Multiple sequence alignment - TraesCS7A01G189500

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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 TraesCS7A01G189500 chr7A 100.000 3590 0 0 1 3590 146907307 146910896 0.000000e+00 6630.0
1 TraesCS7A01G189500 chr7A 98.499 733 7 3 2860 3590 497778857 497779587 0.000000e+00 1290.0
2 TraesCS7A01G189500 chr7B 92.730 2366 118 33 414 2756 108248427 108250761 0.000000e+00 3367.0
3 TraesCS7A01G189500 chr7B 95.631 206 8 1 1 205 635935737 635935532 2.670000e-86 329.0
4 TraesCS7A01G189500 chr7B 82.609 230 20 12 206 415 108248090 108248319 6.120000e-43 185.0
5 TraesCS7A01G189500 chr7D 95.710 1958 66 9 842 2795 146090567 146092510 0.000000e+00 3134.0
6 TraesCS7A01G189500 chr7D 86.312 526 45 18 206 704 146089887 146090412 6.780000e-152 547.0
7 TraesCS7A01G189500 chr7D 100.000 30 0 0 3561 3590 395357969 395357940 5.010000e-04 56.5
8 TraesCS7A01G189500 chr3A 86.187 1542 186 15 1000 2523 100959905 100958373 0.000000e+00 1642.0
9 TraesCS7A01G189500 chr3A 86.025 1517 180 21 1012 2510 101608029 101609531 0.000000e+00 1598.0
10 TraesCS7A01G189500 chr3A 85.950 1516 185 18 1012 2510 101569160 101567656 0.000000e+00 1594.0
11 TraesCS7A01G189500 chr3A 84.078 1030 138 13 1001 2008 101102192 101101167 0.000000e+00 970.0
12 TraesCS7A01G189500 chr3A 84.388 474 72 2 2001 2473 101100255 101099783 7.020000e-127 464.0
13 TraesCS7A01G189500 chr3A 85.196 358 24 11 2852 3191 617256844 617256498 1.230000e-89 340.0
14 TraesCS7A01G189500 chr3A 93.478 92 6 0 3499 3590 617256419 617256328 1.740000e-28 137.0
15 TraesCS7A01G189500 chr3B 86.798 1477 177 9 1012 2473 133384566 133386039 0.000000e+00 1631.0
16 TraesCS7A01G189500 chr3B 85.227 1611 203 20 1001 2594 132999447 133001039 0.000000e+00 1624.0
17 TraesCS7A01G189500 chr3B 86.127 346 24 7 2860 3191 508714222 508714557 5.700000e-93 351.0
18 TraesCS7A01G189500 chr3B 96.585 205 7 0 1 205 746289170 746288966 1.230000e-89 340.0
19 TraesCS7A01G189500 chr3B 85.597 243 32 3 2865 3105 153532057 153532298 5.950000e-63 252.0
20 TraesCS7A01G189500 chr3B 92.308 91 7 0 3499 3589 508714636 508714726 2.910000e-26 130.0
21 TraesCS7A01G189500 chr3D 86.391 1477 179 14 1012 2471 84884177 84885648 0.000000e+00 1594.0
22 TraesCS7A01G189500 chr3D 100.000 30 0 0 3561 3590 565656910 565656881 5.010000e-04 56.5
23 TraesCS7A01G189500 chr4B 85.786 401 37 9 2963 3355 629776665 629776277 1.200000e-109 407.0
24 TraesCS7A01G189500 chr4B 94.686 207 10 1 1 206 655078218 655078012 1.610000e-83 320.0
25 TraesCS7A01G189500 chr5D 87.006 354 22 7 2852 3191 326123996 326123653 9.410000e-101 377.0
