Multiple sequence alignment - TraesCS5B01G560200

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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 TraesCS5B01G560200 chr5B 100.000 4905 0 0 495 5399 706709766 706714670 0.000000e+00 9058.0
1 TraesCS5B01G560200 chr5B 85.564 3623 470 36 887 4482 706389079 706385483 0.000000e+00 3744.0
2 TraesCS5B01G560200 chr5B 85.341 3561 470 38 974 4507 706453477 706457012 0.000000e+00 3637.0
3 TraesCS5B01G560200 chr5B 85.439 3482 483 19 954 4416 705984504 705981028 0.000000e+00 3600.0
4 TraesCS5B01G560200 chr5B 100.000 182 0 0 1 182 706709272 706709453 2.410000e-88 337.0
5 TraesCS5B01G560200 chr5B 75.433 635 63 44 4747 5369 706457341 706457894 7.040000e-54 222.0
6 TraesCS5B01G560200 chr5B 100.000 54 0 0 5172 5225 706714404 706714457 3.440000e-17 100.0
7 TraesCS5B01G560200 chr5B 100.000 54 0 0 5133 5186 706714443 706714496 3.440000e-17 100.0
8 TraesCS5B01G560200 chr5B 96.610 59 2 0 4591 4649 706457137 706457195 1.240000e-16 99.0
9 TraesCS5B01G560200 chr5B 94.872 39 2 0 5016 5054 480026671 480026633 1.620000e-05 62.1
10 TraesCS5B01G560200 chr4A 96.527 4376 87 25 838 5186 608271202 608266865 0.000000e+00 7179.0
11 TraesCS5B01G560200 chr4A 86.538 3536 446 20 961 4483 608481519 608478001 0.000000e+00 3866.0
12 TraesCS5B01G560200 chr4A 83.522 3453 540 22 978 4409 608234660 608231216 0.000000e+00 3197.0
13 TraesCS5B01G560200 chr4A 97.758 223 5 0 5173 5395 608266917 608266695 8.480000e-103 385.0
14 TraesCS5B01G560200 chr4A 82.424 165 11 6 504 650 608272301 608272137 1.580000e-25 128.0
15 TraesCS5B01G560200 chr4A 90.278 72 5 1 5236 5307 608477252 608477183 5.760000e-15 93.5
16 TraesCS5B01G560200 chr5D 93.795 4319 202 38 793 5064 564226622 564230921 0.000000e+00 6431.0
17 TraesCS5B01G560200 chr5D 85.671 3650 475 37 859 4482 563979803 563976176 0.000000e+00 3799.0
18 TraesCS5B01G560200 chr5D 92.814 167 9 2 5236 5399 564231039 564231205 6.990000e-59 239.0
19 TraesCS5B01G560200 chr5D 92.157 153 12 0 5241 5393 564290673 564290825 3.270000e-52 217.0
20 TraesCS5B01G560200 chr5D 81.595 163 16 9 780 930 564226462 564226622 7.340000e-24 122.0
21 TraesCS5B01G560200 chr3B 84.030 3638 526 40 870 4474 8039816 8043431 0.000000e+00 3448.0
22 TraesCS5B01G560200 chr3A 81.818 143 15 3 5024 5166 38205802 38205933 5.720000e-20 110.0


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 TraesCS5B01G560200 chr5B 706709272 706714670 5398 False 2398.750000 9058 100.000000 1 5399 4 chr5B.!!$F2 5398
1 TraesCS5B01G560200 chr5B 706385483 706389079 3596 True 3744.000000 3744 85.564000 887 4482 1 chr5B.!!$R3 3595
2 TraesCS5B01G560200 chr5B 705981028 705984504 3476 True 3600.000000 3600 85.439000 954 4416 1 chr5B.!!$R2 3462
3 TraesCS5B01G560200 chr5B 706453477 706457894 4417 False 1319.333333 3637 85.794667 974 5369 3 chr5B.!!$F1 4395
4 TraesCS5B01G560200 chr4A 608231216 608234660 3444 True 3197.000000 3197 83.522000 978 4409 1 chr4A.!!$R1 3431
5 TraesCS5B01G560200 chr4A 608266695 608272301 5606 True 2564.000000 7179 92.236333 504 5395 3 chr4A.!!$R2 4891
6 TraesCS5B01G560200 chr4A 608477183 608481519 4336 True 1979.750000 3866 88.408000 961 5307 2 chr4A.!!$R3 4346
7 TraesCS5B01G560200 chr5D 563976176 563979803 3627 True 3799.000000 3799 85.671000 859 4482 1 chr5D.!!$R1 3623
8 TraesCS5B01G560200 chr5D 564226462 564231205 4743 False 2264.000000 6431 89.401333 780 5399 3 chr5D.!!$F2 4619
9 TraesCS5B01G560200 chr3B 8039816 8043431 3615 False 3448.000000 3448 84.030000 870 4474 1 chr3B.!!$F1 3604

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
116 117 0.037326 AAAATCCTCTCGACGCTGCA 60.037 50.0 0.00 0.00 0.00 4.41 F
119 120 0.037326 ATCCTCTCGACGCTGCAAAA 60.037 50.0 0.00 0.00 0.00 2.44 F
560 561 0.041684 TCTGACATGGGAGCTCCTGA 59.958 55.0 31.36 18.99 36.20 3.86 F
698 717 0.524862 CCATGCTCTGTTGCAAGTCC 59.475 55.0 0.00 0.00 46.61 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1029 1840 1.078918 TGCTGATGAGAAGCCACCG 60.079 57.895 0.00 0.0 40.06 4.94 R
1287 2098 1.667830 CTTGCGCTTTCCGAGGACA 60.668 57.895 9.73 0.0 40.02 4.02 R
3450 4282 3.270027 CTTCACCGATGGCAAGTTATCA 58.730 45.455 0.00 0.0 0.00 2.15 R
4451 5296 4.392921 AAGCATGCTTACAGAGATACGT 57.607 40.909 31.09 2.1 34.05 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
22 23 5.904362 AAGCACTAAGGAAAATTAGGCAG 57.096 39.130 0.00 0.00 37.13 4.85
23 24 3.696548 AGCACTAAGGAAAATTAGGCAGC 59.303 43.478 0.00 0.00 37.13 5.25
24 25 3.487544 GCACTAAGGAAAATTAGGCAGCG 60.488 47.826 0.00 0.00 37.13 5.18
