Multiple sequence alignment - TraesCS2D01G315900

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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 TraesCS2D01G315900 chr2D 100.000 3203 0 0 1 3203 405401855 405398653 0.000000e+00 5915.0
1 TraesCS2D01G315900 chr2D 90.236 635 42 11 2588 3203 633084608 633085241 0.000000e+00 811.0
2 TraesCS2D01G315900 chr2D 91.544 544 28 8 2677 3203 476357711 476358253 0.000000e+00 734.0
3 TraesCS2D01G315900 chr2B 94.396 1499 62 15 851 2346 480809601 480808122 0.000000e+00 2283.0
4 TraesCS2D01G315900 chr2B 87.709 659 33 21 202 822 480810229 480809581 0.000000e+00 725.0
5 TraesCS2D01G315900 chr2B 93.074 231 16 0 2358 2588 480807960 480807730 3.960000e-89 339.0
6 TraesCS2D01G315900 chr2B 80.546 293 46 10 2587 2875 672572101 672572386 6.960000e-52 215.0
7 TraesCS2D01G315900 chr2B 88.235 85 5 2 2445 2524 87536412 87536328 2.630000e-16 97.1
8 TraesCS2D01G315900 chr2A 93.704 1509 66 10 1084 2588 543348670 543347187 0.000000e+00 2233.0
9 TraesCS2D01G315900 chr2A 85.144 626 78 10 2588 3203 680349894 680350514 7.540000e-176 627.0
10 TraesCS2D01G315900 chr2A 89.931 437 8 10 642 1061 543349481 543349064 6.080000e-147 531.0
11 TraesCS2D01G315900 chr2A 87.665 454 35 11 211 645 543351561 543351110 2.850000e-140 508.0
12 TraesCS2D01G315900 chr2A 88.235 85 5 2 2445 2524 664884471 664884387 2.630000e-16 97.1
13 TraesCS2D01G315900 chr5D 93.171 615 38 4 2590 3202 249908406 249909018 0.000000e+00 900.0
14 TraesCS2D01G315900 chr5D 78.967 271 45 10 1453 1722 361650879 361650620 1.180000e-39 174.0
15 TraesCS2D01G315900 chr6D 91.311 633 36 7 2590 3203 101227906 101227274 0.000000e+00 846.0
16 TraesCS2D01G315900 chr4D 91.209 637 35 8 2585 3203 505324659 505324026 0.000000e+00 846.0
17 TraesCS2D01G315900 chr7D 88.715 638 54 10 2583 3203 365395452 365394816 0.000000e+00 763.0
18 TraesCS2D01G315900 chr7D 87.649 251 28 2 1475 1722 575536343 575536593 4.040000e-74 289.0
19 TraesCS2D01G315900 chrUn 91.569 510 33 6 2588 3088 132105350 132104842 0.000000e+00 695.0
20 TraesCS2D01G315900 chr7A 86.721 610 50 15 2612 3203 574751060 574751656 0.000000e+00 649.0
21 TraesCS2D01G315900 chr7A 88.095 252 25 3 1475 1722 665772981 665773231 8.690000e-76 294.0
22 TraesCS2D01G315900 chr7A 88.235 85 5 2 2445 2524 735869705 735869621 2.630000e-16 97.1
23 TraesCS2D01G315900 chr3A 85.603 639 61 22 2590 3203 80626643 80626011 2.690000e-180 641.0
24 TraesCS2D01G315900 chr7B 86.345 249 29 3 1475 1719 637338261 637338508 1.890000e-67 267.0
25 TraesCS2D01G315900 chr7B 77.644 331 52 16 2590 2902 720485851 720486177 7.060000e-42 182.0
26 TraesCS2D01G315900 chr5B 79.336 271 45 9 1453 1722 427248949 427248689 2.540000e-41 180.0
27 TraesCS2D01G315900 chr5B 88.235 85 5 2 2445 2524 609836428 609836512 2.630000e-16 97.1
28 TraesCS2D01G315900 chr5A 78.788 264 45 9 1460 1722 462155871 462155618 1.980000e-37 167.0
29 TraesCS2D01G315900 chr5A 88.235 85 5 2 2445 2524 150804771 150804687 2.630000e-16 97.1
30 TraesCS2D01G315900 chr4A 88.235 85 5 2 2445 2524 619952815 619952731 2.630000e-16 97.1
31 TraesCS2D01G315900 chr1D 93.750 64 4 0 4 67 470517897 470517834 2.630000e-16 97.1
32 TraesCS2D01G315900 chr1D 96.875 32 1 0 85 116 470517831 470517800 2.000000e-03 54.7
33 TraesCS2D01G315900 chr1B 88.235 85 5 2 2445 2524 43280435 43280519 2.630000e-16 97.1
34 TraesCS2D01G315900 chr1B 93.651 63 4 0 2462 2524 297182999 297182937 9.460000e-16 95.3


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 TraesCS2D01G315900 chr2D 405398653 405401855 3202 True 5915.000000 5915 100.000000 1 3203 1 chr2D.!!$R1 3202
1 TraesCS2D01G315900 chr2D 633084608 633085241 633 False 811.000000 811 90.236000 2588 3203 1 chr2D.!!$F2 615
2 TraesCS2D01G315900 chr2D 476357711 476358253 542 False 734.000000 734 91.544000 2677 3203 1 chr2D.!!$F1 526
3 TraesCS2D01G315900 chr2B 480807730 480810229 2499 True 1115.666667 2283 91.726333 202 2588 3 chr2B.!!$R2 2386
