Multiple sequence alignment - TraesCS3A01G463300

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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 TraesCS3A01G463300 chr3A 100.000 1276 0 0 1388 2663 697713496 697712221 0.000000e+00 2357.0
1 TraesCS3A01G463300 chr3A 100.000 1099 0 0 1 1099 697714883 697713785 0.000000e+00 2030.0
2 TraesCS3A01G463300 chr3A 94.984 319 16 0 1 319 64413405 64413723 3.960000e-138 501.0
3 TraesCS3A01G463300 chr3A 94.671 319 17 0 1 319 516037407 516037089 1.840000e-136 496.0
4 TraesCS3A01G463300 chrUn 95.507 779 33 2 320 1098 357362705 357363481 0.000000e+00 1243.0
5 TraesCS3A01G463300 chrUn 95.250 779 35 2 320 1098 418420835 418420059 0.000000e+00 1232.0
6 TraesCS3A01G463300 chrUn 85.581 749 96 9 320 1059 87330532 87331277 0.000000e+00 774.0
7 TraesCS3A01G463300 chrUn 86.170 658 50 15 1406 2032 87331656 87332303 0.000000e+00 673.0
8 TraesCS3A01G463300 chrUn 88.356 146 15 2 918 1063 357363472 357363615 9.800000e-40 174.0
9 TraesCS3A01G463300 chr1B 95.122 779 36 2 320 1098 59998316 59999092 0.000000e+00 1227.0
10 TraesCS3A01G463300 chr1B 92.598 662 17 6 1391 2031 3113991 3113341 0.000000e+00 922.0
11 TraesCS3A01G463300 chr1B 97.111 450 13 0 319 768 3115186 3114737 0.000000e+00 760.0
12 TraesCS3A01G463300 chr1B 84.360 633 94 5 319 948 162228975 162229605 1.350000e-172 616.0
13 TraesCS3A01G463300 chr1B 91.398 279 24 0 821 1099 3114502 3114224 1.500000e-102 383.0
14 TraesCS3A01G463300 chr1B 93.103 145 10 0 1887 2031 162230135 162230279 2.080000e-51 213.0
15 TraesCS3A01G463300 chr1B 89.726 146 13 2 918 1063 3114234 3114091 4.530000e-43 185.0
16 TraesCS3A01G463300 chr7B 91.094 786 41 11 320 1099 651992098 651992860 0.000000e+00 1037.0
17 TraesCS3A01G463300 chr7B 90.133 375 16 3 1677 2031 651993731 651994104 4.010000e-128 468.0
18 TraesCS3A01G463300 chr7B 78.652 356 47 12 1683 2013 535890351 535890702 2.690000e-50 209.0
19 TraesCS3A01G463300 chr7B 83.333 66 9 2 1400 1464 366493787 366493851 2.860000e-05 60.2
20 TraesCS3A01G463300 chr2A 94.620 632 34 0 2032 2663 506607224 506606593 0.000000e+00 979.0
21 TraesCS3A01G463300 chr2A 94.483 145 8 0 1887 2031 483381870 483382014 9.590000e-55 224.0
22 TraesCS3A01G463300 chr6A 94.304 632 36 0 2032 2663 7643121 7642490 0.000000e+00 968.0
23 TraesCS3A01G463300 chr6A 93.997 633 37 1 2032 2663 62722584 62721952 0.000000e+00 957.0
24 TraesCS3A01G463300 chr6A 94.637 317 17 0 3 319 542209155 542208839 2.380000e-135 492.0
25 TraesCS3A01G463300 chr7A 94.146 632 37 0 2032 2663 485037071 485036440 0.000000e+00 963.0
26 TraesCS3A01G463300 chr7A 93.987 632 35 2 2032 2661 543759720 543759090 0.000000e+00 953.0
27 TraesCS3A01G463300 chr7A 95.556 315 14 0 3 317 659445782 659445468 3.060000e-139 505.0
28 TraesCS3A01G463300 chr7A 95.268 317 15 0 3 319 564655227 564654911 1.100000e-138 503.0
29 TraesCS3A01G463300 chr1A 94.146 632 37 0 2032 2663 121064816 121064185 0.000000e+00 963.0
30 TraesCS3A01G463300 chr1A 94.984 319 16 0 1 319 110973755 110974073 3.960000e-138 501.0
31 TraesCS3A01G463300 chr1A 94.984 319 16 0 1 319 354555311 354555629 3.960000e-138 501.0
32 TraesCS3A01G463300 chr1A 94.671 319 17 0 1 319 122666323 122666641 1.840000e-136 496.0
33 TraesCS3A01G463300 chr5A 93.987 632 38 0 2032 2663 278283803 278284434 0.000000e+00 957.0
34 TraesCS3A01G463300 chr5A 93.987 632 38 0 2032 2663 662942514 662943145 0.000000e+00 957.0
35 TraesCS3A01G463300 chr5A 94.984 319 16 0 1 319 392464295 392463977 3.960000e-138 501.0
36 TraesCS3A01G463300 chr4A 93.987 632 38 0 2032 2663 23695656 23696287 0.000000e+00 957.0
37 TraesCS3A01G463300 chr7D 87.270 652 47 12 1406 2032 590953561 590952921 0.000000e+00 712.0
38 TraesCS3A01G463300 chr4D 85.380 684 82 13 319 993 6354048 6354722 0.000000e+00 693.0
39 TraesCS3A01G463300 chr4D 90.435 460 22 9 1392 1843 6354935 6355380 1.060000e-163 586.0
40 TraesCS3A01G463300 chr4D 97.241 145 4 0 1887 2031 6355363 6355507 2.050000e-61 246.0
41 TraesCS3A01G463300 chr2B 96.594 411 14 0 379 789 128428426 128428016 0.000000e+00 682.0
42 TraesCS3A01G463300 chr2B 86.567 603 44 13 1435 2031 123271277 123270706 4.840000e-177 630.0
43 TraesCS3A01G463300 chr2B 84.968 632 80 7 319 947 67913649 67914268 6.260000e-176 627.0
