480 0 0 1 4480 36884848 36889327 0.000000e+00 8274.0
1 TraesCS2D01G085300 chr2D 89.533 3363 289 35 1140 4480 36910973 36914294 0.000000e+00 4202.0
2 TraesCS2D01G085300 chr2D 80.225 622 108 12 256 867 542197736 542198352 1.900000e-123 453.0
3 TraesCS2D01G085300 chr2D 80.198 606 102 13 250 842 53791738 53792338 5.320000e-119 438.0
4 TraesCS2D01G085300 chr2B 87.520 3734 379 44 145 3826 64189899 64193597 0.000000e+00 4233.0
5 TraesCS2D01G085300 chr2B 87.267 3110 332 31 1140 4229 63865183 63862118 0.000000e+00 3491.0
6 TraesCS2D01G085300 chr2B 83.512 2147 287 27 1350 3457 64091421 64089303 0.000000e+00 1941.0
7 TraesCS2D01G085300 chr2B 86.774 499 48 10 3493 3986 64089305 64088820 1.420000e-149 540.0
8 TraesCS2D01G085300 chr2B 91.026 312 22 5 4172 4478 63862135 63861825 2.490000e-112 416.0
9 TraesCS2D01G085300 chr2B 80.741 540 60 22 3972 4474 64088753 64088221 9.090000e-102 381.0
10 TraesCS2D01G085300 chr2B 79.452 438 61 19 864 1293 64091867 64091451 2.640000e-72 283.0
11 TraesCS2D01G085300 chr2B 100.000 35 0 0 951 985 63865334 63865300 1.040000e-06 65.8
12 TraesCS2D01G085300 chr2A 85.465 2353 285 29 1140 3464 41620344 41622667 0.000000e+00 2398.0
13 TraesCS2D01G085300 chr2A 86.364 66 8 1 3981 4045 365907955 365908020 2.240000e-08 71.3
14 TraesCS2D01G085300 chr2A 97.222 36 1 0 3474 3509 41622660 41622695 1.350000e-05 62.1
15 TraesCS2D01G085300 chr6A 88.091 529 42 9 3456 3968 555858248 555857725 3.830000e-170 608.0
16 TraesCS2D01G085300 chr6B 80.380 632 108 11 247 866 508533465 508532838 2.440000e-127 466.0
17 TraesCS2D01G085300 chr5D 80.587 613 104 12 241 840 505372196 505371586 4.080000e-125 459.0
18 TraesCS2D01G085300 chr5A 80.196 611 102 16 244 842 492629120 492629723 1.480000e-119 440.0
19 TraesCS2D01G085300 chr7B 79.091 660 115 19 221 866 332810098 332810748 2.480000e-117 433.0
20 TraesCS2D01G085300 chr1B 79.251 641 107 22 221 843 330838460 330837828 1.490000e-114 424.0
21 TraesCS2D01G085300 chr4B 78.443 668 122 16 220 874 330749477 330748819 2.490000e-112 416.0
22 TraesCS2D01G085300 chr1A 100.000 28 0 0 3283 3310 19400826 19400799 8.000000e-03 52.8


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 TraesCS2D01G085300 chr2D 36884848 36889327 4479 False 8274.000000 8274 100.000000 1 4480 1 chr2D.!!$F1 4479
1 TraesCS2D01G085300 chr2D 36910973 36914294 3321 False 4202.000000 4202 89.533000 1140 4480 1 chr2D.!!$F2 3340
2 TraesCS2D01G085300 chr2D 542197736 542198352 616 False 453.000000 453 80.225000 256 867 1 chr2D.!!$F4 611
3 TraesCS2D01G085300 chr2D 53791738 53792338 600 False 438.000000 438 80.198000 250 842 1 chr2D.!!$F3 592
4 TraesCS2D01G085300 chr2B 64189899 64193597 3698 False 4233.000000 4233 87.520000 145 3826 1 chr2B.!!$F1 3681
5 TraesCS2D01G085300 chr2B 63861825 63865334 3509 True 1324.266667 3491 92.764333 951 4478 3 chr2B.!!$R1 3527
6 TraesCS2D01G085300 chr2B 64088221 64091867 3646 True 786.250000 1941 82.619750 864 4474 4 chr2B.!!$R2 3610
7 TraesCS2D01G085300 chr2A 41620344 41622695 2351 False 1230.050000 2398 91.343500 1140 3509 2 chr2A.!!$F2 2369
8 TraesCS2D01G085300 chr6A 555857725 555858248 523 True 608.000000 608 88.091000 3456 3968 1 chr6A.!!$R1 512
9 TraesCS2D01G085300 chr6B 508532838 508533465 627 True 466.000000 466 80.380000 247 866 1 chr6B.!!$R1 619
10 TraesCS2D01G085300 chr5D 505371586 505372196 610 True 459.000000 459 80.587000 241 840 1 chr5D.!!$R1 599
11 TraesCS2D01G085300 chr5A 492629120 492629723 603 False 440.000000 440 80.196000 244 842 1 chr5A.!!$F1 598
12 TraesCS2D01G085300 chr7B 332810098 332810748 650 False 433.000000 433 79.091000 221 866 1 chr7B.!!$F1 645
13 TraesCS2D01G085300 chr1B 330837828 330838460 632 True 424.000000 424 79.251000 221 843 1 chr1B.!!$R1 622
14 TraesCS2D01G085300 chr4B 330748819 330749477 658 True 416.000000 416 78.443000 220 874 1 chr4B.!!$R1 654

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
34 35 0.032678 CCGGCAGTCGCTTATCTCAT 59.967 55.0 0.00 0.00 38.60 2.90 F
51 52 0.039617 CATCGACAGCCTCTCGATCC 60.040 60.0 1.64 0.00 45.60 3.36 F
54 55 0.173481 CGACAGCCTCTCGATCCAAA 59.827 55.0 0.00 0.00 32.65 3.28 F
1854 1920 0.179040 AAAGCGACCCCGTCAAGAAA 60.179 50.0 0.00 0.00 38.24 2.52 F
2139 2205 0.033504 TTGTGGACGAGCTCTGGTTC 59.966 55.0 12.85 2.44 0.00 3.62 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1838 1904 0.040692 GTTTTTCTTGACGGGGTCGC 60.041 55.000 0.00 0.00 40.63 5.19 R
1923 1989 0.606401 CCAGCTTCTTGGCGAGGAAA 60.606 55.000 0.97 0.00 35.41 3.13 R
2025 2091 0.829333 AGTCGAGAGCATTGCTGGAT 59.171 50.000 17.51 1.24 39.88 3.41 R
2922 3013 0.452987 CCAGGTACGCGCAGTAGTAA 59.547 55.000 5.73 0.00 35.72 2.24 R
3747 3872 1.544246 GTGGGTAGTTTGGCCATGTTC 59.456 52.381 6.09 0.00 0.00 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