26 TraesCS7A01G189500 chr5D 94.565 92 5 0 3499 3590 326123574 326123483 3.740000e-30 143.0
27 TraesCS7A01G189500 chr1B 85.756 344 23 8 2863 3191 640059672 640059340 1.230000e-89 340.0
28 TraesCS7A01G189500 chr1B 96.117 206 8 0 1 206 245930012 245929807 1.600000e-88 337.0
29 TraesCS7A01G189500 chr1B 95.610 205 9 0 1 205 683396692 683396896 2.670000e-86 329.0
30 TraesCS7A01G189500 chr1B 93.478 92 6 0 3499 3590 640059261 640059170 1.740000e-28 137.0
31 TraesCS7A01G189500 chr6B 96.117 206 7 1 1 205 624403564 624403359 5.740000e-88 335.0
32 TraesCS7A01G189500 chr6B 86.400 250 29 5 2865 3111 498843914 498843667 5.910000e-68 268.0
33 TraesCS7A01G189500 chr2B 95.631 206 8 1 1 205 666634284 666634079 2.670000e-86 329.0
34 TraesCS7A01G189500 chr6A 95.146 206 9 1 1 205 124710764 124710969 1.240000e-84 324.0
35 TraesCS7A01G189500 chr2A 95.146 206 9 1 1 205 86312804 86313009 1.240000e-84 324.0
36 TraesCS7A01G189500 chr2A 86.897 145 7 3 3049 3191 742559492 742559626 6.210000e-33 152.0
37 TraesCS7A01G189500 chr4D 86.420 243 30 3 2865 3105 361371204 361371445 2.750000e-66 263.0
38 TraesCS7A01G189500 chr1D 80.102 196 30 8 3128 3320 445395599 445395788 1.740000e-28 137.0
39 TraesCS7A01G189500 chr6D 100.000 30 0 0 3561 3590 6347139 6347168 5.010000e-04 56.5


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 TraesCS7A01G189500 chr7A 146907307 146910896 3589 False 6630.0 6630 100.0000 1 3590 1 chr7A.!!$F1 3589
1 TraesCS7A01G189500 chr7A 497778857 497779587 730 False 1290.0 1290 98.4990 2860 3590 1 chr7A.!!$F2 730
2 TraesCS7A01G189500 chr7B 108248090 108250761 2671 False 1776.0 3367 87.6695 206 2756 2 chr7B.!!$F1 2550
3 TraesCS7A01G189500 chr7D 146089887 146092510 2623 False 1840.5 3134 91.0110 206 2795 2 chr7D.!!$F1 2589
4 TraesCS7A01G189500 chr3A 100958373 100959905 1532 True 1642.0 1642 86.1870 1000 2523 1 chr3A.!!$R1 1523
5 TraesCS7A01G189500 chr3A 101608029 101609531 1502 False 1598.0 1598 86.0250 1012 2510 1 chr3A.!!$F1 1498
6 TraesCS7A01G189500 chr3A 101567656 101569160 1504 True 1594.0 1594 85.9500 1012 2510 1 chr3A.!!$R2 1498
7 TraesCS7A01G189500 chr3A 101099783 101102192 2409 True 717.0 970 84.2330 1001 2473 2 chr3A.!!$R3 1472
8 TraesCS7A01G189500 chr3A 617256328 617256844 516 True 238.5 340 89.3370 2852 3590 2 chr3A.!!$R4 738
9 TraesCS7A01G189500 chr3B 133384566 133386039 1473 False 1631.0 1631 86.7980 1012 2473 1 chr3B.!!$F2 1461
10 TraesCS7A01G189500 chr3B 132999447 133001039 1592 False 1624.0 1624 85.2270 1001 2594 1 chr3B.!!$F1 1593