44 TraesCS3A01G463300 chr2B 84.234 666 57 18 1388 2031 67914526 67915165 2.930000e-169 604.0
45 TraesCS3A01G463300 chr2B 96.094 128 5 0 821 948 128427773 128427646 2.690000e-50 209.0
46 TraesCS3A01G463300 chr3B 85.868 651 41 15 1406 2031 47161691 47161067 0.000000e+00 645.0
47 TraesCS3A01G463300 chr3B 85.570 298 16 12 1388 1682 755462087 755462360 1.210000e-73 287.0
48 TraesCS3A01G463300 chr6B 73.184 358 70 15 1678 2031 646025670 646025335 3.630000e-19 106.0


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 TraesCS3A01G463300 chr3A 697712221 697714883 2662 True 2193.500000 2357 100.000000 1 2663 2 chr3A.!!$R2 2662
1 TraesCS3A01G463300 chrUn 418420059 418420835 776 True 1232.000000 1232 95.250000 320 1098 1 chrUn.!!$R1 778
2 TraesCS3A01G463300 chrUn 87330532 87332303 1771 False 723.500000 774 85.875500 320 2032 2 chrUn.!!$F1 1712
3 TraesCS3A01G463300 chrUn 357362705 357363615 910 False 708.500000 1243 91.931500 320 1098 2 chrUn.!!$F2 778
4 TraesCS3A01G463300 chr1B 59998316 59999092 776 False 1227.000000 1227 95.122000 320 1098 1 chr1B.!!$F1 778
5 TraesCS3A01G463300 chr1B 3113341 3115186 1845 True 562.500000 922 92.708250 319 2031 4 chr1B.!!$R1 1712
6 TraesCS3A01G463300 chr1B 162228975 162230279 1304 False 414.500000 616 88.731500 319 2031 2 chr1B.!!$F2 1712
7 TraesCS3A01G463300 chr7B 651992098 651994104 2006 False 752.500000 1037 90.613500 320 2031 2 chr7B.!!$F3 1711
8 TraesCS3A01G463300 chr2A 506606593 506607224 631 True 979.000000 979 94.620000 2032 2663 1 chr2A.!!$R1 631
9 TraesCS3A01G463300 chr6A 7642490 7643121 631 True 968.000000 968 94.304000 2032 2663 1 chr6A.!!$R1 631
10 TraesCS3A01G463300 chr6A 62721952 62722584 632 True 957.000000 957 93.997000 2032 2663 1 chr6A.!!$R2 631
11 TraesCS3A01G463300 chr7A 485036440 485037071 631 True 963.000000 963 94.146000 2032 2663 1 chr7A.!!$R1 631
12 TraesCS3A01G463300 chr7A 543759090 543759720 630 True 953.000000 953 93.987000 2032 2661 1 chr7A.!!$R2 629
13 TraesCS3A01G463300 chr1A 121064185 121064816 631 True 963.000000 963 94.146000 2032 2663 1 chr1A.!!$R1 631
14 TraesCS3A01G463300 chr5A 278283803 278284434 631 False 957.000000 957 93.987000 2032 2663 1 chr5A.!!$F1 631
15 TraesCS3A01G463300 chr5A 662942514 662943145 631 False 957.000000 957 93.987000 2032 2663 1 chr5A.!!$F2 631
16 TraesCS3A01G463300 chr4A 23695656 23696287 631 False 957.000000 957 93.987000 2032 2663 1 chr4A.!!$F1 631
17 TraesCS3A01G463300 chr7D 590952921 590953561 640 True 712.000000 712 87.270000 1406 2032 1 chr7D.!!$R1 626
18 TraesCS3A01G463300 chr4D 6354048 6355507 1459 False 508.333333 693 91.018667 319 2031 3 chr4D.!!$F1 1712
19 TraesCS3A01G463300 chr2B 123270706 123271277 571 True 630.000000 630 86.567000 1435 2031 1 chr2B.!!$R1 596
20 TraesCS3A01G463300 chr2B 67913649 67915165 1516 False 615.500000 627 84.601000 319 2031 2 chr2B.!!$F1 1712
21 TraesCS3A01G463300 chr2B 128427646 128428426 780 True 445.500000 682 96.344000 379 948 2 chr2B.!!$R2 569
22 TraesCS3A01G463300 chr3B 47161067 47161691 624 True 645.000000 645 85.868000 1406 2031 1 chr3B.!!$R1 625

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
189 190 0.038159 GACTTCGGTCCACCTGTCTG 60.038 60.0 0.0 0.0 38.93 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2076 3111 1.219124 GCAGCAGATGGAGAACCGA 59.781 57.895 0.0 0.0 39.42 4.69 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
21 22 2.413453 GTCTGAACTTTAGGCTGAAGCG 59.587 50.000 17.97 5.61 43.26 4.68
22 23 1.129437 CTGAACTTTAGGCTGAAGCGC 59.871 52.381 17.97 10.98 43.26 5.92
29 30 2.511145 GGCTGAAGCGCCTCTCTG 60.511 66.667 2.29 3.96 46.63 3.35
30 31 2.511145 GCTGAAGCGCCTCTCTGG 60.511 66.667 2.29 0.00 39.35 3.86
53 54 4.823419 CCGCGTAATGGCCGGTCA 62.823 66.667 13.22 13.22 0.00 4.02
54 55 3.261951 CGCGTAATGGCCGGTCAG 61.262 66.667 16.89 0.75 0.00 3.51
55 56 3.573491 GCGTAATGGCCGGTCAGC 61.573 66.667 16.89 8.86 0.00 4.26
66 67 4.294523 GGTCAGCCGCATTGTACA 57.705 55.556 0.00 0.00 0.00 2.90
67 68 1.794222 GGTCAGCCGCATTGTACAC 59.206 57.895 0.00 0.00 0.00 2.90
68 69 0.673644 GGTCAGCCGCATTGTACACT 60.674 55.000 0.00 0.00 0.00 3.55
69 70 1.404986 GGTCAGCCGCATTGTACACTA 60.405 52.381 0.00 0.00 0.00 2.74
70 71 1.927174 GTCAGCCGCATTGTACACTAG 59.073 52.381 0.00 0.00 0.00 2.57