4 TraesCS2D01G315900 chr2A 543347187 543351561 4374 True 1090.666667 2233 90.433333 211 2588 3 chr2A.!!$R2 2377
5 TraesCS2D01G315900 chr2A 680349894 680350514 620 False 627.000000 627 85.144000 2588 3203 1 chr2A.!!$F1 615
6 TraesCS2D01G315900 chr5D 249908406 249909018 612 False 900.000000 900 93.171000 2590 3202 1 chr5D.!!$F1 612
7 TraesCS2D01G315900 chr6D 101227274 101227906 632 True 846.000000 846 91.311000 2590 3203 1 chr6D.!!$R1 613
8 TraesCS2D01G315900 chr4D 505324026 505324659 633 True 846.000000 846 91.209000 2585 3203 1 chr4D.!!$R1 618
9 TraesCS2D01G315900 chr7D 365394816 365395452 636 True 763.000000 763 88.715000 2583 3203 1 chr7D.!!$R1 620
10 TraesCS2D01G315900 chrUn 132104842 132105350 508 True 695.000000 695 91.569000 2588 3088 1 chrUn.!!$R1 500
11 TraesCS2D01G315900 chr7A 574751060 574751656 596 False 649.000000 649 86.721000 2612 3203 1 chr7A.!!$F1 591
12 TraesCS2D01G315900 chr3A 80626011 80626643 632 True 641.000000 641 85.603000 2590 3203 1 chr3A.!!$R1 613

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
84 85 0.035739 TCCTCCCGTTCTTTTTCCCG 59.964 55.0 0.00 0.00 0.0 5.14 F
151 152 0.040058 TGGCTAGACTAACCCCACGA 59.960 55.0 0.00 0.00 0.0 4.35 F
474 479 0.109132 GCAAAATGGAGCTCGGTTGG 60.109 55.0 7.83 0.21 0.0 3.77 F
786 2459 0.693622 TCCACTTATCCCGTTTGCCA 59.306 50.0 0.00 0.00 0.0 4.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1236 3335 0.193574 AAGTTCCTCCTCCCTGGTCA 59.806 55.0 0.00 0.00 37.07 4.02 R
1773 3881 0.321387 CATCTGGATCAGCCGATGGG 60.321 60.0 6.03 0.00 40.67 4.00 R
1774 3882 0.395686 ACATCTGGATCAGCCGATGG 59.604 55.0 15.24 2.07 44.61 3.51 R
2481 4743 0.387750 GCAAAGAAAAGAGCAGCCGG 60.388 55.0 0.00 0.00 0.00 6.13 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
25 26 1.920610 AGCCTTGCTGCTTCATTTCT 58.079 45.000 0.00 0.00 38.85 2.52
26 27 2.245582 AGCCTTGCTGCTTCATTTCTT 58.754 42.857 0.00 0.00 38.85 2.52
27 28 2.230750 AGCCTTGCTGCTTCATTTCTTC 59.769 45.455 0.00 0.00 38.85 2.87
28 29 2.230750 GCCTTGCTGCTTCATTTCTTCT 59.769 45.455 0.00 0.00 0.00 2.85
29 30 3.305881 GCCTTGCTGCTTCATTTCTTCTT 60.306 43.478 0.00 0.00 0.00 2.52
30 31 4.483311 CCTTGCTGCTTCATTTCTTCTTC 58.517 43.478 0.00 0.00 0.00 2.87
31 32 4.022589 CCTTGCTGCTTCATTTCTTCTTCA 60.023 41.667 0.00 0.00 0.00 3.02
32 33 5.508489 CCTTGCTGCTTCATTTCTTCTTCAA 60.508 40.000 0.00 0.00 0.00 2.69
33 34 5.717078 TGCTGCTTCATTTCTTCTTCAAT 57.283 34.783 0.00 0.00 0.00 2.57
34 35 5.706916 TGCTGCTTCATTTCTTCTTCAATC 58.293 37.500 0.00 0.00 0.00 2.67
35 36 5.242171 TGCTGCTTCATTTCTTCTTCAATCA 59.758 36.000 0.00 0.00 0.00 2.57
36 37 6.071560 TGCTGCTTCATTTCTTCTTCAATCAT 60.072 34.615 0.00 0.00 0.00 2.45
37 38 6.253727 GCTGCTTCATTTCTTCTTCAATCATG 59.746 38.462 0.00 0.00 0.00 3.07
38 39 7.223260 TGCTTCATTTCTTCTTCAATCATGT 57.777 32.000 0.00 0.00 0.00 3.21
39 40 7.088272 TGCTTCATTTCTTCTTCAATCATGTG 58.912 34.615 0.00 0.00 0.00 3.21
40 41 6.530534 GCTTCATTTCTTCTTCAATCATGTGG 59.469 38.462 0.00 0.00 0.00 4.17
41 42 5.957798 TCATTTCTTCTTCAATCATGTGGC 58.042 37.500 0.00 0.00 0.00 5.01
42 43 4.789012 TTTCTTCTTCAATCATGTGGCC 57.211 40.909 0.00 0.00 0.00 5.36
43 44 2.358957 TCTTCTTCAATCATGTGGCCG 58.641 47.619 0.00 0.00 0.00 6.13
44 45 2.027285 TCTTCTTCAATCATGTGGCCGA 60.027 45.455 0.00 0.00 0.00 5.54
45 46 1.737838 TCTTCAATCATGTGGCCGAC 58.262 50.000 0.00 0.00 0.00 4.79
46 47 0.374758 CTTCAATCATGTGGCCGACG 59.625 55.000 0.00 0.00 0.00 5.12
47 48 1.024046 TTCAATCATGTGGCCGACGG 61.024 55.000 10.29 10.29 0.00 4.79
48 49 2.124736 AATCATGTGGCCGACGGG 60.125 61.111 17.22 0.00 0.00 5.28
49 50 3.697439 AATCATGTGGCCGACGGGG 62.697 63.158 17.22 0.00 39.58 5.73
54 55 4.404098 GTGGCCGACGGGGTGAAT 62.404 66.667 17.22 0.00 38.44 2.57
55 56 3.642503 TGGCCGACGGGGTGAATT 61.643 61.111 17.22 0.00 38.44 2.17
56 57 3.131478 GGCCGACGGGGTGAATTG 61.131 66.667 17.22 0.00 38.44 2.32
57 58 3.810896 GCCGACGGGGTGAATTGC 61.811 66.667 17.22 0.00 38.44 3.56
58 59 2.359354 CCGACGGGGTGAATTGCA 60.359 61.111 5.81 0.00 0.00 4.08