11 TraesCS7A01G189500 chr3B 508714222 508714726 504 False 240.5 351 89.2175 2860 3589 2 chr3B.!!$F4 729
12 TraesCS7A01G189500 chr3D 84884177 84885648 1471 False 1594.0 1594 86.3910 1012 2471 1 chr3D.!!$F1 1459
13 TraesCS7A01G189500 chr5D 326123483 326123996 513 True 260.0 377 90.7855 2852 3590 2 chr5D.!!$R1 738
14 TraesCS7A01G189500 chr1B 640059170 640059672 502 True 238.5 340 89.6170 2863 3590 2 chr1B.!!$R2 727

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
832 1002 0.092351 GTTCCGTACGCGTCACAATG 59.908 55.0 18.63 2.89 36.15 2.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2826 3983 0.178885 TTCCCCGATTCCCCCGATAT 60.179 55.0 0.0 0.0 0.0 1.63 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
19 20 1.263356 TCGAGGAATTTCGGTCCAGT 58.737 50.000 0.00 0.00 40.83 4.00
20 21 1.203994 TCGAGGAATTTCGGTCCAGTC 59.796 52.381 0.00 0.00 40.83 3.51
21 22 1.204941 CGAGGAATTTCGGTCCAGTCT 59.795 52.381 0.00 0.00 37.65 3.24
22 23 2.735762 CGAGGAATTTCGGTCCAGTCTC 60.736 54.545 0.00 0.00 37.65 3.36
23 24 2.498078 GAGGAATTTCGGTCCAGTCTCT 59.502 50.000 0.00 0.00 37.65 3.10
24 25 2.234908 AGGAATTTCGGTCCAGTCTCTG 59.765 50.000 0.00 0.00 37.65 3.35
25 26 2.003301 GAATTTCGGTCCAGTCTCTGC 58.997 52.381 0.00 0.00 0.00 4.26
26 27 0.108615 ATTTCGGTCCAGTCTCTGCG 60.109 55.000 0.00 0.00 0.00 5.18
27 28 1.461091 TTTCGGTCCAGTCTCTGCGT 61.461 55.000 0.00 0.00 0.00 5.24
28 29 1.863662 TTCGGTCCAGTCTCTGCGTC 61.864 60.000 0.00 0.00 0.00 5.19
29 30 2.626780 CGGTCCAGTCTCTGCGTCA 61.627 63.158 0.00 0.00 0.00 4.35
30 31 1.214062 GGTCCAGTCTCTGCGTCAG 59.786 63.158 1.02 1.02 0.00 3.51
31 32 1.445238 GTCCAGTCTCTGCGTCAGC 60.445 63.158 2.45 0.00 45.41 4.26
41 42 2.476051 GCGTCAGCAATGGTGTCG 59.524 61.111 23.04 23.04 42.92 4.35
42 43 2.476051 CGTCAGCAATGGTGTCGC 59.524 61.111 17.35 6.72 36.16 5.19
43 44 2.029288 CGTCAGCAATGGTGTCGCT 61.029 57.895 17.35 0.00 36.16 4.93
44 45 1.568612 CGTCAGCAATGGTGTCGCTT 61.569 55.000 17.35 0.00 36.16 4.68
45 46 0.166814 GTCAGCAATGGTGTCGCTTC 59.833 55.000 12.41 0.00 32.48 3.86
46 47 1.133253 CAGCAATGGTGTCGCTTCG 59.867 57.895 3.99 0.00 32.48 3.79
47 48 1.005037 AGCAATGGTGTCGCTTCGA 60.005 52.632 0.00 0.00 29.87 3.71
77 78 7.506328 GGGGGTGTTGAGATATGTATTTAAC 57.494 40.000 0.00 0.00 0.00 2.01
78 79 7.057894 GGGGGTGTTGAGATATGTATTTAACA 58.942 38.462 0.00 0.00 43.86 2.41
79 80 7.012989 GGGGGTGTTGAGATATGTATTTAACAC 59.987 40.741 0.00 0.00 42.09 3.32
80 81 7.554835 GGGGTGTTGAGATATGTATTTAACACA 59.445 37.037 16.14 0.00 44.77 3.72
81 82 9.120538 GGGTGTTGAGATATGTATTTAACACAT 57.879 33.333 16.14 0.00 44.77 3.21