23 24 6.323203 TGACTATTAGTATTACCGGCAGTC 57.677 41.667 0.00 0.00 0.00 3.51
24 25 5.049198 TGACTATTAGTATTACCGGCAGTCG 60.049 44.000 0.00 0.00 34.10 4.18
25 26 2.497107 TTAGTATTACCGGCAGTCGC 57.503 50.000 0.00 0.00 37.59 5.19
26 27 1.683943 TAGTATTACCGGCAGTCGCT 58.316 50.000 0.00 0.00 38.60 4.93
27 28 0.822164 AGTATTACCGGCAGTCGCTT 59.178 50.000 0.00 0.00 38.60 4.68
28 29 2.026641 AGTATTACCGGCAGTCGCTTA 58.973 47.619 0.00 0.00 38.60 3.09
29 30 2.626743 AGTATTACCGGCAGTCGCTTAT 59.373 45.455 0.00 0.00 38.60 1.73
30 31 2.150397 ATTACCGGCAGTCGCTTATC 57.850 50.000 0.00 0.00 38.60 1.75
31 32 1.108776 TTACCGGCAGTCGCTTATCT 58.891 50.000 0.00 0.00 38.60 1.98
32 33 0.666913 TACCGGCAGTCGCTTATCTC 59.333 55.000 0.00 0.00 38.60 2.75
33 34 1.320344 ACCGGCAGTCGCTTATCTCA 61.320 55.000 0.00 0.00 38.60 3.27
34 35 0.032678 CCGGCAGTCGCTTATCTCAT 59.967 55.000 0.00 0.00 38.60 2.90
35 36 1.413382 CGGCAGTCGCTTATCTCATC 58.587 55.000 0.00 0.00 38.60 2.92
36 37 1.413382 GGCAGTCGCTTATCTCATCG 58.587 55.000 0.00 0.00 38.60 3.84
37 38 1.001268 GGCAGTCGCTTATCTCATCGA 60.001 52.381 0.00 0.00 38.60 3.59
41 42 2.407521 TCGCTTATCTCATCGACAGC 57.592 50.000 0.00 0.00 0.00 4.40
42 43 1.001268 TCGCTTATCTCATCGACAGCC 60.001 52.381 0.00 0.00 30.71 4.85
43 44 1.000827 CGCTTATCTCATCGACAGCCT 60.001 52.381 0.00 0.00 30.71 4.58
44 45 2.671596 GCTTATCTCATCGACAGCCTC 58.328 52.381 0.00 0.00 0.00 4.70
45 46 2.295909 GCTTATCTCATCGACAGCCTCT 59.704 50.000 0.00 0.00 0.00 3.69
46 47 3.611530 GCTTATCTCATCGACAGCCTCTC 60.612 52.174 0.00 0.00 0.00 3.20
47 48 0.950836 ATCTCATCGACAGCCTCTCG 59.049 55.000 0.00 0.00 0.00 4.04
48 49 0.107654 TCTCATCGACAGCCTCTCGA 60.108 55.000 0.00 0.00 43.94 4.04
50 51 0.947960 TCATCGACAGCCTCTCGATC 59.052 55.000 1.64 0.00 45.60 3.69
51 52 0.039617 CATCGACAGCCTCTCGATCC 60.040 60.000 1.64 0.00 45.60 3.36
52 53 0.466372 ATCGACAGCCTCTCGATCCA 60.466 55.000 0.00 0.00 45.60 3.41
53 54 0.679960 TCGACAGCCTCTCGATCCAA 60.680 55.000 0.00 0.00 35.26 3.53
54 55 0.173481 CGACAGCCTCTCGATCCAAA 59.827 55.000 0.00 0.00 32.65 3.28
55 56 1.202463 CGACAGCCTCTCGATCCAAAT 60.202 52.381 0.00 0.00 32.65 2.32
56 57 2.208431 GACAGCCTCTCGATCCAAATG 58.792 52.381 0.00 0.00 0.00 2.32
57 58 1.833630 ACAGCCTCTCGATCCAAATGA 59.166 47.619 0.00 0.00 0.00 2.57
58 59 2.437281 ACAGCCTCTCGATCCAAATGAT 59.563 45.455 0.00 0.00 36.01 2.45
59 60 3.643320 ACAGCCTCTCGATCCAAATGATA 59.357 43.478 0.00 0.00 32.41 2.15
60 61 4.101585 ACAGCCTCTCGATCCAAATGATAA 59.898 41.667 0.00 0.00 32.41 1.75
61 62 5.059161 CAGCCTCTCGATCCAAATGATAAA 58.941 41.667 0.00 0.00 32.41 1.40
62 63 5.704515 CAGCCTCTCGATCCAAATGATAAAT 59.295 40.000 0.00 0.00 32.41 1.40
63 64 6.875726 CAGCCTCTCGATCCAAATGATAAATA 59.124 38.462 0.00 0.00 32.41 1.40
64 65 7.388776 CAGCCTCTCGATCCAAATGATAAATAA 59.611 37.037 0.00 0.00 32.41 1.40
65 66 7.605691 AGCCTCTCGATCCAAATGATAAATAAG 59.394 37.037 0.00 0.00 32.41 1.73
66 67 7.625185 GCCTCTCGATCCAAATGATAAATAAGC 60.625 40.741 0.00 0.00 32.41 3.09
67 68 7.148340 CCTCTCGATCCAAATGATAAATAAGCC 60.148 40.741 0.00 0.00 32.41 4.35
68 69 6.655003 TCTCGATCCAAATGATAAATAAGCCC 59.345 38.462 0.00 0.00 32.41 5.19
69 70 6.303054 TCGATCCAAATGATAAATAAGCCCA 58.697 36.000 0.00 0.00 32.41 5.36
70 71 6.206634 TCGATCCAAATGATAAATAAGCCCAC 59.793 38.462 0.00 0.00 32.41 4.61
71 72 6.016360 CGATCCAAATGATAAATAAGCCCACA 60.016 38.462 0.00 0.00 32.41 4.17
72 73 7.309377 CGATCCAAATGATAAATAAGCCCACAT 60.309 37.037 0.00 0.00 32.41 3.21
73 74 8.954834 ATCCAAATGATAAATAAGCCCACATA 57.045 30.769 0.00 0.00 0.00 2.29
74 75 8.177119 TCCAAATGATAAATAAGCCCACATAC 57.823 34.615 0.00 0.00 0.00 2.39
75 76 7.782168 TCCAAATGATAAATAAGCCCACATACA 59.218 33.333 0.00 0.00 0.00 2.29
76 77 8.587608 CCAAATGATAAATAAGCCCACATACAT 58.412 33.333 0.00 0.00 0.00 2.29
79 80 7.921786 TGATAAATAAGCCCACATACATAGC 57.078 36.000 0.00 0.00 0.00 2.97
80 81 7.457561 TGATAAATAAGCCCACATACATAGCA 58.542 34.615 0.00 0.00 0.00 3.49
81 82 7.607607 TGATAAATAAGCCCACATACATAGCAG 59.392 37.037 0.00 0.00 0.00 4.24
82 83 1.972872 AAGCCCACATACATAGCAGC 58.027 50.000 0.00 0.00 0.00 5.25
83 84 0.839277 AGCCCACATACATAGCAGCA 59.161 50.000 0.00 0.00 0.00 4.41
84 85 1.422781 AGCCCACATACATAGCAGCAT 59.577 47.619 0.00 0.00 0.00 3.79
85 86 2.158564 AGCCCACATACATAGCAGCATT 60.159 45.455 0.00 0.00 0.00 3.56
86 87 2.030540 GCCCACATACATAGCAGCATTG 60.031 50.000 0.00 0.00 0.00 2.82
87 88 2.555325 CCCACATACATAGCAGCATTGG 59.445 50.000 0.00 0.00 0.00 3.16
88 89 3.216800 CCACATACATAGCAGCATTGGT 58.783 45.455 0.00 0.00 38.79 3.67
89 90 4.388485 CCACATACATAGCAGCATTGGTA 58.612 43.478 0.00 0.00 41.16 3.25
90 91 4.214119 CCACATACATAGCAGCATTGGTAC 59.786 45.833 0.00 0.00 39.86 3.34
91 92 5.059161 CACATACATAGCAGCATTGGTACT 58.941 41.667 0.00 0.00 39.86 2.73
92 93 5.049886 CACATACATAGCAGCATTGGTACTG 60.050 44.000 0.00 0.00 39.86 2.74