59 60 2.686816 CCGACGGGGTGAATTGCAC 61.687 63.158 5.81 0.00 46.98 4.57
67 68 3.092081 GTGAATTGCACGTTGCTCC 57.908 52.632 10.54 0.45 45.31 4.70
68 69 0.593128 GTGAATTGCACGTTGCTCCT 59.407 50.000 10.54 0.00 45.31 3.69
69 70 0.874390 TGAATTGCACGTTGCTCCTC 59.126 50.000 10.54 5.61 45.31 3.71
70 71 0.169009 GAATTGCACGTTGCTCCTCC 59.831 55.000 10.54 0.00 45.31 4.30
71 72 1.244019 AATTGCACGTTGCTCCTCCC 61.244 55.000 10.54 0.00 45.31 4.30
72 73 4.680237 TGCACGTTGCTCCTCCCG 62.680 66.667 10.54 0.00 45.31 5.14
73 74 4.681978 GCACGTTGCTCCTCCCGT 62.682 66.667 0.00 0.00 40.96 5.28
74 75 2.030562 CACGTTGCTCCTCCCGTT 59.969 61.111 0.00 0.00 0.00 4.44
75 76 2.027625 CACGTTGCTCCTCCCGTTC 61.028 63.158 0.00 0.00 0.00 3.95
76 77 2.207924 ACGTTGCTCCTCCCGTTCT 61.208 57.895 0.00 0.00 0.00 3.01
77 78 1.004918 CGTTGCTCCTCCCGTTCTT 60.005 57.895 0.00 0.00 0.00 2.52
78 79 0.602905 CGTTGCTCCTCCCGTTCTTT 60.603 55.000 0.00 0.00 0.00 2.52
79 80 1.605753 GTTGCTCCTCCCGTTCTTTT 58.394 50.000 0.00 0.00 0.00 2.27
80 81 1.954382 GTTGCTCCTCCCGTTCTTTTT 59.046 47.619 0.00 0.00 0.00 1.94
81 82 1.892209 TGCTCCTCCCGTTCTTTTTC 58.108 50.000 0.00 0.00 0.00 2.29
82 83 1.166129 GCTCCTCCCGTTCTTTTTCC 58.834 55.000 0.00 0.00 0.00 3.13
83 84 1.822506 CTCCTCCCGTTCTTTTTCCC 58.177 55.000 0.00 0.00 0.00 3.97
84 85 0.035739 TCCTCCCGTTCTTTTTCCCG 59.964 55.000 0.00 0.00 0.00 5.14
85 86 1.583495 CCTCCCGTTCTTTTTCCCGC 61.583 60.000 0.00 0.00 0.00 6.13
86 87 0.887387 CTCCCGTTCTTTTTCCCGCA 60.887 55.000 0.00 0.00 0.00 5.69
87 88 1.167781 TCCCGTTCTTTTTCCCGCAC 61.168 55.000 0.00 0.00 0.00 5.34
88 89 1.284715 CCGTTCTTTTTCCCGCACC 59.715 57.895 0.00 0.00 0.00 5.01
89 90 1.082366 CGTTCTTTTTCCCGCACCG 60.082 57.895 0.00 0.00 0.00 4.94
90 91 1.500512 CGTTCTTTTTCCCGCACCGA 61.501 55.000 0.00 0.00 0.00 4.69
91 92 0.237498 GTTCTTTTTCCCGCACCGAG 59.763 55.000 0.00 0.00 0.00 4.63
92 93 0.887387 TTCTTTTTCCCGCACCGAGG 60.887 55.000 0.00 0.00 0.00 4.63
93 94 2.978018 CTTTTTCCCGCACCGAGGC 61.978 63.158 0.00 0.00 0.00 4.70
112 113 4.443266 GTCCAGCCGCTCGAGCTT 62.443 66.667 32.88 16.84 38.95 3.74
113 114 4.441695 TCCAGCCGCTCGAGCTTG 62.442 66.667 32.88 25.58 38.95 4.01
114 115 4.441695 CCAGCCGCTCGAGCTTGA 62.442 66.667 32.88 2.99 38.95 3.02
115 116 2.884685 CAGCCGCTCGAGCTTGAG 60.885 66.667 32.88 24.58 38.95 3.02
116 117 3.377759 AGCCGCTCGAGCTTGAGT 61.378 61.111 32.88 11.80 37.24 3.41
117 118 2.883253 GCCGCTCGAGCTTGAGTC 60.883 66.667 32.88 19.85 38.28 3.36
118 119 2.568612 CCGCTCGAGCTTGAGTCA 59.431 61.111 32.88 0.00 38.28 3.41
119 120 1.515952 CCGCTCGAGCTTGAGTCAG 60.516 63.158 32.88 19.83 38.28 3.51
120 121 1.515952 CGCTCGAGCTTGAGTCAGG 60.516 63.158 32.88 12.00 38.28 3.86
121 122 1.153667 GCTCGAGCTTGAGTCAGGG 60.154 63.158 29.88 7.01 38.28 4.45
122 123 1.599606 GCTCGAGCTTGAGTCAGGGA 61.600 60.000 29.88 0.00 38.28 4.20
123 124 0.172352 CTCGAGCTTGAGTCAGGGAC 59.828 60.000 21.27 0.00 0.00 4.46
124 125 1.153939 CGAGCTTGAGTCAGGGACG 60.154 63.158 4.22 1.49 37.67 4.79
125 126 1.867919 CGAGCTTGAGTCAGGGACGT 61.868 60.000 4.22 0.00 37.67 4.34
126 127 0.109039 GAGCTTGAGTCAGGGACGTC 60.109 60.000 7.13 7.13 37.67 4.34
127 128 0.827925 AGCTTGAGTCAGGGACGTCA 60.828 55.000 18.91 0.00 37.67 4.35
128 129 0.247736 GCTTGAGTCAGGGACGTCAT 59.752 55.000 18.91 1.75 37.67 3.06
129 130 2.001812 CTTGAGTCAGGGACGTCATG 57.998 55.000 18.91 15.24 37.67 3.07
130 131 1.273606 CTTGAGTCAGGGACGTCATGT 59.726 52.381 18.91 0.40 37.67 3.21
131 132 2.209690 TGAGTCAGGGACGTCATGTA 57.790 50.000 18.91 3.41 37.67 2.29
132 133 2.735151 TGAGTCAGGGACGTCATGTAT 58.265 47.619 18.91 8.38 37.67 2.29
133 134 2.427095 TGAGTCAGGGACGTCATGTATG 59.573 50.000 18.91 8.00 37.67 2.39
134 135 1.757118 AGTCAGGGACGTCATGTATGG 59.243 52.381 18.91 0.00 37.67 2.74
135 136 0.464036 TCAGGGACGTCATGTATGGC 59.536 55.000 18.91 0.00 0.00 4.40
136 137 0.465705 CAGGGACGTCATGTATGGCT 59.534 55.000 18.91 0.00 0.00 4.75
137 138 1.686587 CAGGGACGTCATGTATGGCTA 59.313 52.381 18.91 0.00 0.00 3.93