82 83 9.935682 GGTGTTGAGATATGTATTTAACACATG 57.064 33.333 16.14 0.00 44.77 3.21
97 98 9.733556 ATTTAACACATGTATTCTTGTACTCCA 57.266 29.630 0.00 0.00 32.05 3.86
98 99 9.562408 TTTAACACATGTATTCTTGTACTCCAA 57.438 29.630 0.00 0.00 32.05 3.53
99 100 9.562408 TTAACACATGTATTCTTGTACTCCAAA 57.438 29.630 0.00 0.00 32.05 3.28
100 101 8.635765 AACACATGTATTCTTGTACTCCAAAT 57.364 30.769 0.00 0.00 32.05 2.32
101 102 8.268850 ACACATGTATTCTTGTACTCCAAATC 57.731 34.615 0.00 0.00 32.05 2.17
102 103 8.103305 ACACATGTATTCTTGTACTCCAAATCT 58.897 33.333 0.00 0.00 32.05 2.40
103 104 8.607459 CACATGTATTCTTGTACTCCAAATCTC 58.393 37.037 0.00 0.00 32.05 2.75
104 105 7.770897 ACATGTATTCTTGTACTCCAAATCTCC 59.229 37.037 0.00 0.00 31.20 3.71
105 106 7.496346 TGTATTCTTGTACTCCAAATCTCCT 57.504 36.000 0.00 0.00 31.20 3.69
106 107 7.556844 TGTATTCTTGTACTCCAAATCTCCTC 58.443 38.462 0.00 0.00 31.20 3.71
107 108 5.422214 TTCTTGTACTCCAAATCTCCTCC 57.578 43.478 0.00 0.00 31.20 4.30
108 109 4.689062 TCTTGTACTCCAAATCTCCTCCT 58.311 43.478 0.00 0.00 31.20 3.69
109 110 5.094387 TCTTGTACTCCAAATCTCCTCCTT 58.906 41.667 0.00 0.00 31.20 3.36
110 111 4.826274 TGTACTCCAAATCTCCTCCTTG 57.174 45.455 0.00 0.00 0.00 3.61
111 112 4.168101 TGTACTCCAAATCTCCTCCTTGT 58.832 43.478 0.00 0.00 0.00 3.16
112 113 5.338632 TGTACTCCAAATCTCCTCCTTGTA 58.661 41.667 0.00 0.00 0.00 2.41
113 114 5.964477 TGTACTCCAAATCTCCTCCTTGTAT 59.036 40.000 0.00 0.00 0.00 2.29
114 115 7.130099 TGTACTCCAAATCTCCTCCTTGTATA 58.870 38.462 0.00 0.00 0.00 1.47
115 116 7.789831 TGTACTCCAAATCTCCTCCTTGTATAT 59.210 37.037 0.00 0.00 0.00 0.86
116 117 9.310449 GTACTCCAAATCTCCTCCTTGTATATA 57.690 37.037 0.00 0.00 0.00 0.86
117 118 8.429237 ACTCCAAATCTCCTCCTTGTATATAG 57.571 38.462 0.00 0.00 0.00 1.31
118 119 8.013667 ACTCCAAATCTCCTCCTTGTATATAGT 58.986 37.037 0.00 0.00 0.00 2.12
119 120 8.798975 TCCAAATCTCCTCCTTGTATATAGTT 57.201 34.615 0.00 0.00 0.00 2.24
120 121 8.651389 TCCAAATCTCCTCCTTGTATATAGTTG 58.349 37.037 0.00 0.00 0.00 3.16
121 122 8.651389 CCAAATCTCCTCCTTGTATATAGTTGA 58.349 37.037 0.00 0.00 0.00 3.18
122 123 9.703892 CAAATCTCCTCCTTGTATATAGTTGAG 57.296 37.037 0.00 0.00 0.00 3.02
123 124 8.429237 AATCTCCTCCTTGTATATAGTTGAGG 57.571 38.462 9.66 9.66 39.38 3.86
124 125 7.162973 TCTCCTCCTTGTATATAGTTGAGGA 57.837 40.000 14.73 14.73 43.35 3.71
125 126 7.770662 TCTCCTCCTTGTATATAGTTGAGGAT 58.229 38.462 15.41 0.00 44.20 3.24
126 127 8.901841 TCTCCTCCTTGTATATAGTTGAGGATA 58.098 37.037 15.41 9.42 44.20 2.59
127 128 9.707957 CTCCTCCTTGTATATAGTTGAGGATAT 57.292 37.037 15.41 0.00 44.20 1.63
136 137 9.819267 GTATATAGTTGAGGATATAACTTGCCC 57.181 37.037 0.00 0.00 38.11 5.36