93 94 2.923121 ACATAGCAGCATTGGTACTGG 58.077 47.619 0.00 0.00 39.86 4.00
94 95 2.505407 ACATAGCAGCATTGGTACTGGA 59.495 45.455 0.00 0.00 39.86 3.86
95 96 3.054434 ACATAGCAGCATTGGTACTGGAA 60.054 43.478 0.00 0.00 39.86 3.53
96 97 2.814805 AGCAGCATTGGTACTGGAAT 57.185 45.000 0.00 0.00 34.38 3.01
97 98 3.091633 AGCAGCATTGGTACTGGAATT 57.908 42.857 0.00 0.00 34.38 2.17
98 99 3.019564 AGCAGCATTGGTACTGGAATTC 58.980 45.455 0.00 0.00 34.38 2.17
99 100 2.223340 GCAGCATTGGTACTGGAATTCG 60.223 50.000 0.00 0.00 34.38 3.34
100 101 3.270027 CAGCATTGGTACTGGAATTCGA 58.730 45.455 0.00 0.00 0.00 3.71
101 102 3.310774 CAGCATTGGTACTGGAATTCGAG 59.689 47.826 15.18 15.18 0.00 4.04
102 103 3.055094 AGCATTGGTACTGGAATTCGAGT 60.055 43.478 24.02 24.02 38.48 4.18
103 104 4.161565 AGCATTGGTACTGGAATTCGAGTA 59.838 41.667 22.11 22.11 36.35 2.59
104 105 5.057149 GCATTGGTACTGGAATTCGAGTAT 58.943 41.667 26.68 13.65 38.94 2.12
105 106 5.177696 GCATTGGTACTGGAATTCGAGTATC 59.822 44.000 26.68 26.20 38.94 2.24
106 107 5.925506 TTGGTACTGGAATTCGAGTATCA 57.074 39.130 29.26 29.26 43.40 2.15
107 108 6.479972 TTGGTACTGGAATTCGAGTATCAT 57.520 37.500 31.71 11.99 44.10 2.45
108 109 7.591421 TTGGTACTGGAATTCGAGTATCATA 57.409 36.000 31.71 22.82 44.10 2.15
109 110 7.776618 TGGTACTGGAATTCGAGTATCATAT 57.223 36.000 29.26 8.96 41.32 1.78
110 111 7.827701 TGGTACTGGAATTCGAGTATCATATC 58.172 38.462 29.26 17.39 41.32 1.63
111 112 7.450323 TGGTACTGGAATTCGAGTATCATATCA 59.550 37.037 29.26 16.05 41.32 2.15
112 113 8.470805 GGTACTGGAATTCGAGTATCATATCAT 58.529 37.037 26.87 5.80 38.94 2.45
113 114 9.509855 GTACTGGAATTCGAGTATCATATCATC 57.490 37.037 26.68 11.64 38.94 2.92
114 115 7.551585 ACTGGAATTCGAGTATCATATCATCC 58.448 38.462 20.16 0.00 33.06 3.51
115 116 6.564328 TGGAATTCGAGTATCATATCATCCG 58.436 40.000 0.00 0.00 33.17 4.18
116 117 5.980116 GGAATTCGAGTATCATATCATCCGG 59.020 44.000 0.00 0.00 33.17 5.14
117 118 4.983671 TTCGAGTATCATATCATCCGGG 57.016 45.455 0.00 0.00 33.17 5.73
118 119 3.964411 TCGAGTATCATATCATCCGGGT 58.036 45.455 0.00 0.00 33.17 5.28
119 120 3.945921 TCGAGTATCATATCATCCGGGTC 59.054 47.826 0.00 0.00 33.17 4.46
120 121 3.694566 CGAGTATCATATCATCCGGGTCA 59.305 47.826 0.00 0.00 33.17 4.02
121 122 4.157840 CGAGTATCATATCATCCGGGTCAA 59.842 45.833 0.00 0.00 33.17 3.18
122 123 5.655488 GAGTATCATATCATCCGGGTCAAG 58.345 45.833 0.00 0.00 33.17 3.02
123 124 5.087323 AGTATCATATCATCCGGGTCAAGT 58.913 41.667 0.00 0.00 0.00 3.16
124 125 4.543590 ATCATATCATCCGGGTCAAGTC 57.456 45.455 0.00 0.00 0.00 3.01
125 126 3.304829 TCATATCATCCGGGTCAAGTCA 58.695 45.455 0.00 0.00 0.00 3.41
126 127 3.709141 TCATATCATCCGGGTCAAGTCAA 59.291 43.478 0.00 0.00 0.00 3.18
127 128 2.403252 ATCATCCGGGTCAAGTCAAC 57.597 50.000 0.00 0.00 0.00 3.18
128 129 0.323629 TCATCCGGGTCAAGTCAACC 59.676 55.000 0.00 0.00 35.97 3.77
129 130 0.324943 CATCCGGGTCAAGTCAACCT 59.675 55.000 0.00 0.00 36.97 3.50
130 131 1.553248 CATCCGGGTCAAGTCAACCTA 59.447 52.381 0.00 0.00 36.97 3.08
131 132 1.946984 TCCGGGTCAAGTCAACCTAT 58.053 50.000 0.00 0.00 36.97 2.57
132 133 3.104519 TCCGGGTCAAGTCAACCTATA 57.895 47.619 0.00 0.00 36.97 1.31
133 134 3.649843 TCCGGGTCAAGTCAACCTATAT 58.350 45.455 0.00 0.00 36.97 0.86
134 135 3.640029 TCCGGGTCAAGTCAACCTATATC 59.360 47.826 0.00 0.00 36.97 1.63
135 136 3.244112 CCGGGTCAAGTCAACCTATATCC 60.244 52.174 0.00 0.00 36.97 2.59
136 137 3.386726 CGGGTCAAGTCAACCTATATCCA 59.613 47.826 0.00 0.00 36.97 3.41
137 138 4.704965 GGGTCAAGTCAACCTATATCCAC 58.295 47.826 0.00 0.00 36.97 4.02
138 139 4.163458 GGGTCAAGTCAACCTATATCCACA 59.837 45.833 0.00 0.00 36.97 4.17
139 140 5.338871 GGGTCAAGTCAACCTATATCCACAA 60.339 44.000 0.00 0.00 36.97 3.33
140 141 6.177610 GGTCAAGTCAACCTATATCCACAAA 58.822 40.000 0.00 0.00 33.78 2.83
141 142 6.828785 GGTCAAGTCAACCTATATCCACAAAT 59.171 38.462 0.00 0.00 33.78 2.32
142 143 7.012421 GGTCAAGTCAACCTATATCCACAAATC 59.988 40.741 0.00 0.00 33.78 2.17
143 144 7.552687 GTCAAGTCAACCTATATCCACAAATCA 59.447 37.037 0.00 0.00 0.00 2.57
183 184 5.230306 TGTTTACGCAAAATTTTCAACTCCG 59.770 36.000 0.00 0.66 0.00 4.63
185 186 3.368495 ACGCAAAATTTTCAACTCCGTC 58.632 40.909 0.00 0.00 0.00 4.79
193 194 9.893305 CAAAATTTTCAACTCCGTCTACTTATT 57.107 29.630 0.00 0.00 0.00 1.40
208 210 9.931210 CGTCTACTTATTTTCCAAAATCATACC 57.069 33.333 0.45 0.00 39.24 2.73
223 225 4.672587 TCATACCTAAGGTTAGCAGCTG 57.327 45.455 10.11 10.11 37.09 4.24
224 226 2.981859 TACCTAAGGTTAGCAGCTGC 57.018 50.000 31.53 31.53 37.09 5.25
305 314 1.977544 CCGGTCCACCTCGTCTCTT 60.978 63.158 0.00 0.00 0.00 2.85
318 327 1.134965 CGTCTCTTGTGGCCTTAGGAG 60.135 57.143 3.32 8.43 0.00 3.69
367 380 1.288037 GGGGGAGGGCTCTGTTTTTAT 59.712 52.381 0.00 0.00 0.00 1.40
374 387 6.831868 GGGAGGGCTCTGTTTTTATATGTTTA 59.168 38.462 0.00 0.00 0.00 2.01
402 417 9.868277 TTGAGTTTTGTTATGATTTGTGTCTTT 57.132 25.926 0.00 0.00 0.00 2.52