138 139 1.964223 AGGGACGTCATGTATGGCTAG 59.036 52.381 18.91 0.00 0.00 3.42
139 140 1.961394 GGGACGTCATGTATGGCTAGA 59.039 52.381 18.91 0.00 0.00 2.43
140 141 2.288273 GGGACGTCATGTATGGCTAGAC 60.288 54.545 18.91 0.00 0.00 2.59
141 142 2.623889 GGACGTCATGTATGGCTAGACT 59.376 50.000 18.91 0.00 0.00 3.24
142 143 3.819337 GGACGTCATGTATGGCTAGACTA 59.181 47.826 18.91 0.00 0.00 2.59
143 144 4.277672 GGACGTCATGTATGGCTAGACTAA 59.722 45.833 18.91 0.00 0.00 2.24
144 145 5.184340 ACGTCATGTATGGCTAGACTAAC 57.816 43.478 0.00 0.00 0.00 2.34
145 146 4.037684 ACGTCATGTATGGCTAGACTAACC 59.962 45.833 0.00 0.00 0.00 2.85
146 147 4.558898 CGTCATGTATGGCTAGACTAACCC 60.559 50.000 0.00 0.00 0.00 4.11
147 148 3.901844 TCATGTATGGCTAGACTAACCCC 59.098 47.826 0.00 0.00 0.00 4.95
148 149 3.408157 TGTATGGCTAGACTAACCCCA 57.592 47.619 0.00 0.00 0.00 4.96
149 150 3.036091 TGTATGGCTAGACTAACCCCAC 58.964 50.000 0.00 0.00 0.00 4.61
150 151 1.120530 ATGGCTAGACTAACCCCACG 58.879 55.000 0.00 0.00 0.00 4.94
151 152 0.040058 TGGCTAGACTAACCCCACGA 59.960 55.000 0.00 0.00 0.00 4.35
152 153 1.342674 TGGCTAGACTAACCCCACGAT 60.343 52.381 0.00 0.00 0.00 3.73
153 154 1.340568 GGCTAGACTAACCCCACGATC 59.659 57.143 0.00 0.00 0.00 3.69
154 155 2.308690 GCTAGACTAACCCCACGATCT 58.691 52.381 0.00 0.00 0.00 2.75
155 156 3.484407 GCTAGACTAACCCCACGATCTA 58.516 50.000 0.00 0.00 0.00 1.98
156 157 4.080687 GCTAGACTAACCCCACGATCTAT 58.919 47.826 0.00 0.00 0.00 1.98
157 158 4.523558 GCTAGACTAACCCCACGATCTATT 59.476 45.833 0.00 0.00 0.00 1.73
158 159 5.335819 GCTAGACTAACCCCACGATCTATTC 60.336 48.000 0.00 0.00 0.00 1.75
159 160 3.896272 AGACTAACCCCACGATCTATTCC 59.104 47.826 0.00 0.00 0.00 3.01
160 161 3.640029 GACTAACCCCACGATCTATTCCA 59.360 47.826 0.00 0.00 0.00 3.53
161 162 3.387050 ACTAACCCCACGATCTATTCCAC 59.613 47.826 0.00 0.00 0.00 4.02
162 163 2.176247 ACCCCACGATCTATTCCACT 57.824 50.000 0.00 0.00 0.00 4.00
163 164 1.762957 ACCCCACGATCTATTCCACTG 59.237 52.381 0.00 0.00 0.00 3.66
164 165 1.762957 CCCCACGATCTATTCCACTGT 59.237 52.381 0.00 0.00 0.00 3.55
165 166 2.963101 CCCCACGATCTATTCCACTGTA 59.037 50.000 0.00 0.00 0.00 2.74
166 167 3.578716 CCCCACGATCTATTCCACTGTAT 59.421 47.826 0.00 0.00 0.00 2.29
167 168 4.560128 CCCACGATCTATTCCACTGTATG 58.440 47.826 0.00 0.00 0.00 2.39
168 169 4.039245 CCCACGATCTATTCCACTGTATGT 59.961 45.833 0.00 0.00 0.00 2.29
169 170 4.984785 CCACGATCTATTCCACTGTATGTG 59.015 45.833 0.00 0.00 45.80 3.21
374 378 3.583086 AGTTTTTAGTGCTAGCCAGAGGA 59.417 43.478 13.29 0.00 0.00 3.71
469 474 1.017387 GGGTAGCAAAATGGAGCTCG 58.983 55.000 7.83 0.00 42.05 5.03
470 475 1.017387 GGTAGCAAAATGGAGCTCGG 58.983 55.000 7.83 0.00 42.05 4.63
471 476 1.679032 GGTAGCAAAATGGAGCTCGGT 60.679 52.381 7.83 0.61 42.05 4.69
473 478 0.883833 AGCAAAATGGAGCTCGGTTG 59.116 50.000 7.83 9.85 36.00 3.77
474 479 0.109132 GCAAAATGGAGCTCGGTTGG 60.109 55.000 7.83 0.21 0.00 3.77
475 480 1.533625 CAAAATGGAGCTCGGTTGGA 58.466 50.000 7.83 0.00 0.00 3.53
476 481 1.470098 CAAAATGGAGCTCGGTTGGAG 59.530 52.381 7.83 0.00 46.06 3.86
477 482 0.984230 AAATGGAGCTCGGTTGGAGA 59.016 50.000 7.83 0.00 46.23 3.71
478 483 0.984230 AATGGAGCTCGGTTGGAGAA 59.016 50.000 7.83 0.00 46.23 2.87
479 484 0.984230 ATGGAGCTCGGTTGGAGAAA 59.016 50.000 7.83 0.00 46.23 2.52
480 485 0.762418 TGGAGCTCGGTTGGAGAAAA 59.238 50.000 7.83 0.00 46.23 2.29
481 486 1.142060 TGGAGCTCGGTTGGAGAAAAA 59.858 47.619 7.83 0.00 46.23 1.94
511 521 3.206964 ACTTCAGATCAGATCGCTCGTA 58.793 45.455 4.67 0.00 0.00 3.43
512 522 3.818210 ACTTCAGATCAGATCGCTCGTAT 59.182 43.478 4.67 0.00 0.00 3.06
514 524 5.645929 ACTTCAGATCAGATCGCTCGTATAT 59.354 40.000 4.67 0.00 0.00 0.86
516 526 6.836577 TCAGATCAGATCGCTCGTATATAG 57.163 41.667 4.67 0.00 0.00 1.31
520 544 7.223777 CAGATCAGATCGCTCGTATATAGAAGA 59.776 40.741 4.67 0.00 0.00 2.87
546 573 1.621814 TGACAAGTAGTACCACCAGCC 59.378 52.381 0.00 0.00 0.00 4.85
579 606 3.883489 CCATCACATCACATCAGCTCATT 59.117 43.478 0.00 0.00 0.00 2.57