71 72 1.548719 TCAGCCGCATTGTACACTAGT 59.451 47.619 0.00 0.00 0.00 2.57
72 73 1.660607 CAGCCGCATTGTACACTAGTG 59.339 52.381 21.44 21.44 0.00 2.74
73 74 1.548719 AGCCGCATTGTACACTAGTGA 59.451 47.619 29.30 10.19 0.00 3.41
74 75 2.028476 AGCCGCATTGTACACTAGTGAA 60.028 45.455 29.30 13.55 0.00 3.18
75 76 2.348666 GCCGCATTGTACACTAGTGAAG 59.651 50.000 29.30 12.04 0.00 3.02
76 77 2.930040 CCGCATTGTACACTAGTGAAGG 59.070 50.000 29.30 15.34 0.00 3.46
77 78 3.368013 CCGCATTGTACACTAGTGAAGGA 60.368 47.826 29.30 12.24 0.00 3.36
78 79 3.859961 CGCATTGTACACTAGTGAAGGAG 59.140 47.826 29.30 12.54 0.00 3.69
79 80 4.184629 GCATTGTACACTAGTGAAGGAGG 58.815 47.826 29.30 13.98 0.00 4.30
80 81 4.322801 GCATTGTACACTAGTGAAGGAGGT 60.323 45.833 29.30 7.49 0.00 3.85
81 82 5.794894 CATTGTACACTAGTGAAGGAGGTT 58.205 41.667 29.30 6.73 0.00 3.50
82 83 5.881923 TTGTACACTAGTGAAGGAGGTTT 57.118 39.130 29.30 5.99 0.00 3.27
83 84 5.464030 TGTACACTAGTGAAGGAGGTTTC 57.536 43.478 29.30 2.95 0.00 2.78
84 85 4.897076 TGTACACTAGTGAAGGAGGTTTCA 59.103 41.667 29.30 5.56 34.83 2.69
85 86 5.364446 TGTACACTAGTGAAGGAGGTTTCAA 59.636 40.000 29.30 0.00 38.69 2.69
86 87 5.568620 ACACTAGTGAAGGAGGTTTCAAT 57.431 39.130 29.30 0.00 38.69 2.57
87 88 5.308825 ACACTAGTGAAGGAGGTTTCAATG 58.691 41.667 29.30 0.00 38.69 2.82
88 89 4.154918 CACTAGTGAAGGAGGTTTCAATGC 59.845 45.833 18.45 0.00 38.69 3.56
89 90 3.515602 AGTGAAGGAGGTTTCAATGCT 57.484 42.857 0.00 0.00 38.69 3.79
90 91 3.837355 AGTGAAGGAGGTTTCAATGCTT 58.163 40.909 0.00 0.00 38.69 3.91
91 92 3.823304 AGTGAAGGAGGTTTCAATGCTTC 59.177 43.478 0.17 0.17 38.69 3.86
92 93 3.057245 GTGAAGGAGGTTTCAATGCTTCC 60.057 47.826 4.36 0.00 38.69 3.46
93 94 3.181429 TGAAGGAGGTTTCAATGCTTCCT 60.181 43.478 4.36 0.00 42.05 3.36
94 95 3.078891 AGGAGGTTTCAATGCTTCCTC 57.921 47.619 0.00 0.00 36.64 3.71
96 97 3.078891 GAGGTTTCAATGCTTCCTCCT 57.921 47.619 0.00 0.00 38.81 3.69
97 98 3.013219 GAGGTTTCAATGCTTCCTCCTC 58.987 50.000 0.00 0.00 38.81 3.71
98 99 1.740025 GGTTTCAATGCTTCCTCCTCG 59.260 52.381 0.00 0.00 0.00 4.63
99 100 2.615493 GGTTTCAATGCTTCCTCCTCGA 60.615 50.000 0.00 0.00 0.00 4.04
100 101 2.675348 GTTTCAATGCTTCCTCCTCGAG 59.325 50.000 5.13 5.13 0.00 4.04
113 114 3.723554 CTCGAGGTGAGGTAGCAAC 57.276 57.895 3.91 0.00 41.29 4.17
126 127 2.811799 GCAACCTGCGTTTTGGGT 59.188 55.556 0.00 0.00 31.71 4.51
127 128 2.034607 GCAACCTGCGTTTTGGGTA 58.965 52.632 0.00 0.00 31.71 3.69
128 129 0.386113 GCAACCTGCGTTTTGGGTAA 59.614 50.000 0.00 0.00 31.71 2.85
129 130 1.866471 GCAACCTGCGTTTTGGGTAAC 60.866 52.381 0.00 0.00 31.71 2.50
130 131 1.679153 CAACCTGCGTTTTGGGTAACT 59.321 47.619 0.00 0.00 32.50 2.24
131 132 1.601166 ACCTGCGTTTTGGGTAACTC 58.399 50.000 0.00 0.00 0.00 3.01
132 133 1.142262 ACCTGCGTTTTGGGTAACTCT 59.858 47.619 0.00 0.00 0.00 3.24
133 134 2.227194 CCTGCGTTTTGGGTAACTCTT 58.773 47.619 0.00 0.00 0.00 2.85
134 135 3.181452 ACCTGCGTTTTGGGTAACTCTTA 60.181 43.478 0.00 0.00 0.00 2.10
135 136 3.435671 CCTGCGTTTTGGGTAACTCTTAG 59.564 47.826 0.00 0.00 0.00 2.18
136 137 4.312443 CTGCGTTTTGGGTAACTCTTAGA 58.688 43.478 0.00 0.00 0.00 2.10
137 138 4.060205 TGCGTTTTGGGTAACTCTTAGAC 58.940 43.478 0.00 0.00 0.00 2.59
138 139 3.122445 GCGTTTTGGGTAACTCTTAGACG 59.878 47.826 0.00 0.00 0.00 4.18
139 140 3.676646 CGTTTTGGGTAACTCTTAGACGG 59.323 47.826 0.00 0.00 0.00 4.79
140 141 3.967332 TTTGGGTAACTCTTAGACGGG 57.033 47.619 0.00 0.00 0.00 5.28
141 142 1.188863 TGGGTAACTCTTAGACGGGC 58.811 55.000 0.00 0.00 0.00 6.13
142 143 0.101939 GGGTAACTCTTAGACGGGCG 59.898 60.000 0.00 0.00 0.00 6.13
143 144 0.527169 GGTAACTCTTAGACGGGCGC 60.527 60.000 0.00 0.00 0.00 6.53
144 145 0.455005 GTAACTCTTAGACGGGCGCT 59.545 55.000 7.64 0.00 0.00 5.92
145 146 0.737219 TAACTCTTAGACGGGCGCTC 59.263 55.000 7.64 0.06 0.00 5.03
146 147 2.024871 CTCTTAGACGGGCGCTCG 59.975 66.667 31.23 31.23 0.00 5.03
147 148 2.437180 TCTTAGACGGGCGCTCGA 60.437 61.111 39.76 12.15 0.00 4.04
148 149 2.024871 CTTAGACGGGCGCTCGAG 59.975 66.667 39.76 20.18 0.00 4.04
149 150 2.749044 TTAGACGGGCGCTCGAGT 60.749 61.111 39.76 24.69 0.00 4.18
150 151 2.267681 CTTAGACGGGCGCTCGAGTT 62.268 60.000 39.76 22.55 0.00 3.01
151 152 2.262471 TTAGACGGGCGCTCGAGTTC 62.262 60.000 39.76 24.14 0.00 3.01
152 153 4.415332 GACGGGCGCTCGAGTTCA 62.415 66.667 39.76 0.00 0.00 3.18