403 418 9.868277 TGAGTTTTGTTATGATTTGTGTCTTTT 57.132 25.926 0.00 0.00 0.00 2.27
464 479 2.443390 GTACTCCCCGCCTAGCCA 60.443 66.667 0.00 0.00 0.00 4.75
465 480 1.837499 GTACTCCCCGCCTAGCCAT 60.837 63.158 0.00 0.00 0.00 4.40
517 537 2.292569 GACGTGTGAAGGTGTGTCTCTA 59.707 50.000 0.00 0.00 0.00 2.43
518 538 2.691526 ACGTGTGAAGGTGTGTCTCTAA 59.308 45.455 0.00 0.00 0.00 2.10
538 558 6.586344 TCTAATGGATCTGTCTTTGATGGAC 58.414 40.000 0.00 0.00 0.00 4.02
581 601 5.735427 CGTTTGTCTATGTTCGTGTGTTTTT 59.265 36.000 0.00 0.00 0.00 1.94
591 611 5.821470 TGTTCGTGTGTTTTTAGGTTGGATA 59.179 36.000 0.00 0.00 0.00 2.59
621 641 2.554142 CATGCTACTCTTCATCGGCAA 58.446 47.619 0.00 0.00 33.44 4.52
665 685 0.249322 CATACGGGGACTTAGCACGG 60.249 60.000 0.00 0.00 0.00 4.94
672 692 0.517316 GGACTTAGCACGGCAACTTG 59.483 55.000 0.00 0.00 39.23 3.16
702 722 5.419155 TGTCTACCACAACAAATTTTGTCCA 59.581 36.000 14.80 0.19 44.59 4.02
763 783 3.485877 CGGCTTGCTTTAGTGCTTGTATC 60.486 47.826 0.00 0.00 0.00 2.24
765 785 3.440173 GCTTGCTTTAGTGCTTGTATCCA 59.560 43.478 0.00 0.00 0.00 3.41
772 792 3.819564 AGTGCTTGTATCCATCGCTAA 57.180 42.857 0.00 0.00 0.00 3.09
828 854 9.946165 CTAGTGTTCGTTGTACTATCATGATTA 57.054 33.333 14.65 0.00 0.00 1.75
893 921 1.398390 GTAAGATTGCTTGGTGCCGAG 59.602 52.381 1.07 1.07 42.00 4.63
943 983 0.383949 TTTCAGTGGCTCCAAAACGC 59.616 50.000 0.00 0.00 0.00 4.84
993 1035 1.520342 GGCACGCTCCATCACTCTC 60.520 63.158 0.00 0.00 0.00 3.20
996 1038 0.459237 CACGCTCCATCACTCTCCAC 60.459 60.000 0.00 0.00 0.00 4.02
1021 1071 0.523125 CAACACACTTGCACACACCG 60.523 55.000 0.00 0.00 0.00 4.94
1105 1168 1.876156 CTGCTGTGAAGAAGGTCCAAC 59.124 52.381 0.00 0.00 0.00 3.77
1138 1201 1.691195 TTTCGTGCAGGTCCAGGTGA 61.691 55.000 6.26 0.00 0.00 4.02
1248 1311 1.367471 CGCCTCCATCGCCTTCATA 59.633 57.895 0.00 0.00 0.00 2.15
1257 1320 2.230940 CGCCTTCATACCGCTCACG 61.231 63.158 0.00 0.00 39.67 4.35
1294 1357 2.203983 TGCTGGGGCAGAGGAAGA 60.204 61.111 0.00 0.00 44.28 2.87
1318 1381 1.599071 TCAAGCTGTTGAAAGAGTGCG 59.401 47.619 0.00 0.00 39.85 5.34
1416 1482 3.139584 TCATCCTCATCATCAAGGGCAAT 59.860 43.478 0.00 0.00 33.21 3.56
1515 1581 2.363795 CGGACCCCAGTGGAGCTA 60.364 66.667 11.95 0.00 38.00 3.32
1584 1650 1.886542 GAGGCGGAATGGTTGAAGTTT 59.113 47.619 0.00 0.00 0.00 2.66
1603 1669 3.658757 TTGAGGGAAAGGCAATTTTCG 57.341 42.857 0.00 0.00 37.82 3.46
1681 1747 2.571757 CGAGCAACTCCTACGCCA 59.428 61.111 0.00 0.00 0.00 5.69
1815 1881 1.302192 CGTCGAGGAAAAGCCCCAA 60.302 57.895 0.00 0.00 37.37 4.12
1850 1916 2.356553 CGAAAGCGACCCCGTCAA 60.357 61.111 0.00 0.00 40.82 3.18
1851 1917 2.380410 CGAAAGCGACCCCGTCAAG 61.380 63.158 0.00 0.00 40.82 3.02
1852 1918 1.005394 GAAAGCGACCCCGTCAAGA 60.005 57.895 0.00 0.00 38.24 3.02
1853 1919 0.601841 GAAAGCGACCCCGTCAAGAA 60.602 55.000 0.00 0.00 38.24 2.52
1854 1920 0.179040 AAAGCGACCCCGTCAAGAAA 60.179 50.000 0.00 0.00 38.24 2.52
1855 1921 0.179040 AAGCGACCCCGTCAAGAAAA 60.179 50.000 0.00 0.00 38.24 2.29
1856 1922 0.179040 AGCGACCCCGTCAAGAAAAA 60.179 50.000 0.00 0.00 38.24 1.94
1893 1959 2.278206 CTCATCACGCTCGACCGG 60.278 66.667 0.00 0.00 0.00 5.28
1902 1968 3.299977 CTCGACCGGGTGTGGACA 61.300 66.667 3.30 0.00 0.00 4.02
1936 2002 1.005394 GACGGTTTCCTCGCCAAGA 60.005 57.895 0.00 0.00 0.00 3.02
1937 2003 0.601841 GACGGTTTCCTCGCCAAGAA 60.602 55.000 0.00 0.00 0.00 2.52
1940 2006 0.606673 GGTTTCCTCGCCAAGAAGCT 60.607 55.000 0.00 0.00 0.00 3.74
1959 2025 2.676748 CTGGAGCTAAGGGATCTCTGT 58.323 52.381 0.00 0.00 0.00 3.41
1989 2055 0.820871 CCCTCTTCAAGAGTCTCCGG 59.179 60.000 13.58 3.11 40.72 5.14
1995 2061 4.117661 AAGAGTCTCCGGCGTCGC 62.118 66.667 9.22 9.22 34.56 5.19
2025 2091 2.280552 CCCGTTGACCGAGGAAGGA 61.281 63.158 0.00 0.00 39.56 3.36
2037 2103 3.509517 GGAAGGATCCAGCAATGCT 57.490 52.632 15.82 0.00 45.79 3.79
2098 2164 2.180017 GCAAAGCAGGCGTGGATG 59.820 61.111 8.72 0.00 0.00 3.51
2139 2205 0.033504 TTGTGGACGAGCTCTGGTTC 59.966 55.000 12.85 2.44 0.00 3.62
2169 2235 2.894565 CTACTACTCGCCGCTCCCG 61.895 68.421 0.00 0.00 0.00 5.14
2208 2274 3.781307 TGCGCCGCCCTCAACTAT 61.781 61.111 6.63 0.00 0.00 2.12
2214 2280 0.390860 CCGCCCTCAACTATCTCCTG 59.609 60.000 0.00 0.00 0.00 3.86
2241 2307 0.969149 TCATCATCGCCGGAGCTATT 59.031 50.000 5.05 0.00 36.60 1.73
2244 2310 1.112916 TCATCGCCGGAGCTATTGGA 61.113 55.000 5.05 0.00 36.60 3.53
2254 2320 0.543749 AGCTATTGGAGTGGGAGTGC 59.456 55.000 0.00 0.00 0.00 4.40
2281 2348 5.119931 TCAAATCAAAAGGGTGATCGTTG 57.880 39.130 0.00 0.00 37.25 4.10
2284 2351 2.139917 TCAAAAGGGTGATCGTTGTCG 58.860 47.619 0.00 0.00 38.55 4.35
2286 2353 0.395312 AAAGGGTGATCGTTGTCGGT 59.605 50.000 0.00 0.00 37.69 4.69
2305 2372 3.702048 CCGACCGGGCCAAAGAGA 61.702 66.667 6.32 0.00 0.00 3.10
2310 2380 2.434331 CGGGCCAAAGAGAACCCA 59.566 61.111 4.39 0.00 42.97 4.51