666 2325 1.078143 ATTGACGGGAGAGGCAAGC 60.078 57.895 0.00 0.00 0.00 4.01
782 2455 3.352648 CAACCATCCACTTATCCCGTTT 58.647 45.455 0.00 0.00 0.00 3.60
783 2456 2.999331 ACCATCCACTTATCCCGTTTG 58.001 47.619 0.00 0.00 0.00 2.93
784 2457 1.676006 CCATCCACTTATCCCGTTTGC 59.324 52.381 0.00 0.00 0.00 3.68
785 2458 1.676006 CATCCACTTATCCCGTTTGCC 59.324 52.381 0.00 0.00 0.00 4.52
786 2459 0.693622 TCCACTTATCCCGTTTGCCA 59.306 50.000 0.00 0.00 0.00 4.92
787 2460 1.094785 CCACTTATCCCGTTTGCCAG 58.905 55.000 0.00 0.00 0.00 4.85
788 2461 1.339631 CCACTTATCCCGTTTGCCAGA 60.340 52.381 0.00 0.00 0.00 3.86
841 2514 3.462678 GCCTCCCCCAGTCGAGTC 61.463 72.222 0.00 0.00 0.00 3.36
842 2515 3.141488 CCTCCCCCAGTCGAGTCG 61.141 72.222 6.09 6.09 0.00 4.18
843 2516 2.045242 CTCCCCCAGTCGAGTCGA 60.045 66.667 12.09 12.09 0.00 4.20
893 2619 1.616994 CCTCCGCCTCCAAAGGAAAAT 60.617 52.381 0.00 0.00 46.67 1.82
1063 2793 4.028490 CTTGGTACGGCTGCCCCA 62.028 66.667 14.12 12.16 0.00 4.96
1098 3191 1.140134 CCTTCTTCACCCCTTCCCCA 61.140 60.000 0.00 0.00 0.00 4.96
1101 3194 0.919289 TCTTCACCCCTTCCCCATCC 60.919 60.000 0.00 0.00 0.00 3.51
1130 3229 3.983494 CTCTCCGCCGCCGATCAT 61.983 66.667 0.00 0.00 36.29 2.45
1146 3245 0.780637 TCATATCGCCTCCTCCTCCT 59.219 55.000 0.00 0.00 0.00 3.69
1147 3246 1.181786 CATATCGCCTCCTCCTCCTC 58.818 60.000 0.00 0.00 0.00 3.71
1158 3257 1.681486 CTCCTCCTCCTTCGCCTTCC 61.681 65.000 0.00 0.00 0.00 3.46
1179 3278 7.093727 CCTTCCTTTTCTTTCTATTTCCCTTCC 60.094 40.741 0.00 0.00 0.00 3.46
1180 3279 6.253758 TCCTTTTCTTTCTATTTCCCTTCCC 58.746 40.000 0.00 0.00 0.00 3.97
1206 3305 2.125512 CTTGCTCCGTCCCCTTCG 60.126 66.667 0.00 0.00 0.00 3.79
1354 3456 3.610669 CCCTCATCCTCCTCGGCG 61.611 72.222 0.00 0.00 0.00 6.46
1355 3457 4.292178 CCTCATCCTCCTCGGCGC 62.292 72.222 0.00 0.00 0.00 6.53
1765 3873 4.933064 GAGCCGGCATCGAGTCCG 62.933 72.222 31.54 18.02 44.89 4.79
1776 3884 3.677527 GAGTCCGACTCGAACCCA 58.322 61.111 12.74 0.00 35.28 4.51
1777 3885 2.190756 GAGTCCGACTCGAACCCAT 58.809 57.895 12.74 0.00 35.28 4.00
1778 3886 0.100861 GAGTCCGACTCGAACCCATC 59.899 60.000 12.74 0.00 35.28 3.51
1860 3968 1.416813 CGCTGGAGCATGAAGACGAC 61.417 60.000 0.00 0.00 42.21 4.34
1896 4007 2.736995 CCGCGCGTGGAAGAAGAA 60.737 61.111 34.65 0.00 0.00 2.52
1919 4030 2.979676 CGAGCAGCAGCAACCCAA 60.980 61.111 3.17 0.00 45.49 4.12
2013 4124 3.554692 GCGGCGATGGTCTCAACG 61.555 66.667 12.98 0.00 41.24 4.10
2075 4186 3.075005 CGAAGGGGAGGAGCGGAA 61.075 66.667 0.00 0.00 0.00 4.30
2248 4360 7.502226 TGAATTTTGATCCTAGTCGCCAATAAT 59.498 33.333 0.00 0.00 0.00 1.28
2249 4361 6.618287 TTTTGATCCTAGTCGCCAATAATG 57.382 37.500 0.00 0.00 0.00 1.90
2346 4458 1.123038 CGCGAAATGCAGCAAAGAAAC 59.877 47.619 0.00 0.00 46.97 2.78
2354 4616 2.031595 TGCAGCAAAGAAACGCGAAATA 60.032 40.909 15.93 0.00 0.00 1.40
2356 4618 3.001758 GCAGCAAAGAAACGCGAAATATG 60.002 43.478 15.93 5.62 0.00 1.78
2661 4925 2.700773 GGCGCTGAAAAATCGGCCT 61.701 57.895 7.64 0.00 41.93 5.19
2666 4930 2.356135 GCTGAAAAATCGGCCTAGTCA 58.644 47.619 0.00 0.00 36.06 3.41
2674 4939 2.423898 CGGCCTAGTCACGTCCCAT 61.424 63.158 0.00 0.00 0.00 4.00
2831 5117 2.434331 CTTCCCCCAAACGCCTCA 59.566 61.111 0.00 0.00 0.00 3.86
2986 5274 0.921256 ATAAGCTGGTGGCCTCCCTT 60.921 55.000 21.06 18.40 43.05 3.95
3060 5366 2.123640 CGAGACCTCCCTCTCCCC 60.124 72.222 0.00 0.00 34.23 4.81
3106 5436 2.125106 GATGGCCGAGCGTTTCCT 60.125 61.111 0.00 0.00 0.00 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 2.230750 AGAAGAAATGAAGCAGCAAGGC 59.769 45.455 0.00 0.00 0.00 4.35
8 9 4.022589 TGAAGAAGAAATGAAGCAGCAAGG 60.023 41.667 0.00 0.00 0.00 3.61
9 10 5.117355 TGAAGAAGAAATGAAGCAGCAAG 57.883 39.130 0.00 0.00 0.00 4.01
10 11 5.518848 TTGAAGAAGAAATGAAGCAGCAA 57.481 34.783 0.00 0.00 0.00 3.91
11 12 5.242171 TGATTGAAGAAGAAATGAAGCAGCA 59.758 36.000 0.00 0.00 0.00 4.41
12 13 5.706916 TGATTGAAGAAGAAATGAAGCAGC 58.293 37.500 0.00 0.00 0.00 5.25
13 14 7.273598 CACATGATTGAAGAAGAAATGAAGCAG 59.726 37.037 0.00 0.00 0.00 4.24