137 138 8.686739 ATATAGTTGAGGATATAACTTGCCCT 57.313 34.615 0.00 0.00 38.11 5.19
138 139 9.784376 ATATAGTTGAGGATATAACTTGCCCTA 57.216 33.333 0.00 0.00 38.11 3.53
139 140 8.686739 ATAGTTGAGGATATAACTTGCCCTAT 57.313 34.615 0.00 0.00 38.11 2.57
140 141 6.773638 AGTTGAGGATATAACTTGCCCTATG 58.226 40.000 0.00 0.00 33.59 2.23
141 142 6.330250 AGTTGAGGATATAACTTGCCCTATGT 59.670 38.462 0.00 0.00 33.59 2.29
142 143 7.512746 AGTTGAGGATATAACTTGCCCTATGTA 59.487 37.037 0.00 0.00 33.59 2.29
143 144 7.241042 TGAGGATATAACTTGCCCTATGTAC 57.759 40.000 0.00 0.00 0.00 2.90
144 145 7.016914 TGAGGATATAACTTGCCCTATGTACT 58.983 38.462 0.00 0.00 0.00 2.73
145 146 8.174757 TGAGGATATAACTTGCCCTATGTACTA 58.825 37.037 0.00 0.00 0.00 1.82
146 147 9.203163 GAGGATATAACTTGCCCTATGTACTAT 57.797 37.037 0.00 0.00 0.00 2.12
158 159 8.692710 TGCCCTATGTACTATATATACTTGTGC 58.307 37.037 0.00 0.00 0.00 4.57
159 160 8.692710 GCCCTATGTACTATATATACTTGTGCA 58.307 37.037 0.00 4.60 0.00 4.57
181 182 7.381766 GCATATGCACCTATCAATACATTGA 57.618 36.000 22.84 7.08 44.65 2.57
182 183 7.120138 TGCATATGCACCTATCAATACATTGAG 59.880 37.037 26.32 0.60 46.74 3.02
183 184 7.335171 GCATATGCACCTATCAATACATTGAGA 59.665 37.037 22.84 5.15 44.22 3.27
203 204 5.862678 AGAGTTGCCTCTTATTCCTCTAC 57.137 43.478 0.00 0.00 46.08 2.59
204 205 5.273208 AGAGTTGCCTCTTATTCCTCTACA 58.727 41.667 0.00 0.00 46.08 2.74
222 223 2.370349 ACACCGAGGACTAGATCACTG 58.630 52.381 0.00 0.00 0.00 3.66
241 246 1.272425 TGGACCCTCCATTCGCAAAAT 60.272 47.619 0.00 0.00 42.67 1.82
247 252 6.183360 GGACCCTCCATTCGCAAAATAAAATA 60.183 38.462 0.00 0.00 36.28 1.40
248 253 7.360113 ACCCTCCATTCGCAAAATAAAATAT 57.640 32.000 0.00 0.00 0.00 1.28
257 263 6.950545 TCGCAAAATAAAATATGAGGGTACG 58.049 36.000 0.00 0.00 0.00 3.67
261 267 7.645402 CAAAATAAAATATGAGGGTACGGGAC 58.355 38.462 0.00 0.00 0.00 4.46
279 285 3.068691 CCTCTTGGACCGGCTCGA 61.069 66.667 0.00 0.00 34.57 4.04
281 287 1.446272 CTCTTGGACCGGCTCGAAC 60.446 63.158 0.00 0.00 0.00 3.95
282 288 2.809601 CTTGGACCGGCTCGAACG 60.810 66.667 0.00 2.46 0.00 3.95
283 289 3.277211 CTTGGACCGGCTCGAACGA 62.277 63.158 0.00 0.00 0.00 3.85
291 307 4.849329 GCTCGAACGACCGGCGAT 62.849 66.667 22.10 12.28 44.57 4.58
324 349 2.202837 GCCCGTACACGATCACCC 60.203 66.667 2.76 0.00 43.02 4.61
421 557 1.000145 GCTTCCGCTTCTAGAAACCG 59.000 55.000 6.63 11.64 0.00 4.44
446 582 2.736719 CGAATCTCGATCCACACAGCTT 60.737 50.000 0.00 0.00 43.74 3.74
448 584 0.171231 TCTCGATCCACACAGCTTCG 59.829 55.000 0.00 0.00 0.00 3.79
449 585 0.109086 CTCGATCCACACAGCTTCGT 60.109 55.000 2.02 0.00 0.00 3.85