25 26 3.065371 CACTAAGGAAAATTAGGCAGCGG 59.935 47.826 0.00 0.00 37.13 5.52
26 27 2.215942 AAGGAAAATTAGGCAGCGGT 57.784 45.000 0.00 0.00 0.00 5.68
27 28 2.215942 AGGAAAATTAGGCAGCGGTT 57.784 45.000 0.00 0.00 0.00 4.44
28 29 2.525368 AGGAAAATTAGGCAGCGGTTT 58.475 42.857 0.00 0.00 0.00 3.27
29 30 2.897326 AGGAAAATTAGGCAGCGGTTTT 59.103 40.909 0.00 0.00 0.00 2.43
30 31 2.993220 GGAAAATTAGGCAGCGGTTTTG 59.007 45.455 0.00 0.00 0.00 2.44
31 32 2.741759 AAATTAGGCAGCGGTTTTGG 57.258 45.000 0.00 0.00 0.00 3.28
32 33 0.246360 AATTAGGCAGCGGTTTTGGC 59.754 50.000 0.00 0.00 41.05 4.52
33 34 0.897863 ATTAGGCAGCGGTTTTGGCA 60.898 50.000 1.68 0.00 42.98 4.92
34 35 1.109920 TTAGGCAGCGGTTTTGGCAA 61.110 50.000 0.00 0.00 42.98 4.52
35 36 1.523154 TAGGCAGCGGTTTTGGCAAG 61.523 55.000 0.00 0.00 42.98 4.01
36 37 2.417097 GCAGCGGTTTTGGCAAGT 59.583 55.556 0.00 0.00 0.00 3.16
37 38 1.657556 GCAGCGGTTTTGGCAAGTA 59.342 52.632 0.00 0.00 0.00 2.24
38 39 0.387239 GCAGCGGTTTTGGCAAGTAG 60.387 55.000 0.00 0.00 0.00 2.57
39 40 0.240945 CAGCGGTTTTGGCAAGTAGG 59.759 55.000 0.00 0.00 0.00 3.18
40 41 0.109723 AGCGGTTTTGGCAAGTAGGA 59.890 50.000 0.00 0.00 0.00 2.94
41 42 1.173913 GCGGTTTTGGCAAGTAGGAT 58.826 50.000 0.00 0.00 0.00 3.24
42 43 1.135402 GCGGTTTTGGCAAGTAGGATG 60.135 52.381 0.00 0.00 0.00 3.51
43 44 2.159382 CGGTTTTGGCAAGTAGGATGT 58.841 47.619 0.00 0.00 0.00 3.06
44 45 2.095263 CGGTTTTGGCAAGTAGGATGTG 60.095 50.000 0.00 0.00 0.00 3.21
45 46 2.890945 GGTTTTGGCAAGTAGGATGTGT 59.109 45.455 0.00 0.00 0.00 3.72
46 47 3.057526 GGTTTTGGCAAGTAGGATGTGTC 60.058 47.826 0.00 0.00 0.00 3.67
47 48 2.489938 TTGGCAAGTAGGATGTGTCC 57.510 50.000 0.00 0.00 45.45 4.02
60 61 4.798574 GGATGTGTCCATGTCAAAAGAAC 58.201 43.478 0.00 0.00 44.42 3.01
61 62 4.278170 GGATGTGTCCATGTCAAAAGAACA 59.722 41.667 0.00 0.00 44.42 3.18
62 63 4.898829 TGTGTCCATGTCAAAAGAACAG 57.101 40.909 0.00 0.00 0.00 3.16
63 64 4.269183 TGTGTCCATGTCAAAAGAACAGT 58.731 39.130 0.00 0.00 0.00 3.55
64 65 4.096231 TGTGTCCATGTCAAAAGAACAGTG 59.904 41.667 0.00 0.00 0.00 3.66
65 66 4.335315 GTGTCCATGTCAAAAGAACAGTGA 59.665 41.667 0.00 0.00 0.00 3.41
66 67 4.946772 TGTCCATGTCAAAAGAACAGTGAA 59.053 37.500 0.00 0.00 0.00 3.18
67 68 5.593909 TGTCCATGTCAAAAGAACAGTGAAT 59.406 36.000 0.00 0.00 0.00 2.57
68 69 5.916883 GTCCATGTCAAAAGAACAGTGAATG 59.083 40.000 0.00 0.00 0.00 2.67
69 70 5.827267 TCCATGTCAAAAGAACAGTGAATGA 59.173 36.000 0.00 0.00 0.00 2.57
70 71 6.320926 TCCATGTCAAAAGAACAGTGAATGAA 59.679 34.615 0.00 0.00 0.00 2.57
71 72 6.418819 CCATGTCAAAAGAACAGTGAATGAAC 59.581 38.462 0.00 0.00 0.00 3.18
72 73 5.890334 TGTCAAAAGAACAGTGAATGAACC 58.110 37.500 0.00 0.00 0.00 3.62
73 74 5.163561 TGTCAAAAGAACAGTGAATGAACCC 60.164 40.000 0.00 0.00 0.00 4.11
74 75 4.340950 TCAAAAGAACAGTGAATGAACCCC 59.659 41.667 0.00 0.00 0.00 4.95
75 76 2.185004 AGAACAGTGAATGAACCCCG 57.815 50.000 0.00 0.00 0.00 5.73
76 77 0.521735 GAACAGTGAATGAACCCCGC 59.478 55.000 0.00 0.00 0.00 6.13
77 78 0.179004 AACAGTGAATGAACCCCGCA 60.179 50.000 0.00 0.00 0.00 5.69
78 79 0.179004 ACAGTGAATGAACCCCGCAA 60.179 50.000 0.00 0.00 0.00 4.85
79 80 0.958091 CAGTGAATGAACCCCGCAAA 59.042 50.000 0.00 0.00 0.00 3.68
80 81 1.339610 CAGTGAATGAACCCCGCAAAA 59.660 47.619 0.00 0.00 0.00 2.44
81 82 2.035632 AGTGAATGAACCCCGCAAAAA 58.964 42.857 0.00 0.00 0.00 1.94
111 112 7.932120 AACTATGATAAAAATCCTCTCGACG 57.068 36.000 0.00 0.00 0.00 5.12
112 113 5.921408 ACTATGATAAAAATCCTCTCGACGC 59.079 40.000 0.00 0.00 0.00 5.19
113 114 4.386867 TGATAAAAATCCTCTCGACGCT 57.613 40.909 0.00 0.00 0.00 5.07
114 115 4.112634 TGATAAAAATCCTCTCGACGCTG 58.887 43.478 0.00 0.00 0.00 5.18
115 116 1.079503 AAAAATCCTCTCGACGCTGC 58.920 50.000 0.00 0.00 0.00 5.25
116 117 0.037326 AAAATCCTCTCGACGCTGCA 60.037 50.000 0.00 0.00 0.00 4.41
117 118 0.037326 AAATCCTCTCGACGCTGCAA 60.037 50.000 0.00 0.00 0.00 4.08
118 119 0.037326 AATCCTCTCGACGCTGCAAA 60.037 50.000 0.00 0.00 0.00 3.68
119 120 0.037326 ATCCTCTCGACGCTGCAAAA 60.037 50.000 0.00 0.00 0.00 2.44
120 121 0.944311 TCCTCTCGACGCTGCAAAAC 60.944 55.000 0.00 0.00 0.00 2.43
121 122 1.128611 CTCTCGACGCTGCAAAACG 59.871 57.895 0.00 2.23 0.00 3.60
122 123 2.170985 CTCGACGCTGCAAAACGG 59.829 61.111 0.00 0.00 0.00 4.44
123 124 2.279584 TCGACGCTGCAAAACGGA 60.280 55.556 0.00 0.00 0.00 4.69
124 125 1.626654 CTCGACGCTGCAAAACGGAT 61.627 55.000 0.00 0.00 0.00 4.18
125 126 0.388778 TCGACGCTGCAAAACGGATA 60.389 50.000 0.00 0.00 0.00 2.59
126 127 0.247145 CGACGCTGCAAAACGGATAC 60.247 55.000 0.00 0.00 0.00 2.24
127 128 0.793861 GACGCTGCAAAACGGATACA 59.206 50.000 0.00 0.00 0.00 2.29