14 15 7.088272 CACATGATTGAAGAAGAAATGAAGCA 58.912 34.615 0.00 0.00 0.00 3.91
15 16 6.530534 CCACATGATTGAAGAAGAAATGAAGC 59.469 38.462 0.00 0.00 0.00 3.86
16 17 6.530534 GCCACATGATTGAAGAAGAAATGAAG 59.469 38.462 0.00 0.00 0.00 3.02
17 18 6.392354 GCCACATGATTGAAGAAGAAATGAA 58.608 36.000 0.00 0.00 0.00 2.57
18 19 5.105635 GGCCACATGATTGAAGAAGAAATGA 60.106 40.000 0.00 0.00 0.00 2.57
19 20 5.107133 GGCCACATGATTGAAGAAGAAATG 58.893 41.667 0.00 0.00 0.00 2.32
20 21 4.142315 CGGCCACATGATTGAAGAAGAAAT 60.142 41.667 2.24 0.00 0.00 2.17
21 22 3.191162 CGGCCACATGATTGAAGAAGAAA 59.809 43.478 2.24 0.00 0.00 2.52
22 23 2.749076 CGGCCACATGATTGAAGAAGAA 59.251 45.455 2.24 0.00 0.00 2.52
23 24 2.027285 TCGGCCACATGATTGAAGAAGA 60.027 45.455 2.24 0.00 0.00 2.87
24 25 2.096496 GTCGGCCACATGATTGAAGAAG 59.904 50.000 2.24 0.00 0.00 2.85
25 26 2.083774 GTCGGCCACATGATTGAAGAA 58.916 47.619 2.24 0.00 0.00 2.52
26 27 1.737838 GTCGGCCACATGATTGAAGA 58.262 50.000 2.24 0.00 0.00 2.87
27 28 0.374758 CGTCGGCCACATGATTGAAG 59.625 55.000 2.24 0.00 0.00 3.02
28 29 1.024046 CCGTCGGCCACATGATTGAA 61.024 55.000 2.24 0.00 0.00 2.69
29 30 1.449423 CCGTCGGCCACATGATTGA 60.449 57.895 2.24 0.00 0.00 2.57
30 31 2.472059 CCCGTCGGCCACATGATTG 61.472 63.158 5.50 0.00 0.00 2.67
31 32 2.124736 CCCGTCGGCCACATGATT 60.125 61.111 5.50 0.00 0.00 2.57
32 33 4.175337 CCCCGTCGGCCACATGAT 62.175 66.667 5.50 0.00 0.00 2.45
37 38 3.912745 AATTCACCCCGTCGGCCAC 62.913 63.158 5.50 0.00 33.26 5.01
38 39 3.642503 AATTCACCCCGTCGGCCA 61.643 61.111 5.50 0.00 33.26 5.36
39 40 3.131478 CAATTCACCCCGTCGGCC 61.131 66.667 5.50 0.00 33.26 6.13
40 41 3.810896 GCAATTCACCCCGTCGGC 61.811 66.667 5.50 0.00 33.26 5.54
41 42 2.359354 TGCAATTCACCCCGTCGG 60.359 61.111 3.60 3.60 37.81 4.79
42 43 2.867472 GTGCAATTCACCCCGTCG 59.133 61.111 0.00 0.00 39.79 5.12
43 44 1.512156 AACGTGCAATTCACCCCGTC 61.512 55.000 0.00 0.00 42.69 4.79
44 45 1.527380 AACGTGCAATTCACCCCGT 60.527 52.632 0.00 0.00 42.69 5.28
45 46 1.081509 CAACGTGCAATTCACCCCG 60.082 57.895 0.00 0.00 42.69 5.73
46 47 1.372872 GCAACGTGCAATTCACCCC 60.373 57.895 0.00 0.00 44.26 4.95
47 48 4.243383 GCAACGTGCAATTCACCC 57.757 55.556 0.00 0.00 44.26 4.61
56 57 4.681978 ACGGGAGGAGCAACGTGC 62.682 66.667 0.00 0.00 45.46 5.34
57 58 2.027625 GAACGGGAGGAGCAACGTG 61.028 63.158 0.00 0.00 39.76 4.49
58 59 1.755393 AAGAACGGGAGGAGCAACGT 61.755 55.000 0.00 0.00 41.88 3.99
59 60 0.602905 AAAGAACGGGAGGAGCAACG 60.603 55.000 0.00 0.00 0.00 4.10
60 61 1.605753 AAAAGAACGGGAGGAGCAAC 58.394 50.000 0.00 0.00 0.00 4.17
61 62 2.227194 GAAAAAGAACGGGAGGAGCAA 58.773 47.619 0.00 0.00 0.00 3.91
62 63 1.544759 GGAAAAAGAACGGGAGGAGCA 60.545 52.381 0.00 0.00 0.00 4.26
63 64 1.166129 GGAAAAAGAACGGGAGGAGC 58.834 55.000 0.00 0.00 0.00 4.70
64 65 1.822506 GGGAAAAAGAACGGGAGGAG 58.177 55.000 0.00 0.00 0.00 3.69
65 66 0.035739 CGGGAAAAAGAACGGGAGGA 59.964 55.000 0.00 0.00 0.00 3.71
66 67 1.583495 GCGGGAAAAAGAACGGGAGG 61.583 60.000 0.00 0.00 0.00 4.30
67 68 0.887387 TGCGGGAAAAAGAACGGGAG 60.887 55.000 0.00 0.00 0.00 4.30
68 69 1.148723 TGCGGGAAAAAGAACGGGA 59.851 52.632 0.00 0.00 0.00 5.14
69 70 1.284715 GTGCGGGAAAAAGAACGGG 59.715 57.895 0.00 0.00 0.00 5.28
70 71 1.284715 GGTGCGGGAAAAAGAACGG 59.715 57.895 0.00 0.00 0.00 4.44
71 72 1.082366 CGGTGCGGGAAAAAGAACG 60.082 57.895 0.00 0.00 0.00 3.95
72 73 0.237498 CTCGGTGCGGGAAAAAGAAC 59.763 55.000 0.00 0.00 0.00 3.01
73 74 0.887387 CCTCGGTGCGGGAAAAAGAA 60.887 55.000 0.00 0.00 0.00 2.52
74 75 1.302192 CCTCGGTGCGGGAAAAAGA 60.302 57.895 0.00 0.00 0.00 2.52
75 76 2.978018 GCCTCGGTGCGGGAAAAAG 61.978 63.158 0.00 0.00 0.00 2.27
76 77 2.981350 GCCTCGGTGCGGGAAAAA 60.981 61.111 0.00 0.00 0.00 1.94
103 104 1.153667 CCCTGACTCAAGCTCGAGC 60.154 63.158 30.01 30.01 42.49 5.03
104 105 0.172352 GTCCCTGACTCAAGCTCGAG 59.828 60.000 8.45 8.45 39.05 4.04
105 106 1.587043 CGTCCCTGACTCAAGCTCGA 61.587 60.000 0.00 0.00 0.00 4.04
106 107 1.153939 CGTCCCTGACTCAAGCTCG 60.154 63.158 0.00 0.00 0.00 5.03