2314 2390 0.328258 GGCCAAAGAGAACCCAGCTA 59.672 55.000 0.00 0.00 0.00 3.32
2315 2391 1.271926 GGCCAAAGAGAACCCAGCTAA 60.272 52.381 0.00 0.00 0.00 3.09
2324 2400 4.480480 CCCAGCTAAGGGTCCAGA 57.520 61.111 0.68 0.00 44.24 3.86
2327 2403 1.566231 CCCAGCTAAGGGTCCAGAATT 59.434 52.381 0.68 0.00 44.24 2.17
2334 2410 3.721087 AAGGGTCCAGAATTGTACCAG 57.279 47.619 0.00 0.00 33.46 4.00
2335 2411 1.916181 AGGGTCCAGAATTGTACCAGG 59.084 52.381 0.00 0.00 33.46 4.45
2336 2412 1.633945 GGGTCCAGAATTGTACCAGGT 59.366 52.381 0.00 0.00 33.46 4.00
2355 2431 4.038162 CAGGTAGCCTACTACTTCATCACC 59.962 50.000 1.24 0.00 46.77 4.02
2367 2443 4.168101 ACTTCATCACCTTGTTCCTCCTA 58.832 43.478 0.00 0.00 0.00 2.94
2370 2446 3.769844 TCATCACCTTGTTCCTCCTACTC 59.230 47.826 0.00 0.00 0.00 2.59
2436 2512 1.308069 CCAACTGGACCAAGATGGCG 61.308 60.000 6.86 0.00 42.67 5.69
2440 2516 0.321564 CTGGACCAAGATGGCGTTGA 60.322 55.000 0.00 0.00 42.67 3.18
2509 2591 4.539083 TGGACACGGTGCTGCGTT 62.539 61.111 8.30 0.00 0.00 4.84
2517 2599 4.043200 GTGCTGCGTTTCAGGCCC 62.043 66.667 0.00 0.00 43.06 5.80
2559 2641 4.459089 GGGCAGACCTCGGTGCTC 62.459 72.222 0.00 0.00 39.76 4.26
2646 2737 4.115270 AGGTCGGTGGAACTCTCC 57.885 61.111 0.00 0.00 34.17 3.71
2648 2739 1.911766 GGTCGGTGGAACTCTCCCA 60.912 63.158 0.00 0.00 41.64 4.37
2655 2746 2.593956 GGAACTCTCCCAGGCCGTT 61.594 63.158 0.00 0.00 35.42 4.44
2685 2776 1.346068 GTGCTCAGGTCCTTGAAGAGT 59.654 52.381 0.00 0.00 0.00 3.24
2715 2806 1.239347 GACTGGACAAAGGAAGCACC 58.761 55.000 0.00 0.00 39.35 5.01
2717 2808 0.111253 CTGGACAAAGGAAGCACCCT 59.889 55.000 0.00 0.00 40.05 4.34
2718 2809 0.110486 TGGACAAAGGAAGCACCCTC 59.890 55.000 0.00 0.00 40.05 4.30
2721 2812 2.034221 AAAGGAAGCACCCTCGCC 59.966 61.111 0.00 0.00 40.05 5.54
2877 2968 4.029186 TACTCGAACGCGGCGTGT 62.029 61.111 30.10 21.86 39.99 4.49
2922 3013 3.064324 GCCGCCTGCCATTTGTCT 61.064 61.111 0.00 0.00 0.00 3.41
3294 3385 4.754667 GGCGGGGAGTTCGTCACC 62.755 72.222 0.00 0.00 46.93 4.02
3576 3700 4.991153 TTACTACTCTCAGCATGTCTGG 57.009 45.455 14.50 7.77 43.06 3.86
3661 3786 8.918202 AAAACTATCAAATACTCTGACACCAA 57.082 30.769 0.00 0.00 0.00 3.67
3747 3872 7.141100 AGTAATTGTGATGGTTTTTCCTACG 57.859 36.000 0.00 0.00 37.07 3.51
3769 3894 0.251564 CATGGCCAAACTACCCACCA 60.252 55.000 10.96 0.00 0.00 4.17
3821 3950 6.447084 TCTTTTGAGATGGAGGGGTAGTATTT 59.553 38.462 0.00 0.00 0.00 1.40
3822 3951 7.626084 TCTTTTGAGATGGAGGGGTAGTATTTA 59.374 37.037 0.00 0.00 0.00 1.40
3823 3952 6.996180 TTGAGATGGAGGGGTAGTATTTAG 57.004 41.667 0.00 0.00 0.00 1.85
3824 3953 6.039415 TGAGATGGAGGGGTAGTATTTAGT 57.961 41.667 0.00 0.00 0.00 2.24
3825 3954 7.170554 TGAGATGGAGGGGTAGTATTTAGTA 57.829 40.000 0.00 0.00 0.00 1.82
3826 3955 7.008941 TGAGATGGAGGGGTAGTATTTAGTAC 58.991 42.308 0.00 0.00 0.00 2.73
3865 3994 6.261603 GCAGTGGATAATGATCTTCATGACAA 59.738 38.462 0.00 0.00 37.15 3.18
3931 4060 9.512435 CCTCTTTGATTAGCATGATTGTAAAAG 57.488 33.333 0.00 0.00 0.00 2.27
4102 4320 1.865340 GGGTTCGTTCCTATGAATCGC 59.135 52.381 0.00 0.00 32.21 4.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 0.032678 ATGAGATAAGCGACTGCCGG 59.967 55.000 0.00 0.00 44.31 6.13
16 17 1.413382 GATGAGATAAGCGACTGCCG 58.587 55.000 0.00 0.00 44.31 5.69
17 18 1.001268 TCGATGAGATAAGCGACTGCC 60.001 52.381 0.00 0.00 44.31 4.85
18 19 2.047769 GTCGATGAGATAAGCGACTGC 58.952 52.381 7.65 0.00 46.74 4.40
22 23 1.001268 GGCTGTCGATGAGATAAGCGA 60.001 52.381 0.00 0.00 40.34 4.93
23 24 1.000827 AGGCTGTCGATGAGATAAGCG 60.001 52.381 0.00 0.00 40.34 4.68
24 25 2.295909 AGAGGCTGTCGATGAGATAAGC 59.704 50.000 0.00 0.00 39.36 3.09
25 26 3.364864 CGAGAGGCTGTCGATGAGATAAG 60.365 52.174 27.87 0.00 39.92 1.73
26 27 2.550180 CGAGAGGCTGTCGATGAGATAA 59.450 50.000 27.87 0.00 39.92 1.75
27 28 2.147150 CGAGAGGCTGTCGATGAGATA 58.853 52.381 27.87 0.00 39.92 1.98
28 29 0.950836 CGAGAGGCTGTCGATGAGAT 59.049 55.000 27.87 0.00 39.92 2.75
29 30 0.107654 TCGAGAGGCTGTCGATGAGA 60.108 55.000 29.90 10.32 41.41 3.27
30 31 2.398803 TCGAGAGGCTGTCGATGAG 58.601 57.895 29.90 4.95 41.41 2.90
31 32 4.637771 TCGAGAGGCTGTCGATGA 57.362 55.556 29.90 11.08 41.41 2.92
35 36 0.173481 TTTGGATCGAGAGGCTGTCG 59.827 55.000 26.24 26.24 38.84 4.35
36 37 2.159043 TCATTTGGATCGAGAGGCTGTC 60.159 50.000 0.68 0.68 0.00 3.51
37 38 1.833630 TCATTTGGATCGAGAGGCTGT 59.166 47.619 0.00 0.00 0.00 4.40
38 39 2.609427 TCATTTGGATCGAGAGGCTG 57.391 50.000 0.00 0.00 0.00 4.85
39 40 4.963318 TTATCATTTGGATCGAGAGGCT 57.037 40.909 0.00 0.00 37.44 4.58
40 41 7.625185 GCTTATTTATCATTTGGATCGAGAGGC 60.625 40.741 0.00 0.00 37.44 4.70
41 42 7.148340 GGCTTATTTATCATTTGGATCGAGAGG 60.148 40.741 0.00 0.00 37.44 3.69
42 43 7.148340 GGGCTTATTTATCATTTGGATCGAGAG 60.148 40.741 0.00 0.00 37.44 3.20
43 44 6.655003 GGGCTTATTTATCATTTGGATCGAGA 59.345 38.462 0.00 0.00 37.44 4.04