128 129 0.515564 ACGCTGCAAAACGGATACAC 59.484 50.000 0.00 0.00 0.00 2.90
129 130 0.518355 CGCTGCAAAACGGATACACG 60.518 55.000 0.00 0.00 40.31 4.49
130 131 0.793861 GCTGCAAAACGGATACACGA 59.206 50.000 0.00 0.00 37.61 4.35
131 132 1.201921 GCTGCAAAACGGATACACGAG 60.202 52.381 0.00 0.00 37.61 4.18
132 133 2.333926 CTGCAAAACGGATACACGAGA 58.666 47.619 0.00 0.00 37.61 4.04
133 134 2.734606 CTGCAAAACGGATACACGAGAA 59.265 45.455 0.00 0.00 37.61 2.87
134 135 3.132160 TGCAAAACGGATACACGAGAAA 58.868 40.909 0.00 0.00 37.61 2.52
135 136 3.560481 TGCAAAACGGATACACGAGAAAA 59.440 39.130 0.00 0.00 37.61 2.29
136 137 4.035324 TGCAAAACGGATACACGAGAAAAA 59.965 37.500 0.00 0.00 37.61 1.94
155 156 4.733972 AAAAAGAGAAACTACTCGCTGC 57.266 40.909 0.00 0.00 41.25 5.25
156 157 3.386768 AAAGAGAAACTACTCGCTGCA 57.613 42.857 0.00 0.00 41.25 4.41
157 158 3.386768 AAGAGAAACTACTCGCTGCAA 57.613 42.857 0.00 0.00 41.25 4.08
158 159 3.601443 AGAGAAACTACTCGCTGCAAT 57.399 42.857 0.00 0.00 41.25 3.56
159 160 3.516615 AGAGAAACTACTCGCTGCAATC 58.483 45.455 0.00 0.00 41.25 2.67
160 161 2.263077 AGAAACTACTCGCTGCAATCG 58.737 47.619 0.00 1.97 0.00 3.34
161 162 0.721718 AAACTACTCGCTGCAATCGC 59.278 50.000 0.00 0.00 39.24 4.58
162 163 1.084370 AACTACTCGCTGCAATCGCC 61.084 55.000 0.00 0.00 37.32 5.54
163 164 2.580470 CTACTCGCTGCAATCGCCG 61.580 63.158 0.00 0.82 37.32 6.46
164 165 3.350909 TACTCGCTGCAATCGCCGT 62.351 57.895 0.00 5.84 37.32 5.68
165 166 2.829043 TACTCGCTGCAATCGCCGTT 62.829 55.000 0.00 0.00 37.32 4.44
166 167 3.707156 CTCGCTGCAATCGCCGTTG 62.707 63.158 0.00 0.00 37.32 4.10
527 528 2.444895 GGAGGAGCTGGGTCGGAT 60.445 66.667 0.00 0.00 0.00 4.18
536 537 0.464452 CTGGGTCGGATTGGGTACTC 59.536 60.000 0.00 0.00 0.00 2.59
557 558 0.177604 CAGTCTGACATGGGAGCTCC 59.822 60.000 25.59 25.59 0.00 4.70
560 561 0.041684 TCTGACATGGGAGCTCCTGA 59.958 55.000 31.36 18.99 36.20 3.86
562 563 1.489649 CTGACATGGGAGCTCCTGAAT 59.510 52.381 31.36 19.36 36.20 2.57
567 568 3.053095 ACATGGGAGCTCCTGAATTTCAT 60.053 43.478 31.36 20.47 36.20 2.57
568 569 3.287867 TGGGAGCTCCTGAATTTCATC 57.712 47.619 31.36 11.71 36.20 2.92
569 570 2.577563 TGGGAGCTCCTGAATTTCATCA 59.422 45.455 31.36 14.24 36.20 3.07
570 571 3.212685 GGGAGCTCCTGAATTTCATCAG 58.787 50.000 31.36 0.51 45.19 2.90
593 611 7.064609 TCAGGAAAACTTAGATACGCTTCATTG 59.935 37.037 0.00 0.00 0.00 2.82
608 627 3.564235 TCATTGTGAAAGCTGTGATGC 57.436 42.857 0.00 0.00 0.00 3.91
650 669 2.799017 AGATTGCATCTGTTGAAGCCA 58.201 42.857 0.00 0.00 38.44 4.75
657 676 5.851720 TGCATCTGTTGAAGCCAAATTTTA 58.148 33.333 0.00 0.00 36.21 1.52
659 678 5.928264 GCATCTGTTGAAGCCAAATTTTACT 59.072 36.000 0.00 0.00 33.49 2.24
660 679 7.090173 GCATCTGTTGAAGCCAAATTTTACTA 58.910 34.615 0.00 0.00 33.49 1.82
661 680 7.598493 GCATCTGTTGAAGCCAAATTTTACTAA 59.402 33.333 0.00 0.00 33.49 2.24
662 681 9.643693 CATCTGTTGAAGCCAAATTTTACTAAT 57.356 29.630 0.00 0.00 33.49 1.73
686 705 6.530019 TTTTTCCTAATTCCTTCCATGCTC 57.470 37.500 0.00 0.00 0.00 4.26
687 706 5.456921 TTTCCTAATTCCTTCCATGCTCT 57.543 39.130 0.00 0.00 0.00 4.09
688 707 4.428294 TCCTAATTCCTTCCATGCTCTG 57.572 45.455 0.00 0.00 0.00 3.35
689 708 3.782523 TCCTAATTCCTTCCATGCTCTGT 59.217 43.478 0.00 0.00 0.00 3.41
690 709 4.228210 TCCTAATTCCTTCCATGCTCTGTT 59.772 41.667 0.00 0.00 0.00 3.16
691 710 4.337555 CCTAATTCCTTCCATGCTCTGTTG 59.662 45.833 0.00 0.00 0.00 3.33
692 711 1.538047 TTCCTTCCATGCTCTGTTGC 58.462 50.000 0.00 0.00 0.00 4.17
694 713 1.202915 TCCTTCCATGCTCTGTTGCAA 60.203 47.619 0.00 0.00 46.61 4.08
695 714 1.201647 CCTTCCATGCTCTGTTGCAAG 59.798 52.381 0.00 0.00 46.61 4.01
696 715 1.884579 CTTCCATGCTCTGTTGCAAGT 59.115 47.619 0.00 0.00 46.61 3.16
697 716 1.527034 TCCATGCTCTGTTGCAAGTC 58.473 50.000 0.00 0.00 46.61 3.01
698 717 0.524862 CCATGCTCTGTTGCAAGTCC 59.475 55.000 0.00 0.00 46.61 3.85
699 718 1.241165 CATGCTCTGTTGCAAGTCCA 58.759 50.000 0.00 0.00 46.61 4.02
700 719 1.816835 CATGCTCTGTTGCAAGTCCAT 59.183 47.619 0.00 0.00 46.61 3.41
701 720 1.985473 TGCTCTGTTGCAAGTCCATT 58.015 45.000 0.00 0.00 40.29 3.16
702 721 1.610038 TGCTCTGTTGCAAGTCCATTG 59.390 47.619 0.00 0.00 40.29 2.82
703 722 1.610522 GCTCTGTTGCAAGTCCATTGT 59.389 47.619 0.00 0.00 41.29 2.71
704 723 2.606308 GCTCTGTTGCAAGTCCATTGTG 60.606 50.000 0.00 0.00 41.29 3.33
705 724 2.620115 CTCTGTTGCAAGTCCATTGTGT 59.380 45.455 0.00 0.00 41.29 3.72
706 725 3.023119 TCTGTTGCAAGTCCATTGTGTT 58.977 40.909 0.00 0.00 41.29 3.32
707 726 3.446873 TCTGTTGCAAGTCCATTGTGTTT 59.553 39.130 0.00 0.00 41.29 2.83
708 727 4.081752 TCTGTTGCAAGTCCATTGTGTTTT 60.082 37.500 0.00 0.00 41.29 2.43