153 154 3.701604 GACGGGCGCTCGAGTTCAT 62.702 63.158 39.76 13.58 0.00 2.57
154 155 3.257561 CGGGCGCTCGAGTTCATG 61.258 66.667 29.20 0.00 0.00 3.07
155 156 3.567797 GGGCGCTCGAGTTCATGC 61.568 66.667 15.13 10.28 0.00 4.06
156 157 2.510238 GGCGCTCGAGTTCATGCT 60.510 61.111 15.13 0.00 0.00 3.79
157 158 2.520904 GGCGCTCGAGTTCATGCTC 61.521 63.158 15.13 0.00 0.00 4.26
158 159 2.520904 GCGCTCGAGTTCATGCTCC 61.521 63.158 15.13 0.00 32.11 4.70
159 160 1.140589 CGCTCGAGTTCATGCTCCT 59.859 57.895 15.13 0.00 32.11 3.69
160 161 0.869454 CGCTCGAGTTCATGCTCCTC 60.869 60.000 15.13 0.00 32.11 3.71
162 163 0.248825 CTCGAGTTCATGCTCCTCGG 60.249 60.000 20.67 12.19 46.03 4.63
163 164 1.880340 CGAGTTCATGCTCCTCGGC 60.880 63.158 16.09 0.00 43.20 5.54
164 165 1.522580 GAGTTCATGCTCCTCGGCC 60.523 63.158 0.00 0.00 0.00 6.13
165 166 2.892425 GTTCATGCTCCTCGGCCG 60.892 66.667 22.12 22.12 0.00 6.13
166 167 4.838152 TTCATGCTCCTCGGCCGC 62.838 66.667 23.51 6.41 0.00 6.53
169 170 4.845580 ATGCTCCTCGGCCGCAAG 62.846 66.667 23.51 18.00 37.20 4.01
187 188 4.990288 GACTTCGGTCCACCTGTC 57.010 61.111 0.00 0.00 38.93 3.51
188 189 2.352817 GACTTCGGTCCACCTGTCT 58.647 57.895 0.00 0.00 38.93 3.41
189 190 0.038159 GACTTCGGTCCACCTGTCTG 60.038 60.000 0.00 0.00 38.93 3.51
190 191 1.374758 CTTCGGTCCACCTGTCTGC 60.375 63.158 0.00 0.00 0.00 4.26
191 192 1.821061 CTTCGGTCCACCTGTCTGCT 61.821 60.000 0.00 0.00 0.00 4.24
192 193 0.541063 TTCGGTCCACCTGTCTGCTA 60.541 55.000 0.00 0.00 0.00 3.49
193 194 0.965866 TCGGTCCACCTGTCTGCTAG 60.966 60.000 0.00 0.00 0.00 3.42
194 195 1.219393 GGTCCACCTGTCTGCTAGC 59.781 63.158 8.10 8.10 0.00 3.42
195 196 1.544825 GGTCCACCTGTCTGCTAGCA 61.545 60.000 18.22 18.22 0.00 3.49
196 197 0.321671 GTCCACCTGTCTGCTAGCAA 59.678 55.000 19.86 7.18 0.00 3.91
197 198 0.610174 TCCACCTGTCTGCTAGCAAG 59.390 55.000 19.86 13.22 0.00 4.01
198 199 0.322975 CCACCTGTCTGCTAGCAAGT 59.677 55.000 19.86 8.38 0.00 3.16
199 200 1.674221 CCACCTGTCTGCTAGCAAGTC 60.674 57.143 19.86 12.03 0.00 3.01
200 201 1.274728 CACCTGTCTGCTAGCAAGTCT 59.725 52.381 19.86 0.00 0.00 3.24
201 202 1.974236 ACCTGTCTGCTAGCAAGTCTT 59.026 47.619 19.86 0.00 0.00 3.01
202 203 2.289320 ACCTGTCTGCTAGCAAGTCTTG 60.289 50.000 19.86 8.31 0.00 3.02
203 204 2.028658 CCTGTCTGCTAGCAAGTCTTGA 60.029 50.000 19.86 8.46 0.00 3.02
204 205 3.369261 CCTGTCTGCTAGCAAGTCTTGAT 60.369 47.826 19.86 12.83 0.00 2.57
205 206 3.854666 TGTCTGCTAGCAAGTCTTGATC 58.145 45.455 19.86 6.89 0.00 2.92
206 207 3.259123 TGTCTGCTAGCAAGTCTTGATCA 59.741 43.478 19.86 9.13 0.00 2.92
207 208 3.864583 GTCTGCTAGCAAGTCTTGATCAG 59.135 47.826 19.86 13.77 0.00 2.90
208 209 2.608546 CTGCTAGCAAGTCTTGATCAGC 59.391 50.000 19.86 18.25 0.00 4.26
209 210 2.235650 TGCTAGCAAGTCTTGATCAGCT 59.764 45.455 16.84 13.98 36.20 4.24
210 211 3.269178 GCTAGCAAGTCTTGATCAGCTT 58.731 45.455 16.99 6.78 33.83 3.74
211 212 3.063725 GCTAGCAAGTCTTGATCAGCTTG 59.936 47.826 16.99 21.93 38.59 4.01
212 213 3.413846 AGCAAGTCTTGATCAGCTTGA 57.586 42.857 26.61 11.29 38.18 3.02
213 214 3.748083 AGCAAGTCTTGATCAGCTTGAA 58.252 40.909 26.61 2.49 38.18 2.69
214 215 3.752222 AGCAAGTCTTGATCAGCTTGAAG 59.248 43.478 26.61 10.87 38.18 3.02
215 216 3.670091 GCAAGTCTTGATCAGCTTGAAGC 60.670 47.826 26.61 9.59 42.84 3.86
233 234 1.775869 GCTGTTGCTGCTTTTTCTCC 58.224 50.000 0.00 0.00 36.03 3.71
234 235 1.067516 GCTGTTGCTGCTTTTTCTCCA 59.932 47.619 0.00 0.00 36.03 3.86
235 236 2.861360 GCTGTTGCTGCTTTTTCTCCAG 60.861 50.000 0.00 0.00 36.03 3.86
236 237 1.682854 TGTTGCTGCTTTTTCTCCAGG 59.317 47.619 0.00 0.00 0.00 4.45
237 238 0.675633 TTGCTGCTTTTTCTCCAGGC 59.324 50.000 0.00 0.00 0.00 4.85
238 239 0.178981 TGCTGCTTTTTCTCCAGGCT 60.179 50.000 0.00 0.00 0.00 4.58
239 240 1.073763 TGCTGCTTTTTCTCCAGGCTA 59.926 47.619 0.00 0.00 0.00 3.93
240 241 2.291153 TGCTGCTTTTTCTCCAGGCTAT 60.291 45.455 0.00 0.00 0.00 2.97
241 242 2.757314 GCTGCTTTTTCTCCAGGCTATT 59.243 45.455 0.00 0.00 0.00 1.73
242 243 3.194329 GCTGCTTTTTCTCCAGGCTATTT 59.806 43.478 0.00 0.00 0.00 1.40
243 244 4.741342 CTGCTTTTTCTCCAGGCTATTTG 58.259 43.478 0.00 0.00 0.00 2.32
244 245 3.056607 TGCTTTTTCTCCAGGCTATTTGC 60.057 43.478 0.00 0.00 41.94 3.68
256 257 3.308438 GCTATTTGCCATGGCCATAAG 57.692 47.619 33.44 24.19 41.09 1.73
257 258 2.611224 GCTATTTGCCATGGCCATAAGC 60.611 50.000 33.44 28.90 41.09 3.09