107 108 0.109039 GACGTCCCTGACTCAAGCTC 60.109 60.000 3.51 0.00 0.00 4.09
108 109 0.827925 TGACGTCCCTGACTCAAGCT 60.828 55.000 14.12 0.00 0.00 3.74
109 110 0.247736 ATGACGTCCCTGACTCAAGC 59.752 55.000 14.12 0.00 0.00 4.01
110 111 1.273606 ACATGACGTCCCTGACTCAAG 59.726 52.381 14.12 0.00 0.00 3.02
111 112 1.338107 ACATGACGTCCCTGACTCAA 58.662 50.000 14.12 0.00 0.00 3.02
112 113 2.209690 TACATGACGTCCCTGACTCA 57.790 50.000 14.12 0.00 0.00 3.41
113 114 2.223829 CCATACATGACGTCCCTGACTC 60.224 54.545 14.12 0.00 0.00 3.36
114 115 1.757118 CCATACATGACGTCCCTGACT 59.243 52.381 14.12 1.46 0.00 3.41
115 116 1.806623 GCCATACATGACGTCCCTGAC 60.807 57.143 14.12 0.00 0.00 3.51
116 117 0.464036 GCCATACATGACGTCCCTGA 59.536 55.000 14.12 0.00 0.00 3.86
117 118 0.465705 AGCCATACATGACGTCCCTG 59.534 55.000 14.12 13.02 0.00 4.45
118 119 1.964223 CTAGCCATACATGACGTCCCT 59.036 52.381 14.12 0.00 0.00 4.20
119 120 1.961394 TCTAGCCATACATGACGTCCC 59.039 52.381 14.12 0.00 0.00 4.46
120 121 2.623889 AGTCTAGCCATACATGACGTCC 59.376 50.000 14.12 0.00 33.40 4.79
121 122 3.992260 AGTCTAGCCATACATGACGTC 57.008 47.619 9.11 9.11 33.40 4.34
122 123 4.037684 GGTTAGTCTAGCCATACATGACGT 59.962 45.833 7.83 0.00 33.40 4.34
123 124 4.547532 GGTTAGTCTAGCCATACATGACG 58.452 47.826 7.83 0.00 33.40 4.35
124 125 4.262506 GGGGTTAGTCTAGCCATACATGAC 60.263 50.000 14.11 0.00 37.42 3.06
125 126 3.901844 GGGGTTAGTCTAGCCATACATGA 59.098 47.826 14.11 0.00 37.42 3.07
126 127 3.646162 TGGGGTTAGTCTAGCCATACATG 59.354 47.826 14.11 0.00 37.42 3.21
127 128 3.646637 GTGGGGTTAGTCTAGCCATACAT 59.353 47.826 14.11 0.00 37.42 2.29
128 129 3.036091 GTGGGGTTAGTCTAGCCATACA 58.964 50.000 14.11 7.34 37.42 2.29
129 130 2.035576 CGTGGGGTTAGTCTAGCCATAC 59.964 54.545 14.11 10.62 37.42 2.39
130 131 2.091720 TCGTGGGGTTAGTCTAGCCATA 60.092 50.000 14.11 0.35 37.42 2.74
131 132 1.120530 CGTGGGGTTAGTCTAGCCAT 58.879 55.000 14.11 0.00 37.42 4.40
132 133 0.040058 TCGTGGGGTTAGTCTAGCCA 59.960 55.000 14.11 0.00 37.42 4.75
133 134 1.340568 GATCGTGGGGTTAGTCTAGCC 59.659 57.143 4.18 4.18 34.91 3.93
134 135 2.308690 AGATCGTGGGGTTAGTCTAGC 58.691 52.381 0.00 0.00 0.00 3.42
135 136 5.183522 GGAATAGATCGTGGGGTTAGTCTAG 59.816 48.000 0.00 0.00 0.00 2.43
136 137 5.075493 GGAATAGATCGTGGGGTTAGTCTA 58.925 45.833 0.00 0.00 0.00 2.59
137 138 3.896272 GGAATAGATCGTGGGGTTAGTCT 59.104 47.826 0.00 0.00 0.00 3.24
138 139 3.640029 TGGAATAGATCGTGGGGTTAGTC 59.360 47.826 0.00 0.00 0.00 2.59
139 140 3.387050 GTGGAATAGATCGTGGGGTTAGT 59.613 47.826 0.00 0.00 0.00 2.24
140 141 3.641906 AGTGGAATAGATCGTGGGGTTAG 59.358 47.826 0.00 0.00 0.00 2.34
141 142 3.386726 CAGTGGAATAGATCGTGGGGTTA 59.613 47.826 0.00 0.00 0.00 2.85
142 143 2.170607 CAGTGGAATAGATCGTGGGGTT 59.829 50.000 0.00 0.00 0.00 4.11
143 144 1.762957 CAGTGGAATAGATCGTGGGGT 59.237 52.381 0.00 0.00 0.00 4.95
144 145 1.762957 ACAGTGGAATAGATCGTGGGG 59.237 52.381 0.00 0.00 0.00 4.96
145 146 4.039245 ACATACAGTGGAATAGATCGTGGG 59.961 45.833 0.00 0.00 0.00 4.61
146 147 4.984785 CACATACAGTGGAATAGATCGTGG 59.015 45.833 0.00 0.00 44.69 4.94
340 344 4.518217 CACTAAAAACTCGTGCAGACTTG 58.482 43.478 0.00 0.00 0.00 3.16
364 368 1.007118 TGTGGAGATGTCCTCTGGCTA 59.993 52.381 10.72 0.00 44.30 3.93
374 378 2.416747 CGTGTGATTGTGTGGAGATGT 58.583 47.619 0.00 0.00 0.00 3.06
486 496 4.290155 GAGCGATCTGATCTGAAGTTCTC 58.710 47.826 15.16 7.36 0.00 2.87
494 504 6.836577 TCTATATACGAGCGATCTGATCTG 57.163 41.667 15.16 9.87 0.00 2.90
511 521 8.911918 ACTACTTGTCAGTCGATCTTCTATAT 57.088 34.615 0.00 0.00 34.06 0.86
512 522 9.258826 GTACTACTTGTCAGTCGATCTTCTATA 57.741 37.037 0.00 0.00 34.06 1.31
514 524 6.538021 GGTACTACTTGTCAGTCGATCTTCTA 59.462 42.308 0.00 0.00 34.06 2.10
516 526 5.123502 TGGTACTACTTGTCAGTCGATCTTC 59.876 44.000 0.00 0.00 34.06 2.87
520 544 3.442977 GGTGGTACTACTTGTCAGTCGAT 59.557 47.826 9.41 0.00 34.06 3.59
546 573 2.614983 TGATGTGATGGTGCATCGAATG 59.385 45.455 0.00 0.00 43.14 2.67