709 728 3.931468 TGTTGCAAGTCCATTGTGTTTTG 59.069 39.130 0.00 0.00 41.29 2.44
710 729 3.176552 TGCAAGTCCATTGTGTTTTGG 57.823 42.857 0.00 0.00 41.29 3.28
711 730 2.762887 TGCAAGTCCATTGTGTTTTGGA 59.237 40.909 0.00 0.00 41.29 3.53
741 760 7.085052 TCATTTCTTGAGAAGATTGCATCTG 57.915 36.000 0.00 0.00 40.13 2.90
743 762 6.738832 TTTCTTGAGAAGATTGCATCTGAG 57.261 37.500 0.00 0.00 40.13 3.35
745 764 5.802465 TCTTGAGAAGATTGCATCTGAGTT 58.198 37.500 0.00 0.00 40.13 3.01
747 766 7.389232 TCTTGAGAAGATTGCATCTGAGTTAA 58.611 34.615 0.00 0.00 40.13 2.01
748 767 7.548427 TCTTGAGAAGATTGCATCTGAGTTAAG 59.452 37.037 0.00 0.00 40.13 1.85
760 805 5.485209 TCTGAGTTAAGTTTTCCTCCCTC 57.515 43.478 0.00 0.00 0.00 4.30
820 1446 8.947055 TCATACATGAAGAAAATTCATCTCGA 57.053 30.769 0.00 0.00 37.06 4.04
854 1496 9.162764 TGCTTGAAATAAGTAATCCTTACAGTC 57.837 33.333 0.39 0.00 38.45 3.51
855 1497 9.162764 GCTTGAAATAAGTAATCCTTACAGTCA 57.837 33.333 0.39 0.00 38.45 3.41
867 1509 6.328641 TCCTTACAGTCAACTAGTCAAGTC 57.671 41.667 0.00 0.00 37.50 3.01
930 1729 5.835819 TCATCTATCCCTTAACAGGAGACAG 59.164 44.000 0.00 0.00 44.19 3.51
931 1730 5.208294 TCTATCCCTTAACAGGAGACAGT 57.792 43.478 0.00 0.00 44.19 3.55
932 1731 5.590818 TCTATCCCTTAACAGGAGACAGTT 58.409 41.667 0.00 0.00 44.19 3.16
952 1752 7.842525 CAGTTTTCTACAACTGCATACAAAG 57.157 36.000 0.83 0.00 45.43 2.77
965 1775 6.264292 ACTGCATACAAAGTACAAACATGGAA 59.736 34.615 0.00 0.00 0.00 3.53
995 1806 5.049405 GGTTCTATCATTATTGCAGGGTTCG 60.049 44.000 0.00 0.00 0.00 3.95
1167 1978 2.496942 CACCATGGTGAAGGCCATC 58.503 57.895 37.05 2.09 45.47 3.51
1268 2079 1.072806 AGCTGAGGATGTGCTTGACAA 59.927 47.619 0.00 0.00 38.36 3.18
1287 2098 5.647658 TGACAAGTTTGACTGTCAAGACATT 59.352 36.000 21.13 12.61 41.01 2.71
3450 4282 4.567971 CTTCACTCAAGCATCTCACTCTT 58.432 43.478 0.00 0.00 0.00 2.85
4450 5295 7.124298 TGTCTCTGCCTCTGTACTACAAATAAT 59.876 37.037 0.00 0.00 0.00 1.28
4451 5296 8.630917 GTCTCTGCCTCTGTACTACAAATAATA 58.369 37.037 0.00 0.00 0.00 0.98
4452 5297 8.630917 TCTCTGCCTCTGTACTACAAATAATAC 58.369 37.037 0.00 0.00 0.00 1.89
4453 5298 7.423199 TCTGCCTCTGTACTACAAATAATACG 58.577 38.462 0.00 0.00 0.00 3.06
4649 5557 6.680874 AACATTGTGCAAATTGTTGATTGT 57.319 29.167 14.78 0.00 36.83 2.71
4650 5558 6.050454 ACATTGTGCAAATTGTTGATTGTG 57.950 33.333 0.00 0.00 36.83 3.33
4652 5560 3.528532 TGTGCAAATTGTTGATTGTGCA 58.471 36.364 0.00 0.00 38.36 4.57
4653 5561 3.937079 TGTGCAAATTGTTGATTGTGCAA 59.063 34.783 0.00 0.00 40.26 4.08
4654 5562 4.393990 TGTGCAAATTGTTGATTGTGCAAA 59.606 33.333 0.00 0.00 40.26 3.68
4656 5564 5.972382 GTGCAAATTGTTGATTGTGCAAATT 59.028 32.000 0.00 0.00 40.26 1.82
4660 5568 7.513814 GCAAATTGTTGATTGTGCAAATTGTTG 60.514 33.333 0.00 0.00 36.17 3.33
4661 5569 6.922247 ATTGTTGATTGTGCAAATTGTTGA 57.078 29.167 0.00 0.00 36.83 3.18
4663 5571 6.922247 TGTTGATTGTGCAAATTGTTGATT 57.078 29.167 0.00 0.00 36.83 2.57
4664 5572 6.716438 TGTTGATTGTGCAAATTGTTGATTG 58.284 32.000 0.00 0.00 36.83 2.67
4733 5720 5.055812 GTGGGCTGAATTGATTTGTTTTCA 58.944 37.500 0.00 0.00 0.00 2.69
4736 5723 6.771749 TGGGCTGAATTGATTTGTTTTCATTT 59.228 30.769 0.00 0.00 0.00 2.32
4795 5784 6.598457 CCTAGGCATTCTATCAATCATTCCTG 59.402 42.308 0.00 0.00 0.00 3.86
4957 6036 2.043625 CAAGGTTGCAGCATGGTGT 58.956 52.632 24.73 2.90 35.86 4.16
5176 6268 0.395586 TTCTGTGTTGCTGTTGGGCT 60.396 50.000 0.00 0.00 0.00 5.19
5177 6269 0.819259 TCTGTGTTGCTGTTGGGCTC 60.819 55.000 0.00 0.00 0.00 4.70
5178 6270 0.820891 CTGTGTTGCTGTTGGGCTCT 60.821 55.000 0.00 0.00 0.00 4.09
5179 6271 0.819259 TGTGTTGCTGTTGGGCTCTC 60.819 55.000 0.00 0.00 0.00 3.20
5180 6272 1.597854 TGTTGCTGTTGGGCTCTCG 60.598 57.895 0.00 0.00 0.00 4.04
5181 6273 2.032528 TTGCTGTTGGGCTCTCGG 59.967 61.111 0.00 0.00 0.00 4.63
5182 6274 2.515979 TTGCTGTTGGGCTCTCGGA 61.516 57.895 0.00 0.00 0.00 4.55
5183 6275 2.435059 GCTGTTGGGCTCTCGGAC 60.435 66.667 0.00 0.00 0.00 4.79
5184 6276 2.948720 GCTGTTGGGCTCTCGGACT 61.949 63.158 0.00 0.00 0.00 3.85
5185 6277 1.216710 CTGTTGGGCTCTCGGACTC 59.783 63.158 0.00 0.00 0.00 3.36
5186 6278 1.228894 TGTTGGGCTCTCGGACTCT 60.229 57.895 0.00 0.00 0.00 3.24
5187 6279 1.216710 GTTGGGCTCTCGGACTCTG 59.783 63.158 0.00 0.00 0.00 3.35
5188 6280 1.228894 TTGGGCTCTCGGACTCTGT 60.229 57.895 0.00 0.00 0.00 3.41
5189 6281 0.832135 TTGGGCTCTCGGACTCTGTT 60.832 55.000 0.00 0.00 0.00 3.16
5190 6282 1.251527 TGGGCTCTCGGACTCTGTTC 61.252 60.000 0.00 0.00 0.00 3.18
5191 6283 1.513622 GGCTCTCGGACTCTGTTCC 59.486 63.158 0.00 0.00 0.00 3.62
5198 6290 3.816580 GGACTCTGTTCCGGTCTTC 57.183 57.895 0.00 0.00 0.00 2.87