44 45 6.430925 TGGGCTTATTTATCATTTGGATCGAG 59.569 38.462 0.00 0.00 37.44 4.04
45 46 6.206634 GTGGGCTTATTTATCATTTGGATCGA 59.793 38.462 0.00 0.00 37.44 3.59
46 47 6.016360 TGTGGGCTTATTTATCATTTGGATCG 60.016 38.462 0.00 0.00 37.44 3.69
47 48 7.288810 TGTGGGCTTATTTATCATTTGGATC 57.711 36.000 0.00 0.00 37.44 3.36
48 49 7.860649 ATGTGGGCTTATTTATCATTTGGAT 57.139 32.000 0.00 0.00 40.14 3.41
49 50 7.782168 TGTATGTGGGCTTATTTATCATTTGGA 59.218 33.333 0.00 0.00 0.00 3.53
50 51 7.950512 TGTATGTGGGCTTATTTATCATTTGG 58.049 34.615 0.00 0.00 0.00 3.28
53 54 8.960591 GCTATGTATGTGGGCTTATTTATCATT 58.039 33.333 0.00 0.00 0.00 2.57
54 55 8.108999 TGCTATGTATGTGGGCTTATTTATCAT 58.891 33.333 0.00 0.00 0.00 2.45
55 56 7.457561 TGCTATGTATGTGGGCTTATTTATCA 58.542 34.615 0.00 0.00 0.00 2.15
56 57 7.414540 GCTGCTATGTATGTGGGCTTATTTATC 60.415 40.741 0.00 0.00 0.00 1.75
57 58 6.375455 GCTGCTATGTATGTGGGCTTATTTAT 59.625 38.462 0.00 0.00 0.00 1.40
58 59 5.705441 GCTGCTATGTATGTGGGCTTATTTA 59.295 40.000 0.00 0.00 0.00 1.40
59 60 4.520492 GCTGCTATGTATGTGGGCTTATTT 59.480 41.667 0.00 0.00 0.00 1.40
60 61 4.074970 GCTGCTATGTATGTGGGCTTATT 58.925 43.478 0.00 0.00 0.00 1.40
61 62 3.072915 TGCTGCTATGTATGTGGGCTTAT 59.927 43.478 0.00 0.00 0.00 1.73
62 63 2.437651 TGCTGCTATGTATGTGGGCTTA 59.562 45.455 0.00 0.00 0.00 3.09
63 64 1.212688 TGCTGCTATGTATGTGGGCTT 59.787 47.619 0.00 0.00 0.00 4.35
64 65 0.839277 TGCTGCTATGTATGTGGGCT 59.161 50.000 0.00 0.00 0.00 5.19
65 66 1.901591 ATGCTGCTATGTATGTGGGC 58.098 50.000 0.00 0.00 0.00 5.36
66 67 2.555325 CCAATGCTGCTATGTATGTGGG 59.445 50.000 0.00 0.00 0.00 4.61
67 68 3.216800 ACCAATGCTGCTATGTATGTGG 58.783 45.455 0.00 0.54 0.00 4.17
68 69 5.049886 CAGTACCAATGCTGCTATGTATGTG 60.050 44.000 0.00 0.00 31.35 3.21
69 70 5.059161 CAGTACCAATGCTGCTATGTATGT 58.941 41.667 0.00 0.00 31.35 2.29
70 71 4.453478 CCAGTACCAATGCTGCTATGTATG 59.547 45.833 0.00 0.00 37.24 2.39
71 72 4.347876 TCCAGTACCAATGCTGCTATGTAT 59.652 41.667 0.00 0.00 37.24 2.29
72 73 3.709141 TCCAGTACCAATGCTGCTATGTA 59.291 43.478 0.00 0.00 37.24 2.29
73 74 2.505407 TCCAGTACCAATGCTGCTATGT 59.495 45.455 0.00 0.00 37.24 2.29
74 75 3.198409 TCCAGTACCAATGCTGCTATG 57.802 47.619 0.00 0.00 37.24 2.23
75 76 3.931907 TTCCAGTACCAATGCTGCTAT 57.068 42.857 0.00 0.00 37.24 2.97
76 77 3.931907 ATTCCAGTACCAATGCTGCTA 57.068 42.857 0.00 0.00 37.24 3.49
77 78 2.814805 ATTCCAGTACCAATGCTGCT 57.185 45.000 0.00 0.00 37.24 4.24
78 79 2.223340 CGAATTCCAGTACCAATGCTGC 60.223 50.000 0.00 0.00 37.24 5.25
79 80 3.270027 TCGAATTCCAGTACCAATGCTG 58.730 45.455 0.00 0.00 38.23 4.41
80 81 3.055094 ACTCGAATTCCAGTACCAATGCT 60.055 43.478 3.66 0.00 0.00 3.79
81 82 3.270877 ACTCGAATTCCAGTACCAATGC 58.729 45.455 3.66 0.00 0.00 3.56
82 83 6.280643 TGATACTCGAATTCCAGTACCAATG 58.719 40.000 14.17 0.00 0.00 2.82
83 84 6.479972 TGATACTCGAATTCCAGTACCAAT 57.520 37.500 14.17 1.03 0.00 3.16
84 85 5.925506 TGATACTCGAATTCCAGTACCAA 57.074 39.130 14.17 2.09 0.00 3.67
85 86 7.450323 TGATATGATACTCGAATTCCAGTACCA 59.550 37.037 14.17 11.81 0.00 3.25
86 87 7.827701 TGATATGATACTCGAATTCCAGTACC 58.172 38.462 14.17 6.38 0.00 3.34
87 88 9.509855 GATGATATGATACTCGAATTCCAGTAC 57.490 37.037 14.17 9.48 0.00 2.73
88 89 8.687242 GGATGATATGATACTCGAATTCCAGTA 58.313 37.037 14.23 14.23 0.00 2.74
89 90 7.551585 GGATGATATGATACTCGAATTCCAGT 58.448 38.462 10.66 10.66 0.00 4.00
90 91 6.694844 CGGATGATATGATACTCGAATTCCAG 59.305 42.308 0.00 0.00 0.00 3.86
91 92 6.405842 CCGGATGATATGATACTCGAATTCCA 60.406 42.308 0.00 0.00 0.00 3.53
92 93 5.980116 CCGGATGATATGATACTCGAATTCC 59.020 44.000 0.00 0.00 0.00 3.01
93 94 5.980116 CCCGGATGATATGATACTCGAATTC 59.020 44.000 0.73 0.00 0.00 2.17
94 95 5.422331 ACCCGGATGATATGATACTCGAATT 59.578 40.000 0.73 0.00 0.00 2.17
95 96 4.956700 ACCCGGATGATATGATACTCGAAT 59.043 41.667 0.73 0.00 0.00 3.34
96 97 4.341487 ACCCGGATGATATGATACTCGAA 58.659 43.478 0.73 0.00 0.00 3.71
97 98 3.945921 GACCCGGATGATATGATACTCGA 59.054 47.826 0.73 0.00 0.00 4.04
98 99 3.694566 TGACCCGGATGATATGATACTCG 59.305 47.826 0.73 0.00 0.00 4.18
99 100 5.186021 ACTTGACCCGGATGATATGATACTC 59.814 44.000 0.73 0.00 0.00 2.59
100 101 5.087323 ACTTGACCCGGATGATATGATACT 58.913 41.667 0.73 0.00 0.00 2.12
101 102 5.047306 TGACTTGACCCGGATGATATGATAC 60.047 44.000 0.73 0.00 0.00 2.24
102 103 5.083821 TGACTTGACCCGGATGATATGATA 58.916 41.667 0.73 0.00 0.00 2.15
103 104 3.903714 TGACTTGACCCGGATGATATGAT 59.096 43.478 0.73 0.00 0.00 2.45
104 105 3.304829 TGACTTGACCCGGATGATATGA 58.695 45.455 0.73 0.00 0.00 2.15
105 106 3.751479 TGACTTGACCCGGATGATATG 57.249 47.619 0.73 0.00 0.00 1.78
106 107 3.181454 GGTTGACTTGACCCGGATGATAT 60.181 47.826 0.73 0.00 0.00 1.63
107 108 2.169769 GGTTGACTTGACCCGGATGATA 59.830 50.000 0.73 0.00 0.00 2.15
108 109 1.065418 GGTTGACTTGACCCGGATGAT 60.065 52.381 0.73 0.00 0.00 2.45