285 286 2.340078 AGCGCTCTTGCTTGACGA 59.660 55.556 2.64 0.00 44.46 4.20
286 287 1.735920 AGCGCTCTTGCTTGACGAG 60.736 57.895 2.64 0.00 44.46 4.18
287 288 2.734673 GCGCTCTTGCTTGACGAGG 61.735 63.158 0.00 0.00 36.97 4.63
288 289 1.373497 CGCTCTTGCTTGACGAGGT 60.373 57.895 0.00 0.00 36.97 3.85
289 290 1.347817 CGCTCTTGCTTGACGAGGTC 61.348 60.000 0.00 0.00 36.97 3.85
290 291 1.016653 GCTCTTGCTTGACGAGGTCC 61.017 60.000 0.00 0.00 36.03 4.46
291 292 0.605589 CTCTTGCTTGACGAGGTCCT 59.394 55.000 0.00 0.00 0.00 3.85
292 293 0.603569 TCTTGCTTGACGAGGTCCTC 59.396 55.000 9.05 9.05 0.00 3.71
293 294 0.318441 CTTGCTTGACGAGGTCCTCA 59.682 55.000 19.15 0.00 0.00 3.86
294 295 0.318441 TTGCTTGACGAGGTCCTCAG 59.682 55.000 19.15 13.31 0.00 3.35
295 296 1.216710 GCTTGACGAGGTCCTCAGG 59.783 63.158 19.15 5.99 0.00 3.86
296 297 1.216710 CTTGACGAGGTCCTCAGGC 59.783 63.158 19.15 13.63 0.00 4.85
297 298 1.533033 TTGACGAGGTCCTCAGGCA 60.533 57.895 19.15 15.95 0.00 4.75
298 299 1.816863 TTGACGAGGTCCTCAGGCAC 61.817 60.000 19.15 5.47 0.00 5.01
299 300 3.343788 GACGAGGTCCTCAGGCACG 62.344 68.421 19.15 6.77 0.00 5.34
300 301 3.062466 CGAGGTCCTCAGGCACGA 61.062 66.667 19.15 0.00 0.00 4.35
301 302 2.418910 CGAGGTCCTCAGGCACGAT 61.419 63.158 19.15 0.00 0.00 3.73
302 303 1.101635 CGAGGTCCTCAGGCACGATA 61.102 60.000 19.15 0.00 0.00 2.92
303 304 1.112113 GAGGTCCTCAGGCACGATAA 58.888 55.000 14.46 0.00 0.00 1.75
304 305 1.480954 GAGGTCCTCAGGCACGATAAA 59.519 52.381 14.46 0.00 0.00 1.40
305 306 1.207329 AGGTCCTCAGGCACGATAAAC 59.793 52.381 0.00 0.00 0.00 2.01
306 307 1.207329 GGTCCTCAGGCACGATAAACT 59.793 52.381 0.00 0.00 0.00 2.66
307 308 2.541556 GTCCTCAGGCACGATAAACTC 58.458 52.381 0.00 0.00 0.00 3.01
315 316 2.911280 CGATAAACTCGTCGCCGC 59.089 61.111 0.00 0.00 42.56 6.53
316 317 2.574222 CGATAAACTCGTCGCCGCC 61.574 63.158 0.00 0.00 42.56 6.13
317 318 2.574222 GATAAACTCGTCGCCGCCG 61.574 63.158 0.00 0.00 0.00 6.46
377 378 4.579869 ACAGATGGCAAAGACGTAAATCT 58.420 39.130 0.00 0.00 0.00 2.40
582 589 2.584608 CCGGGATCCGTCTTTGCT 59.415 61.111 5.45 0.00 46.80 3.91
769 778 9.594478 TTACAGACCAATATATTACACACAGTG 57.406 33.333 0.00 0.00 39.75 3.66
951 1174 4.415150 CCAGTGGCCTGCGGTGAT 62.415 66.667 3.32 0.00 37.38 3.06
1003 1406 3.134127 GGTGAAGACGGGCCATGC 61.134 66.667 4.39 0.00 0.00 4.06
1553 2299 1.765314 AGAAAGAGATCGTGATGGGGG 59.235 52.381 0.00 0.00 0.00 5.40
1554 2300 1.486726 GAAAGAGATCGTGATGGGGGT 59.513 52.381 0.00 0.00 0.00 4.95
1555 2301 1.123928 AAGAGATCGTGATGGGGGTC 58.876 55.000 0.00 0.00 0.00 4.46
1575 2321 3.897122 GGGTGGGTGGGCTGTCAA 61.897 66.667 0.00 0.00 0.00 3.18
1692 2699 2.762327 GGACCAGATTTTGCCATGTCAT 59.238 45.455 0.00 0.00 0.00 3.06
2023 3058 4.155826 CCTGACGGCAAATTAACTGATTCA 59.844 41.667 0.00 0.00 0.00 2.57
2076 3111 3.525199 AGAGGCATGTAATTGTCCTCCTT 59.475 43.478 9.02 0.00 39.09 3.36
2153 3188 1.144298 CATCATGCTGGAGGGGATTGA 59.856 52.381 0.00 0.00 0.00 2.57
2190 3225 6.379386 CGCTATCCGAAGTGTTATTATCTCA 58.621 40.000 0.00 0.00 40.02 3.27
2392 3429 0.318441 CCTGTTCGTCTCTGGCTTCA 59.682 55.000 0.00 0.00 0.00 3.02
2450 3487 1.916000 GAATGTCGGTTAAGTCGTCGG 59.084 52.381 0.00 0.00 0.00 4.79
2455 3492 0.665369 CGGTTAAGTCGTCGGCAGTT 60.665 55.000 0.00 0.00 0.00 3.16
2573 3610 6.708502 GGAGAGAGACCTTAATGAATTTAGCC 59.291 42.308 0.00 0.00 0.00 3.93
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.413453 CGCTTCAGCCTAAAGTTCAGAC 59.587 50.000 0.00 0.00 37.91 3.51
1 2 2.688507 CGCTTCAGCCTAAAGTTCAGA 58.311 47.619 0.00 0.00 37.91 3.27
2 3 1.129437 GCGCTTCAGCCTAAAGTTCAG 59.871 52.381 0.00 0.00 37.91 3.02
3 4 1.156736 GCGCTTCAGCCTAAAGTTCA 58.843 50.000 0.00 0.00 37.91 3.18
4 5 3.978063 GCGCTTCAGCCTAAAGTTC 57.022 52.632 0.00 0.00 37.91 3.01
13 14 2.511145 CCAGAGAGGCGCTTCAGC 60.511 66.667 22.42 12.89 37.78 4.26
36 37 4.823419 TGACCGGCCATTACGCGG 62.823 66.667 12.47 0.00 0.00 6.46
37 38 3.261951 CTGACCGGCCATTACGCG 61.262 66.667 3.53 3.53 0.00 6.01
38 39 3.573491 GCTGACCGGCCATTACGC 61.573 66.667 0.00 0.00 0.00 4.42
49 50 0.673644 AGTGTACAATGCGGCTGACC 60.674 55.000 0.00 0.00 0.00 4.02
50 51 1.927174 CTAGTGTACAATGCGGCTGAC 59.073 52.381 5.98 0.00 0.00 3.51
51 52 1.548719 ACTAGTGTACAATGCGGCTGA 59.451 47.619 5.98 0.00 0.00 4.26
52 53 1.660607 CACTAGTGTACAATGCGGCTG 59.339 52.381 15.06 0.00 0.00 4.85