5199 6291 1.258676 GGACTCTGTTCCGGTCTTCT 58.741 55.000 0.00 0.00 0.00 2.85
5200 6292 1.067495 GGACTCTGTTCCGGTCTTCTG 60.067 57.143 0.00 0.00 0.00 3.02
5201 6293 1.614413 GACTCTGTTCCGGTCTTCTGT 59.386 52.381 0.00 0.00 0.00 3.41
5202 6294 1.341531 ACTCTGTTCCGGTCTTCTGTG 59.658 52.381 0.00 0.00 0.00 3.66
5203 6295 1.341531 CTCTGTTCCGGTCTTCTGTGT 59.658 52.381 0.00 0.00 0.00 3.72
5204 6296 1.760613 TCTGTTCCGGTCTTCTGTGTT 59.239 47.619 0.00 0.00 0.00 3.32
5205 6297 1.867233 CTGTTCCGGTCTTCTGTGTTG 59.133 52.381 0.00 0.00 0.00 3.33
5206 6298 0.586802 GTTCCGGTCTTCTGTGTTGC 59.413 55.000 0.00 0.00 0.00 4.17
5207 6299 0.468226 TTCCGGTCTTCTGTGTTGCT 59.532 50.000 0.00 0.00 0.00 3.91
5208 6300 0.249868 TCCGGTCTTCTGTGTTGCTG 60.250 55.000 0.00 0.00 0.00 4.41
5209 6301 0.532862 CCGGTCTTCTGTGTTGCTGT 60.533 55.000 0.00 0.00 0.00 4.40
5210 6302 1.299541 CGGTCTTCTGTGTTGCTGTT 58.700 50.000 0.00 0.00 0.00 3.16
5211 6303 1.003545 CGGTCTTCTGTGTTGCTGTTG 60.004 52.381 0.00 0.00 0.00 3.33
5212 6304 1.334869 GGTCTTCTGTGTTGCTGTTGG 59.665 52.381 0.00 0.00 0.00 3.77
5213 6305 1.334869 GTCTTCTGTGTTGCTGTTGGG 59.665 52.381 0.00 0.00 0.00 4.12
5214 6306 0.031178 CTTCTGTGTTGCTGTTGGGC 59.969 55.000 0.00 0.00 0.00 5.36
5310 6422 1.243902 CCGTTGTTGCTGGGTATGTT 58.756 50.000 0.00 0.00 0.00 2.71
5383 6495 2.167861 GCCACCTCGTGCGAGAATC 61.168 63.158 21.41 5.52 44.53 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.158579 GCTGCCTAATTTTCCTTAGTGCTT 59.841 41.667 0.00 0.00 31.61 3.91
1 2 3.696548 GCTGCCTAATTTTCCTTAGTGCT 59.303 43.478 0.00 0.00 31.61 4.40
2 3 3.487544 CGCTGCCTAATTTTCCTTAGTGC 60.488 47.826 0.00 0.00 0.00 4.40
3 4 3.065371 CCGCTGCCTAATTTTCCTTAGTG 59.935 47.826 0.00 0.00 0.00 2.74
4 5 3.279434 CCGCTGCCTAATTTTCCTTAGT 58.721 45.455 0.00 0.00 0.00 2.24
5 6 3.279434 ACCGCTGCCTAATTTTCCTTAG 58.721 45.455 0.00 0.00 0.00 2.18
6 7 3.359695 ACCGCTGCCTAATTTTCCTTA 57.640 42.857 0.00 0.00 0.00 2.69
7 8 2.215942 ACCGCTGCCTAATTTTCCTT 57.784 45.000 0.00 0.00 0.00 3.36
8 9 2.215942 AACCGCTGCCTAATTTTCCT 57.784 45.000 0.00 0.00 0.00 3.36
9 10 2.993220 CAAAACCGCTGCCTAATTTTCC 59.007 45.455 0.00 0.00 0.00 3.13
10 11 2.993220 CCAAAACCGCTGCCTAATTTTC 59.007 45.455 0.00 0.00 0.00 2.29
11 12 2.870035 GCCAAAACCGCTGCCTAATTTT 60.870 45.455 0.00 0.00 0.00 1.82
12 13 1.337728 GCCAAAACCGCTGCCTAATTT 60.338 47.619 0.00 0.00 0.00 1.82
13 14 0.246360 GCCAAAACCGCTGCCTAATT 59.754 50.000 0.00 0.00 0.00 1.40
14 15 0.897863 TGCCAAAACCGCTGCCTAAT 60.898 50.000 0.00 0.00 0.00 1.73
15 16 1.109920 TTGCCAAAACCGCTGCCTAA 61.110 50.000 0.00 0.00 0.00 2.69
16 17 1.523154 CTTGCCAAAACCGCTGCCTA 61.523 55.000 0.00 0.00 0.00 3.93
17 18 2.837291 TTGCCAAAACCGCTGCCT 60.837 55.556 0.00 0.00 0.00 4.75
18 19 1.801309 TACTTGCCAAAACCGCTGCC 61.801 55.000 0.00 0.00 0.00 4.85
19 20 0.387239 CTACTTGCCAAAACCGCTGC 60.387 55.000 0.00 0.00 0.00 5.25
20 21 0.240945 CCTACTTGCCAAAACCGCTG 59.759 55.000 0.00 0.00 0.00 5.18
21 22 0.109723 TCCTACTTGCCAAAACCGCT 59.890 50.000 0.00 0.00 0.00 5.52
22 23 1.135402 CATCCTACTTGCCAAAACCGC 60.135 52.381 0.00 0.00 0.00 5.68
23 24 2.095263 CACATCCTACTTGCCAAAACCG 60.095 50.000 0.00 0.00 0.00 4.44
24 25 2.890945 ACACATCCTACTTGCCAAAACC 59.109 45.455 0.00 0.00 0.00 3.27
25 26 3.057526 GGACACATCCTACTTGCCAAAAC 60.058 47.826 0.00 0.00 42.45 2.43
26 27 3.153919 GGACACATCCTACTTGCCAAAA 58.846 45.455 0.00 0.00 42.45 2.44
27 28 2.107378 TGGACACATCCTACTTGCCAAA 59.893 45.455 0.00 0.00 46.43 3.28
28 29 1.702401 TGGACACATCCTACTTGCCAA 59.298 47.619 0.00 0.00 46.43 4.52
29 30 1.357137 TGGACACATCCTACTTGCCA 58.643 50.000 0.00 0.00 46.43 4.92
30 31 2.292267 CATGGACACATCCTACTTGCC 58.708 52.381 0.00 0.00 46.43 4.52
31 32 2.939103 GACATGGACACATCCTACTTGC 59.061 50.000 0.00 0.00 46.43 4.01
32 33 4.206477 TGACATGGACACATCCTACTTG 57.794 45.455 0.00 0.00 46.43 3.16
33 34 4.908601 TTGACATGGACACATCCTACTT 57.091 40.909 0.00 0.00 46.43 2.24
34 35 4.908601 TTTGACATGGACACATCCTACT 57.091 40.909 0.00 0.00 46.43 2.57
35 36 5.245531 TCTTTTGACATGGACACATCCTAC 58.754 41.667 0.00 0.00 46.43 3.18
36 37 5.497464 TCTTTTGACATGGACACATCCTA 57.503 39.130 0.00 0.00 46.43 2.94
37 38 4.371624 TCTTTTGACATGGACACATCCT 57.628 40.909 0.00 0.00 46.43 3.24
38 39 4.278170 TGTTCTTTTGACATGGACACATCC 59.722 41.667 0.00 0.00 46.48 3.51
39 40 5.009010 ACTGTTCTTTTGACATGGACACATC 59.991 40.000 0.00 0.00 34.35 3.06
40 41 4.889409 ACTGTTCTTTTGACATGGACACAT 59.111 37.500 0.00 0.00 37.99 3.21
41 42 4.096231 CACTGTTCTTTTGACATGGACACA 59.904 41.667 0.00 0.00 0.00 3.72
42 43 4.335315 TCACTGTTCTTTTGACATGGACAC 59.665 41.667 0.00 0.00 0.00 3.67