109 110 0.323629 GGTTGACTTGACCCGGATGA 59.676 55.000 0.73 0.00 0.00 2.92
110 111 0.324943 AGGTTGACTTGACCCGGATG 59.675 55.000 0.73 0.00 37.93 3.51
111 112 1.946984 TAGGTTGACTTGACCCGGAT 58.053 50.000 0.73 0.00 37.93 4.18
112 113 1.946984 ATAGGTTGACTTGACCCGGA 58.053 50.000 0.73 0.00 37.93 5.14
113 114 3.244112 GGATATAGGTTGACTTGACCCGG 60.244 52.174 0.00 0.00 37.93 5.73
114 115 3.386726 TGGATATAGGTTGACTTGACCCG 59.613 47.826 0.00 0.00 37.93 5.28
115 116 4.163458 TGTGGATATAGGTTGACTTGACCC 59.837 45.833 0.00 0.00 37.93 4.46
116 117 5.353394 TGTGGATATAGGTTGACTTGACC 57.647 43.478 0.00 0.00 37.44 4.02
117 118 7.552687 TGATTTGTGGATATAGGTTGACTTGAC 59.447 37.037 0.00 0.00 0.00 3.18
118 119 7.629157 TGATTTGTGGATATAGGTTGACTTGA 58.371 34.615 0.00 0.00 0.00 3.02
119 120 7.864108 TGATTTGTGGATATAGGTTGACTTG 57.136 36.000 0.00 0.00 0.00 3.16
120 121 9.784531 CTATGATTTGTGGATATAGGTTGACTT 57.215 33.333 0.00 0.00 0.00 3.01
121 122 8.938883 ACTATGATTTGTGGATATAGGTTGACT 58.061 33.333 0.00 0.00 0.00 3.41
155 156 9.484326 GAGTTGAAAATTTTGCGTAAACATTTT 57.516 25.926 20.29 20.29 33.86 1.82
176 177 8.512138 ATTTTGGAAAATAAGTAGACGGAGTTG 58.488 33.333 0.00 0.00 37.65 3.16
193 194 7.891183 TGCTAACCTTAGGTATGATTTTGGAAA 59.109 33.333 3.55 0.00 33.12 3.13
196 197 6.238759 GCTGCTAACCTTAGGTATGATTTTGG 60.239 42.308 3.55 0.00 33.12 3.28
208 210 1.432270 GCGGCAGCTGCTAACCTTAG 61.432 60.000 35.82 17.87 41.70 2.18
211 213 4.785453 GGCGGCAGCTGCTAACCT 62.785 66.667 35.82 0.00 44.37 3.50
305 314 1.609239 CCATGCTCCTAAGGCCACA 59.391 57.895 5.01 0.00 0.00 4.17
318 327 2.123726 GGATCCACCACCCCATGC 60.124 66.667 6.95 0.00 38.79 4.06
402 417 4.214437 GTCGTCGTCTCGTCTTCTTAAAA 58.786 43.478 0.00 0.00 0.00 1.52
403 418 3.662713 CGTCGTCGTCTCGTCTTCTTAAA 60.663 47.826 0.00 0.00 0.00 1.52
464 479 2.495366 TAGACGCACCGCCGAAACAT 62.495 55.000 0.00 0.00 0.00 2.71
465 480 3.210223 TAGACGCACCGCCGAAACA 62.210 57.895 0.00 0.00 0.00 2.83
517 537 4.229123 AGGTCCATCAAAGACAGATCCATT 59.771 41.667 0.00 0.00 35.89 3.16
518 538 3.784763 AGGTCCATCAAAGACAGATCCAT 59.215 43.478 0.00 0.00 35.89 3.41
538 558 0.177604 GACCACCAGATCTGAGCAGG 59.822 60.000 24.62 19.54 0.00 4.85
591 611 0.824759 GAGTAGCATGGGTCGGAAGT 59.175 55.000 0.00 0.00 0.00 3.01
621 641 0.172352 CACACCAAAACAGCAACCGT 59.828 50.000 0.00 0.00 0.00 4.83
665 685 1.801178 GGTAGACACTCAGCAAGTTGC 59.199 52.381 20.44 20.44 45.46 4.17
677 697 5.746721 GGACAAAATTTGTTGTGGTAGACAC 59.253 40.000 13.00 0.00 46.76 3.67
693 713 0.320374 TCGTCGGAGCTGGACAAAAT 59.680 50.000 13.30 0.00 34.04 1.82
763 783 5.906113 ATCTATAGACCACTTAGCGATGG 57.094 43.478 4.10 0.00 42.13 3.51
765 785 6.493802 TCCAAATCTATAGACCACTTAGCGAT 59.506 38.462 4.10 0.00 0.00 4.58
867 895 5.756195 GCACCAAGCAATCTTACATATGA 57.244 39.130 10.38 0.00 44.79 2.15
893 921 0.669932 CATCGCCTCTGCTAGCCATC 60.670 60.000 13.29 0.00 34.43 3.51
898 926 1.593750 GTGCCATCGCCTCTGCTAG 60.594 63.158 0.00 0.00 34.43 3.42
900 928 4.479993 GGTGCCATCGCCTCTGCT 62.480 66.667 0.00 0.00 39.75 4.24
993 1035 1.601162 GCAAGTGTGTTGATGCAGTGG 60.601 52.381 0.00 0.00 38.63 4.00
1021 1071 3.858247 AGTACAAGAGGTTATCAACGGC 58.142 45.455 0.00 0.00 0.00 5.68
1105 1168 2.268298 CACGAAATCGACCCCTACTTG 58.732 52.381 10.16 0.00 43.02 3.16
1257 1320 3.195698 GCGTTGATGGCGGAGGAC 61.196 66.667 0.00 0.00 0.00 3.85
1294 1357 3.252701 CACTCTTTCAACAGCTTGAGCAT 59.747 43.478 5.70 0.00 45.16 3.79
1318 1381 0.875059 CCTTTGCAAGTCGGGTCTTC 59.125 55.000 0.00 0.00 0.00 2.87
1584 1650 2.556622 GACGAAAATTGCCTTTCCCTCA 59.443 45.455 0.00 0.00 32.63 3.86
1603 1669 0.456995 CCGAGCAGGAAGAAGACGAC 60.457 60.000 0.00 0.00 45.00 4.34
1770 1836 0.116342 TGCTCTCCCCTACAACCAGA 59.884 55.000 0.00 0.00 0.00 3.86
1771 1837 0.984230 TTGCTCTCCCCTACAACCAG 59.016 55.000 0.00 0.00 0.00 4.00
1837 1903 0.179040 TTTTTCTTGACGGGGTCGCT 60.179 50.000 0.00 0.00 40.63 4.93
1838 1904 0.040692 GTTTTTCTTGACGGGGTCGC 60.041 55.000 0.00 0.00 40.63 5.19
1840 1906 2.034179 CCTTGTTTTTCTTGACGGGGTC 59.966 50.000 0.00 0.00 0.00 4.46
1841 1907 2.028876 CCTTGTTTTTCTTGACGGGGT 58.971 47.619 0.00 0.00 0.00 4.95
1842 1908 2.034179 GTCCTTGTTTTTCTTGACGGGG 59.966 50.000 0.00 0.00 0.00 5.73
1843 1909 2.685897 TGTCCTTGTTTTTCTTGACGGG 59.314 45.455 0.00 0.00 0.00 5.28
1844 1910 4.351192 CTTGTCCTTGTTTTTCTTGACGG 58.649 43.478 0.00 0.00 0.00 4.79
1845 1911 3.791353 GCTTGTCCTTGTTTTTCTTGACG 59.209 43.478 0.00 0.00 0.00 4.35
1846 1912 4.998788 AGCTTGTCCTTGTTTTTCTTGAC 58.001 39.130 0.00 0.00 0.00 3.18
1847 1913 4.201910 CGAGCTTGTCCTTGTTTTTCTTGA 60.202 41.667 0.00 0.00 0.00 3.02
1848 1914 4.037690 CGAGCTTGTCCTTGTTTTTCTTG 58.962 43.478 0.00 0.00 0.00 3.02
1849 1915 3.066760 CCGAGCTTGTCCTTGTTTTTCTT 59.933 43.478 0.00 0.00 0.00 2.52
1850 1916 2.618709 CCGAGCTTGTCCTTGTTTTTCT 59.381 45.455 0.00 0.00 0.00 2.52