53 54 1.548719 TCACTAGTGTACAATGCGGCT 59.451 47.619 21.99 0.00 0.00 5.52
54 55 2.004583 TCACTAGTGTACAATGCGGC 57.995 50.000 21.99 0.00 0.00 6.53
55 56 2.930040 CCTTCACTAGTGTACAATGCGG 59.070 50.000 21.99 5.87 0.00 5.69
56 57 3.845178 TCCTTCACTAGTGTACAATGCG 58.155 45.455 21.99 0.00 0.00 4.73
57 58 4.184629 CCTCCTTCACTAGTGTACAATGC 58.815 47.826 21.99 0.00 0.00 3.56
58 59 5.407407 ACCTCCTTCACTAGTGTACAATG 57.593 43.478 21.99 10.78 0.00 2.82
59 60 6.042781 TGAAACCTCCTTCACTAGTGTACAAT 59.957 38.462 21.99 0.00 30.31 2.71
60 61 5.364446 TGAAACCTCCTTCACTAGTGTACAA 59.636 40.000 21.99 8.84 30.31 2.41
61 62 4.897076 TGAAACCTCCTTCACTAGTGTACA 59.103 41.667 21.99 7.29 30.31 2.90
62 63 5.464030 TGAAACCTCCTTCACTAGTGTAC 57.536 43.478 21.99 0.00 30.31 2.90
63 64 6.464222 CATTGAAACCTCCTTCACTAGTGTA 58.536 40.000 21.99 12.28 35.07 2.90
64 65 5.308825 CATTGAAACCTCCTTCACTAGTGT 58.691 41.667 21.99 0.00 35.07 3.55
65 66 4.154918 GCATTGAAACCTCCTTCACTAGTG 59.845 45.833 17.17 17.17 35.07 2.74
66 67 4.042187 AGCATTGAAACCTCCTTCACTAGT 59.958 41.667 0.00 0.00 35.07 2.57
67 68 4.583871 AGCATTGAAACCTCCTTCACTAG 58.416 43.478 0.00 0.00 35.07 2.57
68 69 4.640771 AGCATTGAAACCTCCTTCACTA 57.359 40.909 0.00 0.00 35.07 2.74
69 70 3.515602 AGCATTGAAACCTCCTTCACT 57.484 42.857 0.00 0.00 35.07 3.41
70 71 3.057245 GGAAGCATTGAAACCTCCTTCAC 60.057 47.826 0.00 0.00 35.07 3.18
71 72 3.157087 GGAAGCATTGAAACCTCCTTCA 58.843 45.455 0.00 0.00 33.48 3.02
72 73 3.425659 AGGAAGCATTGAAACCTCCTTC 58.574 45.455 0.00 0.00 0.00 3.46
73 74 3.425659 GAGGAAGCATTGAAACCTCCTT 58.574 45.455 0.00 0.00 40.58 3.36
74 75 3.078891 GAGGAAGCATTGAAACCTCCT 57.921 47.619 0.00 0.00 40.58 3.69
76 77 3.013219 GAGGAGGAAGCATTGAAACCTC 58.987 50.000 0.00 0.00 44.21 3.85
77 78 2.616510 CGAGGAGGAAGCATTGAAACCT 60.617 50.000 0.00 0.00 0.00 3.50
78 79 1.740025 CGAGGAGGAAGCATTGAAACC 59.260 52.381 0.00 0.00 0.00 3.27
79 80 2.675348 CTCGAGGAGGAAGCATTGAAAC 59.325 50.000 3.91 0.00 0.00 2.78
80 81 2.977914 CTCGAGGAGGAAGCATTGAAA 58.022 47.619 3.91 0.00 0.00 2.69
81 82 2.680312 CTCGAGGAGGAAGCATTGAA 57.320 50.000 3.91 0.00 0.00 2.69
95 96 0.173708 GGTTGCTACCTCACCTCGAG 59.826 60.000 10.33 5.13 41.53 4.04
96 97 2.273908 GGTTGCTACCTCACCTCGA 58.726 57.895 10.33 0.00 41.53 4.04
97 98 4.913126 GGTTGCTACCTCACCTCG 57.087 61.111 10.33 0.00 41.53 4.63
105 106 0.039527 CCAAAACGCAGGTTGCTACC 60.040 55.000 9.54 9.54 42.25 3.18
106 107 0.039527 CCCAAAACGCAGGTTGCTAC 60.040 55.000 0.00 0.00 42.25 3.58
107 108 0.466555 ACCCAAAACGCAGGTTGCTA 60.467 50.000 0.00 0.00 42.25 3.49
108 109 0.466555 TACCCAAAACGCAGGTTGCT 60.467 50.000 0.00 0.00 42.25 3.91
109 110 0.386113 TTACCCAAAACGCAGGTTGC 59.614 50.000 0.00 0.00 40.69 4.17
110 111 1.679153 AGTTACCCAAAACGCAGGTTG 59.321 47.619 0.00 0.00 36.25 3.77
111 112 1.951602 GAGTTACCCAAAACGCAGGTT 59.048 47.619 0.00 0.00 38.22 3.50
112 113 1.142262 AGAGTTACCCAAAACGCAGGT 59.858 47.619 0.00 0.00 37.69 4.00
113 114 1.892209 AGAGTTACCCAAAACGCAGG 58.108 50.000 0.00 0.00 34.46 4.85
114 115 4.151867 GTCTAAGAGTTACCCAAAACGCAG 59.848 45.833 0.00 0.00 34.46 5.18
115 116 4.060205 GTCTAAGAGTTACCCAAAACGCA 58.940 43.478 0.00 0.00 34.46 5.24
116 117 3.122445 CGTCTAAGAGTTACCCAAAACGC 59.878 47.826 0.00 0.00 34.46 4.84
117 118 3.676646 CCGTCTAAGAGTTACCCAAAACG 59.323 47.826 0.00 0.00 34.46 3.60
118 119 3.999001 CCCGTCTAAGAGTTACCCAAAAC 59.001 47.826 0.00 0.00 0.00 2.43
119 120 3.557686 GCCCGTCTAAGAGTTACCCAAAA 60.558 47.826 0.00 0.00 0.00 2.44
120 121 2.027837 GCCCGTCTAAGAGTTACCCAAA 60.028 50.000 0.00 0.00 0.00 3.28
121 122 1.551883 GCCCGTCTAAGAGTTACCCAA 59.448 52.381 0.00 0.00 0.00 4.12
122 123 1.188863 GCCCGTCTAAGAGTTACCCA 58.811 55.000 0.00 0.00 0.00 4.51
123 124 0.101939 CGCCCGTCTAAGAGTTACCC 59.898 60.000 0.00 0.00 0.00 3.69
124 125 0.527169 GCGCCCGTCTAAGAGTTACC 60.527 60.000 0.00 0.00 0.00 2.85
125 126 0.455005 AGCGCCCGTCTAAGAGTTAC 59.545 55.000 2.29 0.00 0.00 2.50
126 127 0.737219 GAGCGCCCGTCTAAGAGTTA 59.263 55.000 2.29 0.00 0.00 2.24
127 128 1.511768 GAGCGCCCGTCTAAGAGTT 59.488 57.895 2.29 0.00 0.00 3.01
128 129 2.762234 CGAGCGCCCGTCTAAGAGT 61.762 63.158 1.97 0.00 0.00 3.24
129 130 2.024871 CGAGCGCCCGTCTAAGAG 59.975 66.667 1.97 0.00 0.00 2.85
130 131 2.437180 TCGAGCGCCCGTCTAAGA 60.437 61.111 12.10 0.00 0.00 2.10