43 44 4.522114 TCACTGTTCTTTTGACATGGACA 58.478 39.130 0.00 0.00 0.00 4.02
44 45 5.499139 TTCACTGTTCTTTTGACATGGAC 57.501 39.130 0.00 0.00 0.00 4.02
45 46 5.827267 TCATTCACTGTTCTTTTGACATGGA 59.173 36.000 0.00 0.00 0.00 3.41
46 47 6.075762 TCATTCACTGTTCTTTTGACATGG 57.924 37.500 0.00 0.00 0.00 3.66
47 48 6.418819 GGTTCATTCACTGTTCTTTTGACATG 59.581 38.462 0.00 0.00 0.00 3.21
48 49 6.461509 GGGTTCATTCACTGTTCTTTTGACAT 60.462 38.462 0.00 0.00 0.00 3.06
49 50 5.163561 GGGTTCATTCACTGTTCTTTTGACA 60.164 40.000 0.00 0.00 0.00 3.58
50 51 5.281727 GGGTTCATTCACTGTTCTTTTGAC 58.718 41.667 0.00 0.00 0.00 3.18
51 52 4.340950 GGGGTTCATTCACTGTTCTTTTGA 59.659 41.667 0.00 0.00 0.00 2.69
52 53 4.620982 GGGGTTCATTCACTGTTCTTTTG 58.379 43.478 0.00 0.00 0.00 2.44
53 54 3.317993 CGGGGTTCATTCACTGTTCTTTT 59.682 43.478 0.00 0.00 0.00 2.27
54 55 2.884639 CGGGGTTCATTCACTGTTCTTT 59.115 45.455 0.00 0.00 0.00 2.52
55 56 2.504367 CGGGGTTCATTCACTGTTCTT 58.496 47.619 0.00 0.00 0.00 2.52
56 57 1.882352 GCGGGGTTCATTCACTGTTCT 60.882 52.381 0.00 0.00 0.00 3.01
57 58 0.521735 GCGGGGTTCATTCACTGTTC 59.478 55.000 0.00 0.00 0.00 3.18
58 59 0.179004 TGCGGGGTTCATTCACTGTT 60.179 50.000 0.00 0.00 0.00 3.16
59 60 0.179004 TTGCGGGGTTCATTCACTGT 60.179 50.000 0.00 0.00 0.00 3.55
60 61 0.958091 TTTGCGGGGTTCATTCACTG 59.042 50.000 0.00 0.00 0.00 3.66
61 62 1.698506 TTTTGCGGGGTTCATTCACT 58.301 45.000 0.00 0.00 0.00 3.41
62 63 2.517650 TTTTTGCGGGGTTCATTCAC 57.482 45.000 0.00 0.00 0.00 3.18
85 86 8.818057 CGTCGAGAGGATTTTTATCATAGTTTT 58.182 33.333 0.00 0.00 0.00 2.43
86 87 7.042658 GCGTCGAGAGGATTTTTATCATAGTTT 60.043 37.037 0.00 0.00 0.00 2.66
87 88 6.421202 GCGTCGAGAGGATTTTTATCATAGTT 59.579 38.462 0.00 0.00 0.00 2.24
88 89 5.921408 GCGTCGAGAGGATTTTTATCATAGT 59.079 40.000 0.00 0.00 0.00 2.12
89 90 6.088749 CAGCGTCGAGAGGATTTTTATCATAG 59.911 42.308 0.00 0.00 0.00 2.23
90 91 5.920840 CAGCGTCGAGAGGATTTTTATCATA 59.079 40.000 0.00 0.00 0.00 2.15
91 92 4.747108 CAGCGTCGAGAGGATTTTTATCAT 59.253 41.667 0.00 0.00 0.00 2.45
92 93 4.112634 CAGCGTCGAGAGGATTTTTATCA 58.887 43.478 0.00 0.00 0.00 2.15
93 94 3.060205 GCAGCGTCGAGAGGATTTTTATC 60.060 47.826 0.00 0.00 0.00 1.75
94 95 2.866762 GCAGCGTCGAGAGGATTTTTAT 59.133 45.455 0.00 0.00 0.00 1.40
95 96 2.268298 GCAGCGTCGAGAGGATTTTTA 58.732 47.619 0.00 0.00 0.00 1.52
96 97 1.079503 GCAGCGTCGAGAGGATTTTT 58.920 50.000 0.00 0.00 0.00 1.94
97 98 0.037326 TGCAGCGTCGAGAGGATTTT 60.037 50.000 0.00 0.00 0.00 1.82
98 99 0.037326 TTGCAGCGTCGAGAGGATTT 60.037 50.000 0.00 0.00 0.00 2.17
99 100 0.037326 TTTGCAGCGTCGAGAGGATT 60.037 50.000 0.00 0.00 0.00 3.01
100 101 0.037326 TTTTGCAGCGTCGAGAGGAT 60.037 50.000 0.00 0.00 0.00 3.24
101 102 0.944311 GTTTTGCAGCGTCGAGAGGA 60.944 55.000 0.00 0.00 0.00 3.71
102 103 1.493311 GTTTTGCAGCGTCGAGAGG 59.507 57.895 0.00 0.00 0.00 3.69
103 104 1.128611 CGTTTTGCAGCGTCGAGAG 59.871 57.895 0.00 0.00 0.00 3.20
104 105 2.307309 CCGTTTTGCAGCGTCGAGA 61.307 57.895 0.00 0.00 0.00 4.04
105 106 1.626654 ATCCGTTTTGCAGCGTCGAG 61.627 55.000 0.00 0.00 0.00 4.04
106 107 0.388778 TATCCGTTTTGCAGCGTCGA 60.389 50.000 0.00 0.00 0.00 4.20
107 108 0.247145 GTATCCGTTTTGCAGCGTCG 60.247 55.000 6.64 0.00 0.00 5.12
108 109 0.793861 TGTATCCGTTTTGCAGCGTC 59.206 50.000 6.64 0.00 0.00 5.19
109 110 0.515564 GTGTATCCGTTTTGCAGCGT 59.484 50.000 6.64 0.00 0.00 5.07
110 111 0.518355 CGTGTATCCGTTTTGCAGCG 60.518 55.000 0.00 0.00 0.00 5.18
111 112 0.793861 TCGTGTATCCGTTTTGCAGC 59.206 50.000 0.00 0.00 0.00 5.25
112 113 2.333926 TCTCGTGTATCCGTTTTGCAG 58.666 47.619 0.00 0.00 0.00 4.41
113 114 2.442212 TCTCGTGTATCCGTTTTGCA 57.558 45.000 0.00 0.00 0.00 4.08
114 115 3.799137 TTTCTCGTGTATCCGTTTTGC 57.201 42.857 0.00 0.00 0.00 3.68
134 135 4.127171 TGCAGCGAGTAGTTTCTCTTTTT 58.873 39.130 0.00 0.00 32.83 1.94
135 136 3.728845 TGCAGCGAGTAGTTTCTCTTTT 58.271 40.909 0.00 0.00 32.83 2.27
136 137 3.386768 TGCAGCGAGTAGTTTCTCTTT 57.613 42.857 0.00 0.00 32.83 2.52
137 138 3.386768 TTGCAGCGAGTAGTTTCTCTT 57.613 42.857 0.00 0.00 32.83 2.85
138 139 3.516615 GATTGCAGCGAGTAGTTTCTCT 58.483 45.455 0.00 0.00 32.83 3.10
139 140 2.280183 CGATTGCAGCGAGTAGTTTCTC 59.720 50.000 5.23 0.00 0.00 2.87
140 141 2.263077 CGATTGCAGCGAGTAGTTTCT 58.737 47.619 5.23 0.00 0.00 2.52
141 142 1.267087 GCGATTGCAGCGAGTAGTTTC 60.267 52.381 14.18 0.00 42.15 2.78
142 143 0.721718 GCGATTGCAGCGAGTAGTTT 59.278 50.000 14.18 0.00 42.15 2.66
143 144 1.084370 GGCGATTGCAGCGAGTAGTT 61.084 55.000 14.18 0.00 45.35 2.24
144 145 1.519455 GGCGATTGCAGCGAGTAGT 60.519 57.895 14.18 0.00 45.35 2.73