783 2456 2.785868 CCACTACTTGGCATCTGGC 58.214 57.895 0.00 0.00 39.07 4.85
824 2497 3.462678 GACTCGACTGGGGGAGGC 61.463 72.222 0.00 0.00 34.58 4.70
825 2498 3.141488 CGACTCGACTGGGGGAGG 61.141 72.222 0.00 0.00 34.58 4.30
826 2499 2.045242 TCGACTCGACTGGGGGAG 60.045 66.667 0.00 0.00 36.36 4.30
859 2532 3.462678 GAGGAGGAGGCCGTGGAC 61.463 72.222 0.00 0.00 0.00 4.02
860 2533 4.779733 GGAGGAGGAGGCCGTGGA 62.780 72.222 0.00 0.00 0.00 4.02
867 2540 3.984186 TTGGAGGCGGAGGAGGAGG 62.984 68.421 0.00 0.00 0.00 4.30
868 2541 1.965754 CTTTGGAGGCGGAGGAGGAG 61.966 65.000 0.00 0.00 0.00 3.69
869 2542 1.990060 CTTTGGAGGCGGAGGAGGA 60.990 63.158 0.00 0.00 0.00 3.71
870 2543 2.586792 CTTTGGAGGCGGAGGAGG 59.413 66.667 0.00 0.00 0.00 4.30
871 2544 1.553690 TTCCTTTGGAGGCGGAGGAG 61.554 60.000 0.00 0.00 43.21 3.69
872 2545 1.131303 TTTCCTTTGGAGGCGGAGGA 61.131 55.000 0.00 0.00 43.21 3.71
873 2546 0.251165 TTTTCCTTTGGAGGCGGAGG 60.251 55.000 0.00 0.00 43.21 4.30
874 2547 1.745653 GATTTTCCTTTGGAGGCGGAG 59.254 52.381 0.00 0.00 43.21 4.63
878 2551 1.550524 GGGTGATTTTCCTTTGGAGGC 59.449 52.381 0.00 0.00 43.21 4.70
1007 2737 3.925090 GGATCCGGCGGTAGTGGG 61.925 72.222 27.32 0.00 0.00 4.61
1098 3191 2.446802 GAGGAAGGCGAGGGGGAT 60.447 66.667 0.00 0.00 0.00 3.85
1101 3194 3.157949 GGAGAGGAAGGCGAGGGG 61.158 72.222 0.00 0.00 0.00 4.79
1130 3229 1.068943 AGGAGGAGGAGGAGGCGATA 61.069 60.000 0.00 0.00 0.00 2.92
1146 3245 2.951229 AAGAAAAGGAAGGCGAAGGA 57.049 45.000 0.00 0.00 0.00 3.36
1147 3246 3.149981 AGAAAGAAAAGGAAGGCGAAGG 58.850 45.455 0.00 0.00 0.00 3.46
1158 3257 5.422331 GGGGGAAGGGAAATAGAAAGAAAAG 59.578 44.000 0.00 0.00 0.00 2.27
1236 3335 0.193574 AAGTTCCTCCTCCCTGGTCA 59.806 55.000 0.00 0.00 37.07 4.02
1355 3457 4.609247 GACGGACGGCGATCGAGG 62.609 72.222 21.57 11.88 42.43 4.63
1770 3878 0.533755 CTGGATCAGCCGATGGGTTC 60.534 60.000 0.00 0.00 40.66 3.62
1771 3879 0.982852 TCTGGATCAGCCGATGGGTT 60.983 55.000 0.00 0.00 40.66 4.11
1772 3880 0.765903 ATCTGGATCAGCCGATGGGT 60.766 55.000 0.00 0.00 40.66 4.51
1773 3881 0.321387 CATCTGGATCAGCCGATGGG 60.321 60.000 6.03 0.00 40.67 4.00
1774 3882 0.395686 ACATCTGGATCAGCCGATGG 59.604 55.000 15.24 2.07 44.61 3.51
1775 3883 1.069668 TCACATCTGGATCAGCCGATG 59.930 52.381 10.90 10.90 45.21 3.84
1776 3884 1.417288 TCACATCTGGATCAGCCGAT 58.583 50.000 0.00 0.00 40.66 4.18
1777 3885 1.134699 GTTCACATCTGGATCAGCCGA 60.135 52.381 0.00 0.00 40.66 5.54
1778 3886 1.293924 GTTCACATCTGGATCAGCCG 58.706 55.000 0.00 0.00 40.66 5.52
1779 3887 1.293924 CGTTCACATCTGGATCAGCC 58.706 55.000 0.00 0.00 37.10 4.85
1860 3968 2.896443 GCTTCCTGGTCCTCCTCG 59.104 66.667 0.00 0.00 34.23 4.63
1896 4007 4.614112 TGCTGCTGCTCGTGCTGT 62.614 61.111 17.00 0.00 39.81 4.40
1919 4030 2.188994 GCTCTGGCTCTGGCGAAT 59.811 61.111 0.00 0.00 39.81 3.34
1989 4100 2.871427 GACCATCGCCGCGTTCATC 61.871 63.158 13.39 3.57 0.00 2.92
2072 4183 2.220313 GATGCTTCTCTCTGCCATTCC 58.780 52.381 0.00 0.00 0.00 3.01
2075 4186 3.280295 CTTTGATGCTTCTCTCTGCCAT 58.720 45.455 0.88 0.00 0.00 4.40
2248 4360 0.671163 GGCGTTGATCGGGTAACACA 60.671 55.000 0.00 0.00 40.26 3.72
2249 4361 1.363885 GGGCGTTGATCGGGTAACAC 61.364 60.000 0.00 0.00 40.26 3.32
2346 4458 5.197549 CCAGACAACATAACATATTTCGCG 58.802 41.667 0.00 0.00 0.00 5.87
2354 4616 7.450074 TGAAGTAGAACCAGACAACATAACAT 58.550 34.615 0.00 0.00 0.00 2.71
2356 4618 7.441458 ACTTGAAGTAGAACCAGACAACATAAC 59.559 37.037 0.00 0.00 0.00 1.89
2481 4743 0.387750 GCAAAGAAAAGAGCAGCCGG 60.388 55.000 0.00 0.00 0.00 6.13
2661 4925 1.327690 GGGCTCATGGGACGTGACTA 61.328 60.000 0.00 0.00 0.00 2.59
2666 4930 1.910580 AAATCGGGCTCATGGGACGT 61.911 55.000 0.00 0.00 0.00 4.34
2674 4939 4.178861 CGACGAAAATCGGGCTCA 57.821 55.556 4.66 0.00 45.59 4.26
2813 5099 2.361230 GAGGCGTTTGGGGGAAGG 60.361 66.667 0.00 0.00 0.00 3.46
2822 5108 2.258726 GCGGGAAACTGAGGCGTTT 61.259 57.895 0.00 0.00 39.63 3.60


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

AutoCloner maintained by Alex Coulton.