131 132 2.024871 CTCGAGCGCCCGTCTAAG 59.975 66.667 12.10 0.00 0.00 2.18
132 133 2.262471 GAACTCGAGCGCCCGTCTAA 62.262 60.000 12.10 0.00 0.00 2.10
133 134 2.749044 AACTCGAGCGCCCGTCTA 60.749 61.111 12.10 0.00 0.00 2.59
134 135 4.117661 GAACTCGAGCGCCCGTCT 62.118 66.667 12.10 0.00 0.00 4.18
135 136 3.701604 ATGAACTCGAGCGCCCGTC 62.702 63.158 12.10 1.90 0.00 4.79
136 137 3.760035 ATGAACTCGAGCGCCCGT 61.760 61.111 12.10 0.00 0.00 5.28
137 138 3.257561 CATGAACTCGAGCGCCCG 61.258 66.667 13.61 4.37 0.00 6.13
138 139 3.567797 GCATGAACTCGAGCGCCC 61.568 66.667 13.61 0.00 0.00 6.13
139 140 2.510238 AGCATGAACTCGAGCGCC 60.510 61.111 13.61 2.14 0.00 6.53
140 141 2.520904 GGAGCATGAACTCGAGCGC 61.521 63.158 13.61 0.00 37.57 5.92
141 142 0.869454 GAGGAGCATGAACTCGAGCG 60.869 60.000 13.61 0.00 37.57 5.03
142 143 2.970576 GAGGAGCATGAACTCGAGC 58.029 57.895 13.61 0.00 37.57 5.03
146 147 1.522580 GGCCGAGGAGCATGAACTC 60.523 63.158 0.00 0.00 35.86 3.01
147 148 2.586792 GGCCGAGGAGCATGAACT 59.413 61.111 0.00 0.00 0.00 3.01
148 149 2.892425 CGGCCGAGGAGCATGAAC 60.892 66.667 24.07 0.00 0.00 3.18
149 150 4.838152 GCGGCCGAGGAGCATGAA 62.838 66.667 33.48 0.00 0.00 2.57
152 153 4.845580 CTTGCGGCCGAGGAGCAT 62.846 66.667 33.48 0.00 40.83 3.79
157 158 4.394712 AAGTCCTTGCGGCCGAGG 62.395 66.667 33.48 27.77 43.12 4.63
158 159 2.815647 GAAGTCCTTGCGGCCGAG 60.816 66.667 33.48 18.99 0.00 4.63
159 160 4.735132 CGAAGTCCTTGCGGCCGA 62.735 66.667 33.48 11.82 0.00 5.54
170 171 0.038159 CAGACAGGTGGACCGAAGTC 60.038 60.000 9.66 9.66 42.73 3.01
171 172 2.050269 CAGACAGGTGGACCGAAGT 58.950 57.895 0.00 0.00 42.08 3.01
172 173 1.374758 GCAGACAGGTGGACCGAAG 60.375 63.158 0.00 0.00 42.08 3.79
173 174 0.541063 TAGCAGACAGGTGGACCGAA 60.541 55.000 0.00 0.00 42.08 4.30
174 175 0.965866 CTAGCAGACAGGTGGACCGA 60.966 60.000 0.00 0.00 42.08 4.69
175 176 1.513158 CTAGCAGACAGGTGGACCG 59.487 63.158 0.00 0.00 42.08 4.79
176 177 1.219393 GCTAGCAGACAGGTGGACC 59.781 63.158 10.63 0.00 0.00 4.46
177 178 0.321671 TTGCTAGCAGACAGGTGGAC 59.678 55.000 18.45 0.00 0.00 4.02
178 179 0.610174 CTTGCTAGCAGACAGGTGGA 59.390 55.000 18.45 0.00 0.00 4.02
179 180 0.322975 ACTTGCTAGCAGACAGGTGG 59.677 55.000 18.45 4.82 0.00 4.61
180 181 1.274728 AGACTTGCTAGCAGACAGGTG 59.725 52.381 18.45 6.12 0.00 4.00
181 182 1.638529 AGACTTGCTAGCAGACAGGT 58.361 50.000 18.45 12.35 0.00 4.00
182 183 2.028658 TCAAGACTTGCTAGCAGACAGG 60.029 50.000 18.45 7.67 0.00 4.00
183 184 3.309961 TCAAGACTTGCTAGCAGACAG 57.690 47.619 18.45 15.07 0.00 3.51
184 185 3.259123 TGATCAAGACTTGCTAGCAGACA 59.741 43.478 18.45 2.03 0.00 3.41
185 186 3.854666 TGATCAAGACTTGCTAGCAGAC 58.145 45.455 18.45 12.84 0.00 3.51
186 187 3.678252 GCTGATCAAGACTTGCTAGCAGA 60.678 47.826 20.39 10.97 33.70 4.26
187 188 2.608546 GCTGATCAAGACTTGCTAGCAG 59.391 50.000 18.45 18.82 33.70 4.24
188 189 2.235650 AGCTGATCAAGACTTGCTAGCA 59.764 45.455 25.83 14.93 34.95 3.49
189 190 2.903798 AGCTGATCAAGACTTGCTAGC 58.096 47.619 20.85 20.85 33.69 3.42
190 191 4.502016 TCAAGCTGATCAAGACTTGCTAG 58.498 43.478 20.25 9.05 38.68 3.42
191 192 4.541973 TCAAGCTGATCAAGACTTGCTA 57.458 40.909 20.25 8.22 38.68 3.49
192 193 3.413846 TCAAGCTGATCAAGACTTGCT 57.586 42.857 20.25 11.90 38.68 3.91
193 194 3.670091 GCTTCAAGCTGATCAAGACTTGC 60.670 47.826 20.25 10.11 38.68 4.01
194 195 4.080969 GCTTCAAGCTGATCAAGACTTG 57.919 45.455 19.49 19.49 39.45 3.16
207 208 1.658673 AGCAGCAACAGCTTCAAGC 59.341 52.632 0.00 0.00 39.87 4.01
213 214 1.339291 GGAGAAAAAGCAGCAACAGCT 59.661 47.619 0.00 0.00 45.97 4.24
214 215 1.067516 TGGAGAAAAAGCAGCAACAGC 59.932 47.619 0.00 0.00 0.00 4.40
215 216 2.288030 CCTGGAGAAAAAGCAGCAACAG 60.288 50.000 0.00 0.00 0.00 3.16
216 217 1.682854 CCTGGAGAAAAAGCAGCAACA 59.317 47.619 0.00 0.00 0.00 3.33
217 218 1.603931 GCCTGGAGAAAAAGCAGCAAC 60.604 52.381 0.00 0.00 0.00 4.17
218 219 0.675633 GCCTGGAGAAAAAGCAGCAA 59.324 50.000 0.00 0.00 0.00 3.91
219 220 0.178981 AGCCTGGAGAAAAAGCAGCA 60.179 50.000 0.00 0.00 0.00 4.41
220 221 1.826385 TAGCCTGGAGAAAAAGCAGC 58.174 50.000 0.00 0.00 0.00 5.25
221 222 4.741342 CAAATAGCCTGGAGAAAAAGCAG 58.259 43.478 0.00 0.00 0.00 4.24
222 223 3.056607 GCAAATAGCCTGGAGAAAAAGCA 60.057 43.478 0.00 0.00 37.23 3.91
223 224 3.515630 GCAAATAGCCTGGAGAAAAAGC 58.484 45.455 0.00 0.00 37.23 3.51