145 146 2.580470 CGGCGATTGCAGCGAGTAG 61.580 63.158 14.18 0.00 45.35 2.57
146 147 2.582226 CGGCGATTGCAGCGAGTA 60.582 61.111 14.18 0.00 45.35 2.59
147 148 4.742201 ACGGCGATTGCAGCGAGT 62.742 61.111 16.62 10.01 45.35 4.18
148 149 3.490759 AACGGCGATTGCAGCGAG 61.491 61.111 16.62 9.47 45.35 5.03
149 150 3.787676 CAACGGCGATTGCAGCGA 61.788 61.111 16.62 0.00 45.35 4.93
494 495 2.695666 TCCTCCGGCAATCTTCTTCTAG 59.304 50.000 0.00 0.00 0.00 2.43
495 496 2.695666 CTCCTCCGGCAATCTTCTTCTA 59.304 50.000 0.00 0.00 0.00 2.10
496 497 1.484240 CTCCTCCGGCAATCTTCTTCT 59.516 52.381 0.00 0.00 0.00 2.85
497 498 1.946745 CTCCTCCGGCAATCTTCTTC 58.053 55.000 0.00 0.00 0.00 2.87
498 499 0.107459 GCTCCTCCGGCAATCTTCTT 60.107 55.000 0.00 0.00 0.00 2.52
499 500 0.980231 AGCTCCTCCGGCAATCTTCT 60.980 55.000 0.00 0.00 0.00 2.85
500 501 0.813210 CAGCTCCTCCGGCAATCTTC 60.813 60.000 0.00 0.00 0.00 2.87
501 502 1.222936 CAGCTCCTCCGGCAATCTT 59.777 57.895 0.00 0.00 0.00 2.40
502 503 2.739996 CCAGCTCCTCCGGCAATCT 61.740 63.158 0.00 0.00 0.00 2.40
517 518 0.464452 GAGTACCCAATCCGACCCAG 59.536 60.000 0.00 0.00 0.00 4.45
527 528 2.673258 TGTCAGACTGTGAGTACCCAA 58.327 47.619 1.59 0.00 35.13 4.12
536 537 0.612229 AGCTCCCATGTCAGACTGTG 59.388 55.000 1.59 1.06 0.00 3.66
560 561 8.398665 GCGTATCTAAGTTTTCCTGATGAAATT 58.601 33.333 0.00 0.00 42.38 1.82
562 563 7.103641 AGCGTATCTAAGTTTTCCTGATGAAA 58.896 34.615 0.00 0.00 41.18 2.69
567 568 6.032956 TGAAGCGTATCTAAGTTTTCCTGA 57.967 37.500 0.00 0.00 0.00 3.86
568 569 6.910536 ATGAAGCGTATCTAAGTTTTCCTG 57.089 37.500 0.00 0.00 0.00 3.86
569 570 6.879458 ACAATGAAGCGTATCTAAGTTTTCCT 59.121 34.615 0.00 0.00 0.00 3.36
570 571 6.961554 CACAATGAAGCGTATCTAAGTTTTCC 59.038 38.462 0.00 0.00 0.00 3.13
571 572 7.739295 TCACAATGAAGCGTATCTAAGTTTTC 58.261 34.615 0.00 0.00 0.00 2.29
573 574 7.667043 TTCACAATGAAGCGTATCTAAGTTT 57.333 32.000 0.00 0.00 31.83 2.66
574 575 7.624344 GCTTTCACAATGAAGCGTATCTAAGTT 60.624 37.037 0.00 0.00 37.70 2.66
575 576 6.183360 GCTTTCACAATGAAGCGTATCTAAGT 60.183 38.462 0.00 0.00 37.70 2.24
576 577 6.036517 AGCTTTCACAATGAAGCGTATCTAAG 59.963 38.462 2.82 0.00 37.70 2.18
578 579 5.291858 CAGCTTTCACAATGAAGCGTATCTA 59.708 40.000 2.82 0.00 37.70 1.98
581 582 3.753272 ACAGCTTTCACAATGAAGCGTAT 59.247 39.130 2.82 0.00 37.70 3.06
593 611 6.252228 GCTTAATTTAGCATCACAGCTTTCAC 59.748 38.462 11.44 0.00 43.70 3.18
663 682 6.153340 CAGAGCATGGAAGGAATTAGGAAAAA 59.847 38.462 0.00 0.00 0.00 1.94
664 683 5.653769 CAGAGCATGGAAGGAATTAGGAAAA 59.346 40.000 0.00 0.00 0.00 2.29
669 688 4.201990 GCAACAGAGCATGGAAGGAATTAG 60.202 45.833 0.00 0.00 0.00 1.73
680 699 1.241165 TGGACTTGCAACAGAGCATG 58.759 50.000 0.00 0.00 45.19 4.06
685 704 2.653726 ACACAATGGACTTGCAACAGA 58.346 42.857 0.00 0.00 38.50 3.41
686 705 3.441496 AACACAATGGACTTGCAACAG 57.559 42.857 0.00 0.00 38.50 3.16
687 706 3.883830 AAACACAATGGACTTGCAACA 57.116 38.095 0.00 0.00 38.50 3.33
688 707 3.309410 CCAAAACACAATGGACTTGCAAC 59.691 43.478 0.00 0.00 39.12 4.17
689 708 3.196469 TCCAAAACACAATGGACTTGCAA 59.804 39.130 0.00 0.00 40.74 4.08
690 709 2.762887 TCCAAAACACAATGGACTTGCA 59.237 40.909 0.00 0.00 40.74 4.08
691 710 3.451141 TCCAAAACACAATGGACTTGC 57.549 42.857 0.00 0.00 40.74 4.01
697 716 3.256383 TGAGCAGATCCAAAACACAATGG 59.744 43.478 0.00 0.00 38.09 3.16
698 717 4.508461 TGAGCAGATCCAAAACACAATG 57.492 40.909 0.00 0.00 0.00 2.82
699 718 5.733620 AATGAGCAGATCCAAAACACAAT 57.266 34.783 0.00 0.00 0.00 2.71
700 719 5.302568 AGAAATGAGCAGATCCAAAACACAA 59.697 36.000 0.00 0.00 0.00 3.33
701 720 4.828939 AGAAATGAGCAGATCCAAAACACA 59.171 37.500 0.00 0.00 0.00 3.72
702 721 5.382618 AGAAATGAGCAGATCCAAAACAC 57.617 39.130 0.00 0.00 0.00 3.32
703 722 5.535783 TCAAGAAATGAGCAGATCCAAAACA 59.464 36.000 0.00 0.00 33.04 2.83
704 723 6.017400 TCAAGAAATGAGCAGATCCAAAAC 57.983 37.500 0.00 0.00 33.04 2.43
741 760 7.526142 AAAATGAGGGAGGAAAACTTAACTC 57.474 36.000 0.00 0.00 0.00 3.01
912 1706 5.310857 AGAAAACTGTCTCCTGTTAAGGGAT 59.689 40.000 0.00 0.00 44.62 3.85
930 1729 8.339714 TGTACTTTGTATGCAGTTGTAGAAAAC 58.660 33.333 0.00 0.00 0.00 2.43
931 1730 8.439993 TGTACTTTGTATGCAGTTGTAGAAAA 57.560 30.769 0.00 0.00 0.00 2.29
932 1731 8.439993 TTGTACTTTGTATGCAGTTGTAGAAA 57.560 30.769 0.00 0.00 0.00 2.52
947 1747 8.700973 ACCTTTTATTCCATGTTTGTACTTTGT 58.299 29.630 0.00 0.00 0.00 2.83
948 1748 9.541143 AACCTTTTATTCCATGTTTGTACTTTG 57.459 29.630 0.00 0.00 0.00 2.77
949 1749 9.758651 GAACCTTTTATTCCATGTTTGTACTTT 57.241 29.630 0.00 0.00 0.00 2.66
951 1751 8.706322 AGAACCTTTTATTCCATGTTTGTACT 57.294 30.769 0.00 0.00 0.00 2.73