1851 1917 2.858646 GCCGAGCTTGTCCTTGTTTTTC 60.859 50.000 0.00 0.00 0.00 2.29
1852 1918 1.067060 GCCGAGCTTGTCCTTGTTTTT 59.933 47.619 0.00 0.00 0.00 1.94
1853 1919 0.668535 GCCGAGCTTGTCCTTGTTTT 59.331 50.000 0.00 0.00 0.00 2.43
1854 1920 1.507141 CGCCGAGCTTGTCCTTGTTT 61.507 55.000 0.00 0.00 0.00 2.83
1855 1921 1.961277 CGCCGAGCTTGTCCTTGTT 60.961 57.895 0.00 0.00 0.00 2.83
1856 1922 2.357517 CGCCGAGCTTGTCCTTGT 60.358 61.111 0.00 0.00 0.00 3.16
1875 1941 2.761195 CCGGTCGAGCGTGATGAGA 61.761 63.158 32.11 0.00 0.00 3.27
1879 1945 4.129737 CACCCGGTCGAGCGTGAT 62.130 66.667 32.11 16.35 0.00 3.06
1911 1977 3.562779 GAGGAAACCGTCGCCGTGA 62.563 63.158 0.00 0.00 0.00 4.35
1923 1989 0.606401 CCAGCTTCTTGGCGAGGAAA 60.606 55.000 0.97 0.00 35.41 3.13
1924 1990 1.003355 CCAGCTTCTTGGCGAGGAA 60.003 57.895 0.97 0.00 35.41 3.36
1940 2006 2.246067 AGACAGAGATCCCTTAGCTCCA 59.754 50.000 0.00 0.00 41.81 3.86
1953 2019 3.527253 AGAGGGAGAATGAGAGACAGAGA 59.473 47.826 0.00 0.00 0.00 3.10
1959 2025 4.940483 TCTTGAAGAGGGAGAATGAGAGA 58.060 43.478 0.00 0.00 0.00 3.10
1989 2055 3.138798 TACCCTGAGAGGCGACGC 61.139 66.667 12.43 12.43 32.73 5.19
2010 2076 0.902531 TGGATCCTTCCTCGGTCAAC 59.097 55.000 14.23 0.00 43.07 3.18
2014 2080 0.909610 TTGCTGGATCCTTCCTCGGT 60.910 55.000 14.23 0.00 43.07 4.69
2025 2091 0.829333 AGTCGAGAGCATTGCTGGAT 59.171 50.000 17.51 1.24 39.88 3.41
2034 2100 1.210413 GAGCACGAAGTCGAGAGCA 59.790 57.895 7.87 0.00 41.61 4.26
2037 2103 1.587043 CCCTGAGCACGAAGTCGAGA 61.587 60.000 7.87 0.00 41.61 4.04
2092 2158 3.443045 CACCCGCTTGGCATCCAC 61.443 66.667 0.00 0.00 37.83 4.02
2093 2159 3.505790 AACACCCGCTTGGCATCCA 62.506 57.895 0.00 0.00 37.83 3.41
2094 2160 2.676471 AACACCCGCTTGGCATCC 60.676 61.111 0.00 0.00 37.83 3.51
2139 2205 3.240861 GCGAGTAGTAGAAATCACTTGCG 59.759 47.826 0.00 0.00 38.33 4.85
2169 2235 1.673665 CCCACTGAAGGAGCACAGC 60.674 63.158 0.00 0.00 37.61 4.40
2198 2264 1.683917 CCGACAGGAGATAGTTGAGGG 59.316 57.143 0.00 0.00 41.02 4.30
2208 2274 0.331616 TGATGAGGACCGACAGGAGA 59.668 55.000 0.00 0.00 41.02 3.71
2214 2280 1.300233 GGCGATGATGAGGACCGAC 60.300 63.158 0.00 0.00 0.00 4.79
2241 2307 2.265367 TGATAAAGCACTCCCACTCCA 58.735 47.619 0.00 0.00 0.00 3.86
2244 2310 4.922206 TGATTTGATAAAGCACTCCCACT 58.078 39.130 0.00 0.00 30.84 4.00
2254 2320 7.538575 ACGATCACCCTTTTGATTTGATAAAG 58.461 34.615 0.00 0.00 36.30 1.85
2294 2361 1.979155 GCTGGGTTCTCTTTGGCCC 60.979 63.158 0.00 0.00 41.42 5.80
2310 2380 4.489306 GTACAATTCTGGACCCTTAGCT 57.511 45.455 0.00 0.00 28.93 3.32
2324 2400 5.526434 AGTAGTAGGCTACCTGGTACAATT 58.474 41.667 20.67 1.23 46.60 2.32
2327 2403 4.018141 TGAAGTAGTAGGCTACCTGGTACA 60.018 45.833 20.67 11.44 46.60 2.90
2334 2410 4.216708 AGGTGATGAAGTAGTAGGCTACC 58.783 47.826 20.67 6.92 46.60 3.18
2335 2411 5.127356 ACAAGGTGATGAAGTAGTAGGCTAC 59.873 44.000 16.93 16.93 45.96 3.58
2336 2412 5.269991 ACAAGGTGATGAAGTAGTAGGCTA 58.730 41.667 0.00 0.00 0.00 3.93
2355 2431 0.179134 CGGCGAGTAGGAGGAACAAG 60.179 60.000 0.00 0.00 0.00 3.16
2436 2512 3.466836 TCTGATGTAATGGCCGATCAAC 58.533 45.455 0.00 0.00 0.00 3.18
2440 2516 3.470709 CACTTCTGATGTAATGGCCGAT 58.529 45.455 0.00 0.00 0.00 4.18
2448 2524 1.001974 AGCGTGCCACTTCTGATGTAA 59.998 47.619 0.00 0.00 0.00 2.41
2578 2660 3.116531 GAAAAGCCCCGACCGTCG 61.117 66.667 14.15 14.15 40.07 5.12
2580 2662 2.346365 GAGAAAAGCCCCGACCGT 59.654 61.111 0.00 0.00 0.00 4.83
2625 2716 2.376109 GAGAGTTCCACCGACCTCATA 58.624 52.381 0.00 0.00 0.00 2.15
2655 2746 2.571757 CTGAGCACCGCGTCCTTA 59.428 61.111 4.92 0.00 0.00 2.69
2685 2776 0.639943 TGTCCAGTCCCCCATAGCTA 59.360 55.000 0.00 0.00 0.00 3.32
2796 2887 4.624364 TCCGTGGTGCTGCTGGTG 62.624 66.667 0.00 0.00 0.00 4.17
2797 2888 4.320456 CTCCGTGGTGCTGCTGGT 62.320 66.667 0.00 0.00 0.00 4.00
2922 3013 0.452987 CCAGGTACGCGCAGTAGTAA 59.547 55.000 5.73 0.00 35.72 2.24
3324 3415 3.625897 CCAGGCCTGTCCGTGACA 61.626 66.667 30.63 6.57 40.50 3.58
3382 3480 8.470040 AAAGATGCATGAACAAATTACATGAC 57.530 30.769 2.46 0.00 42.41 3.06
3576 3700 5.986741 TCCGACAAAATTTTAGGCCTTTTTC 59.013 36.000 12.58 0.00 0.00 2.29
3747 3872 1.544246 GTGGGTAGTTTGGCCATGTTC 59.456 52.381 6.09 0.00 0.00 3.18
3821 3950 6.593770 CCACTGCATTTGAACATGTAGTACTA 59.406 38.462 0.00 0.00 45.27 1.82
3822 3951 5.412594 CCACTGCATTTGAACATGTAGTACT 59.587 40.000 0.00 0.00 45.27 2.73
3823 3952 5.411361 TCCACTGCATTTGAACATGTAGTAC 59.589 40.000 0.00 0.00 45.27 2.73
3824 3953 5.555966 TCCACTGCATTTGAACATGTAGTA 58.444 37.500 0.00 0.00 45.27 1.82
3826 3955 5.571784 ATCCACTGCATTTGAACATGTAG 57.428 39.130 0.00 0.00 41.35 2.74
3865 3994 4.262420 GGGTGGAGTTGCATGTTTTATGTT 60.262 41.667 0.00 0.00 0.00 2.71
3931 4060 2.665519 CGTGCTTTTACTGTCCATGCAC 60.666 50.000 14.95 14.95 43.73 4.57


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

AutoCloner maintained by Alex Coulton.