236 237 2.611224 GCTTATGGCCATGGCAAATAGC 60.611 50.000 36.56 30.60 42.43 2.97
237 238 3.308438 GCTTATGGCCATGGCAAATAG 57.692 47.619 36.56 25.96 42.43 1.73
270 271 1.347817 GACCTCGTCAAGCAAGAGCG 61.348 60.000 0.00 0.00 37.97 5.03
271 272 1.016653 GGACCTCGTCAAGCAAGAGC 61.017 60.000 0.00 0.00 36.08 4.09
272 273 0.605589 AGGACCTCGTCAAGCAAGAG 59.394 55.000 0.00 0.00 33.68 2.85
273 274 0.603569 GAGGACCTCGTCAAGCAAGA 59.396 55.000 5.55 0.00 33.68 3.02
274 275 0.318441 TGAGGACCTCGTCAAGCAAG 59.682 55.000 16.81 0.00 37.75 4.01
275 276 0.318441 CTGAGGACCTCGTCAAGCAA 59.682 55.000 16.81 0.00 39.81 3.91
276 277 1.536073 CCTGAGGACCTCGTCAAGCA 61.536 60.000 16.81 0.00 39.81 3.91
277 278 1.216710 CCTGAGGACCTCGTCAAGC 59.783 63.158 16.81 0.00 39.81 4.01
278 279 1.216710 GCCTGAGGACCTCGTCAAG 59.783 63.158 16.81 8.18 39.81 3.02
279 280 1.533033 TGCCTGAGGACCTCGTCAA 60.533 57.895 16.81 0.00 39.81 3.18
280 281 2.117423 TGCCTGAGGACCTCGTCA 59.883 61.111 16.81 10.91 38.29 4.35
281 282 2.574399 GTGCCTGAGGACCTCGTC 59.426 66.667 16.81 8.51 32.35 4.20
282 283 3.374402 CGTGCCTGAGGACCTCGT 61.374 66.667 16.81 0.00 32.35 4.18
283 284 1.101635 TATCGTGCCTGAGGACCTCG 61.102 60.000 16.81 11.05 32.35 4.63
284 285 1.112113 TTATCGTGCCTGAGGACCTC 58.888 55.000 15.13 15.13 0.00 3.85
285 286 1.207329 GTTTATCGTGCCTGAGGACCT 59.793 52.381 0.65 0.00 0.00 3.85
286 287 1.207329 AGTTTATCGTGCCTGAGGACC 59.793 52.381 0.65 0.00 0.00 4.46
287 288 2.541556 GAGTTTATCGTGCCTGAGGAC 58.458 52.381 0.65 0.00 0.00 3.85
288 289 1.134367 CGAGTTTATCGTGCCTGAGGA 59.866 52.381 0.65 0.00 46.62 3.71
289 290 1.560923 CGAGTTTATCGTGCCTGAGG 58.439 55.000 0.00 0.00 46.62 3.86
308 309 4.409218 TGTAGTGTCGGCGGCGAC 62.409 66.667 45.48 45.48 39.16 5.19
309 310 4.111016 CTGTAGTGTCGGCGGCGA 62.111 66.667 31.46 31.46 0.00 5.54
311 312 2.775032 TTTCCTGTAGTGTCGGCGGC 62.775 60.000 3.62 3.62 0.00 6.53
312 313 1.012486 GTTTCCTGTAGTGTCGGCGG 61.012 60.000 7.21 0.00 0.00 6.13
313 314 0.038526 AGTTTCCTGTAGTGTCGGCG 60.039 55.000 0.00 0.00 0.00 6.46
314 315 1.429463 CAGTTTCCTGTAGTGTCGGC 58.571 55.000 0.00 0.00 33.80 5.54
315 316 1.000955 AGCAGTTTCCTGTAGTGTCGG 59.999 52.381 0.00 0.00 41.02 4.79
316 317 2.440539 AGCAGTTTCCTGTAGTGTCG 57.559 50.000 0.00 0.00 41.02 4.35
317 318 4.522722 ACTAGCAGTTTCCTGTAGTGTC 57.477 45.455 0.00 0.00 41.02 3.67
360 361 4.171005 CGTCTAGATTTACGTCTTTGCCA 58.829 43.478 0.00 0.00 34.48 4.92
399 400 3.159472 TGACTTTGCCGTCTACTTCCTA 58.841 45.455 0.00 0.00 35.00 2.94
496 497 4.224433 GACGGCAAAACTTTAGTTTAGCC 58.776 43.478 8.19 0.00 46.47 3.93
582 589 4.806330 GTCTGTGATTTAGGACGAAGACA 58.194 43.478 0.00 0.00 34.36 3.41
769 778 1.726791 CTGTGTAATCCGTCTGTGTGC 59.273 52.381 0.00 0.00 0.00 4.57
950 1173 0.978146 CCGACCCTGTCCTCCTTCAT 60.978 60.000 0.00 0.00 0.00 2.57
951 1174 1.609501 CCGACCCTGTCCTCCTTCA 60.610 63.158 0.00 0.00 0.00 3.02
1039 1442 4.393778 ATCCCCCGTCGTCCCAGT 62.394 66.667 0.00 0.00 0.00 4.00
1575 2321 6.044411 TCCACCTTATCTTCCTTATCCTCT 57.956 41.667 0.00 0.00 0.00 3.69
1692 2699 1.581934 GGATCAATCACGCGGATCAA 58.418 50.000 19.36 8.64 39.30 2.57
2076 3111 1.219124 GCAGCAGATGGAGAACCGA 59.781 57.895 0.00 0.00 39.42 4.69
2153 3188 1.571919 GATAGCGCCGAAGACAACAT 58.428 50.000 2.29 0.00 0.00 2.71
2175 3210 6.418101 ACTGGCACATGAGATAATAACACTT 58.582 36.000 0.00 0.00 38.20 3.16
2190 3225 1.836166 AGAGCAGTGATACTGGCACAT 59.164 47.619 10.62 0.00 46.01 3.21
2247 3282 0.962356 CAGGAAGCAACCCAAGCGAT 60.962 55.000 0.00 0.00 37.01 4.58
2248 3283 1.600636 CAGGAAGCAACCCAAGCGA 60.601 57.895 0.00 0.00 37.01 4.93
2361 3398 3.485346 GAACAGGAACCACCGCCCA 62.485 63.158 0.00 0.00 44.74 5.36
2392 3429 1.332997 GACTTCGACGGTATGGACGAT 59.667 52.381 0.00 0.00 34.85 3.73
2431 3468 1.986698 CCGACGACTTAACCGACATT 58.013 50.000 0.00 0.00 0.00 2.71
2450 3487 2.076863 CACCCACTTAGTAGCAACTGC 58.923 52.381 0.00 0.00 36.36 4.40
2455 3492 0.981183 CCACCACCCACTTAGTAGCA 59.019 55.000 0.00 0.00 0.00 3.49
2573 3610 2.009042 GCACTGACCTTTCGGAGATGG 61.009 57.143 0.00 0.00 35.04 3.51
2588 3625 2.868583 CCGTGGATATCTTTGAGCACTG 59.131 50.000 2.05 0.00 0.00 3.66
2595 3632 3.819564 TCACCTCCGTGGATATCTTTG 57.180 47.619 2.05 0.00 40.65 2.77


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

AutoCloner maintained by Alex Coulton.