965 1775 9.082313 CCCTGCAATAATGATAGAACCTTTTAT 57.918 33.333 0.00 0.00 0.00 1.40
971 1781 5.049405 CGAACCCTGCAATAATGATAGAACC 60.049 44.000 0.00 0.00 0.00 3.62
972 1782 5.758296 TCGAACCCTGCAATAATGATAGAAC 59.242 40.000 0.00 0.00 0.00 3.01
995 1806 2.287069 GCAGCTGCAGACATCATGATTC 60.287 50.000 33.36 7.53 41.59 2.52
1029 1840 1.078918 TGCTGATGAGAAGCCACCG 60.079 57.895 0.00 0.00 40.06 4.94
1035 1846 3.808726 GCTGGATAACTGCTGATGAGAAG 59.191 47.826 0.00 0.00 40.50 2.85
1268 2079 4.576463 GGACAATGTCTTGACAGTCAAACT 59.424 41.667 16.85 3.47 35.73 2.66
1287 2098 1.667830 CTTGCGCTTTCCGAGGACA 60.668 57.895 9.73 0.00 40.02 4.02
3450 4282 3.270027 CTTCACCGATGGCAAGTTATCA 58.730 45.455 0.00 0.00 0.00 2.15
4450 5295 5.515797 AAGCATGCTTACAGAGATACGTA 57.484 39.130 31.09 0.00 34.05 3.57
4451 5296 4.392921 AAGCATGCTTACAGAGATACGT 57.607 40.909 31.09 2.10 34.05 3.57
4452 5297 5.046529 AGAAAGCATGCTTACAGAGATACG 58.953 41.667 32.12 0.00 34.84 3.06
4453 5298 5.277250 GCAGAAAGCATGCTTACAGAGATAC 60.277 44.000 32.12 14.40 44.79 2.24
4511 5358 4.878397 GTGGTTCTGTAATGGATCCTCTTG 59.122 45.833 14.23 0.00 0.00 3.02
4649 5557 4.832266 ACCTAGACCAATCAACAATTTGCA 59.168 37.500 0.00 0.00 32.17 4.08
4650 5558 5.163513 CACCTAGACCAATCAACAATTTGC 58.836 41.667 0.00 0.00 32.17 3.68
4652 5560 6.549364 TCAACACCTAGACCAATCAACAATTT 59.451 34.615 0.00 0.00 0.00 1.82
4653 5561 6.068010 TCAACACCTAGACCAATCAACAATT 58.932 36.000 0.00 0.00 0.00 2.32
4654 5562 5.630121 TCAACACCTAGACCAATCAACAAT 58.370 37.500 0.00 0.00 0.00 2.71
4656 5564 4.698201 TCAACACCTAGACCAATCAACA 57.302 40.909 0.00 0.00 0.00 3.33
4660 5568 6.407202 ACTGTAATCAACACCTAGACCAATC 58.593 40.000 0.00 0.00 33.45 2.67
4661 5569 6.374417 ACTGTAATCAACACCTAGACCAAT 57.626 37.500 0.00 0.00 33.45 3.16
4663 5571 6.014647 AGTACTGTAATCAACACCTAGACCA 58.985 40.000 0.00 0.00 33.45 4.02
4664 5572 6.527057 AGTACTGTAATCAACACCTAGACC 57.473 41.667 0.00 0.00 33.45 3.85
4795 5784 1.463444 GTGCCACTGTTCGTTCATACC 59.537 52.381 0.00 0.00 0.00 2.73
4957 6036 3.052455 TGGAGCAAACGATCTTTAGCA 57.948 42.857 0.00 0.00 0.00 3.49
4984 6076 0.535780 CATGCACCATATCTGCGGGT 60.536 55.000 0.00 0.00 37.46 5.28
5180 6272 1.067495 CAGAAGACCGGAACAGAGTCC 60.067 57.143 9.46 0.00 0.00 3.85
5181 6273 1.614413 ACAGAAGACCGGAACAGAGTC 59.386 52.381 9.46 0.00 0.00 3.36
5182 6274 1.341531 CACAGAAGACCGGAACAGAGT 59.658 52.381 9.46 0.00 0.00 3.24
5183 6275 1.341531 ACACAGAAGACCGGAACAGAG 59.658 52.381 9.46 0.00 0.00 3.35
5184 6276 1.410004 ACACAGAAGACCGGAACAGA 58.590 50.000 9.46 0.00 0.00 3.41
5185 6277 1.867233 CAACACAGAAGACCGGAACAG 59.133 52.381 9.46 0.00 0.00 3.16
5186 6278 1.948104 CAACACAGAAGACCGGAACA 58.052 50.000 9.46 0.00 0.00 3.18
5187 6279 0.586802 GCAACACAGAAGACCGGAAC 59.413 55.000 9.46 0.99 0.00 3.62
5188 6280 0.468226 AGCAACACAGAAGACCGGAA 59.532 50.000 9.46 0.00 0.00 4.30
5189 6281 0.249868 CAGCAACACAGAAGACCGGA 60.250 55.000 9.46 0.00 0.00 5.14
5190 6282 0.532862 ACAGCAACACAGAAGACCGG 60.533 55.000 0.00 0.00 0.00 5.28
5191 6283 1.003545 CAACAGCAACACAGAAGACCG 60.004 52.381 0.00 0.00 0.00 4.79
5192 6284 1.334869 CCAACAGCAACACAGAAGACC 59.665 52.381 0.00 0.00 0.00 3.85
5193 6285 1.334869 CCCAACAGCAACACAGAAGAC 59.665 52.381 0.00 0.00 0.00 3.01
5194 6286 1.679139 CCCAACAGCAACACAGAAGA 58.321 50.000 0.00 0.00 0.00 2.87
5195 6287 0.031178 GCCCAACAGCAACACAGAAG 59.969 55.000 0.00 0.00 0.00 2.85
5196 6288 0.395586 AGCCCAACAGCAACACAGAA 60.396 50.000 0.00 0.00 34.23 3.02
5197 6289 0.819259 GAGCCCAACAGCAACACAGA 60.819 55.000 0.00 0.00 34.23 3.41
5198 6290 0.820891 AGAGCCCAACAGCAACACAG 60.821 55.000 0.00 0.00 34.23 3.66
5199 6291 0.819259 GAGAGCCCAACAGCAACACA 60.819 55.000 0.00 0.00 34.23 3.72
5200 6292 1.845809 CGAGAGCCCAACAGCAACAC 61.846 60.000 0.00 0.00 34.23 3.32
5201 6293 1.597854 CGAGAGCCCAACAGCAACA 60.598 57.895 0.00 0.00 34.23 3.33
5202 6294 2.328099 CCGAGAGCCCAACAGCAAC 61.328 63.158 0.00 0.00 34.23 4.17
5203 6295 2.032528 CCGAGAGCCCAACAGCAA 59.967 61.111 0.00 0.00 34.23 3.91
5204 6296 2.922503 TCCGAGAGCCCAACAGCA 60.923 61.111 0.00 0.00 34.23 4.41
5205 6297 2.435059 GTCCGAGAGCCCAACAGC 60.435 66.667 0.00 0.00 0.00 4.40
5206 6298 1.216710 GAGTCCGAGAGCCCAACAG 59.783 63.158 0.00 0.00 0.00 3.16
5207 6299 2.283529 GGAGTCCGAGAGCCCAACA 61.284 63.158 0.00 0.00 0.00 3.33
5208 6300 2.579738 GGAGTCCGAGAGCCCAAC 59.420 66.667 0.00 0.00 0.00 3.77
5310 6422 2.622942 GCCTGACAGTGTTCCATTTTCA 59.377 45.455 0.00 0.00 0.00 2.69


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

AutoCloner maintained by Alex Coulton.