450 586 1.132453 CTCGATCCACACAGCTTCGTA 59.868 52.381 2.02 0.00 0.00 3.43
463 601 3.092403 TCGTATCGTGACGACCGG 58.908 61.111 22.66 0.00 46.43 5.28
508 646 3.275088 CTGCGTCCACGTAGGTCT 58.725 61.111 9.13 0.00 45.99 3.85
530 668 2.970324 GCCCGCGACTCACACAAA 60.970 61.111 8.23 0.00 0.00 2.83
592 730 1.079543 AGGAGCAGACGCATGTGTC 60.080 57.895 28.12 28.12 42.27 3.67
593 731 2.103042 GGAGCAGACGCATGTGTCC 61.103 63.158 30.72 18.94 42.27 4.02
646 787 2.786495 CGCCTAGCCACCACTCGAT 61.786 63.158 0.00 0.00 0.00 3.59
656 797 1.734465 CACCACTCGATGCTTCCTTTC 59.266 52.381 0.00 0.00 0.00 2.62
699 842 3.368323 CCAGCTTCTCAACTTCTCTCCTC 60.368 52.174 0.00 0.00 0.00 3.71
769 939 1.209383 CACGTCACGTCCGATGTCT 59.791 57.895 0.00 0.00 38.32 3.41
798 968 2.342279 CGAAGCCTCGTGGTGGAA 59.658 61.111 5.26 0.00 40.33 3.53
799 969 1.301401 CGAAGCCTCGTGGTGGAAA 60.301 57.895 5.26 0.00 40.33 3.13
800 970 1.566018 CGAAGCCTCGTGGTGGAAAC 61.566 60.000 5.26 0.00 40.33 2.78
801 971 1.566018 GAAGCCTCGTGGTGGAAACG 61.566 60.000 5.26 0.00 42.36 3.60
831 1001 1.339235 CGTTCCGTACGCGTCACAAT 61.339 55.000 18.63 0.00 44.26 2.71
832 1002 0.092351 GTTCCGTACGCGTCACAATG 59.908 55.000 18.63 2.89 36.15 2.82
835 1005 1.680105 CCGTACGCGTCACAATGACC 61.680 60.000 18.63 0.00 44.20 4.02
836 1006 1.004785 CGTACGCGTCACAATGACCA 61.005 55.000 18.63 0.00 44.20 4.02
837 1007 0.437295 GTACGCGTCACAATGACCAC 59.563 55.000 18.63 0.00 44.20 4.16
839 1009 2.860293 GCGTCACAATGACCACCG 59.140 61.111 3.45 0.00 44.20 4.94
840 1010 1.959226 GCGTCACAATGACCACCGT 60.959 57.895 3.45 0.00 44.20 4.83
845 1035 0.533978 CACAATGACCACCGTGACCA 60.534 55.000 0.00 0.00 0.00 4.02
850 1040 1.369692 GACCACCGTGACCATGTCA 59.630 57.895 0.00 0.00 40.50 3.58
870 1060 0.969149 TAGGTGTCTCACAGCCACTG 59.031 55.000 2.28 0.00 46.99 3.66
903 1093 6.207810 ACGCCACAATTAACCTTCTTAATTCA 59.792 34.615 0.00 0.00 33.66 2.57
939 1143 2.416431 CCGCCGTTACCACTATATAGCC 60.416 54.545 9.78 0.00 0.00 3.93
945 1149 4.154737 CGTTACCACTATATAGCCGCTGTA 59.845 45.833 9.78 0.27 0.00 2.74
966 1170 2.684843 GGAGCAAGCGAGCAACAGG 61.685 63.158 6.21 0.00 36.85 4.00
970 1174 2.032681 AAGCGAGCAACAGGGACC 59.967 61.111 0.00 0.00 0.00 4.46
994 1200 1.306568 AGAAGCAGGGAGAGGGTCC 60.307 63.158 0.00 0.00 46.10 4.46
2013 3164 3.839432 GAGGGGTTCGAGGAGCGG 61.839 72.222 0.00 0.00 41.33 5.52
2478 3629 1.748122 GAGGAGCCACGAGTACGGA 60.748 63.158 0.00 0.00 44.46 4.69
2607 3758 1.071228 TGAGCTGCATCTCGCCATTAT 59.929 47.619 12.62 0.00 41.33 1.28
2659 3810 5.503498 TCCGTACAACAATTCTTTTCAACG 58.497 37.500 0.00 0.00 0.00 4.10
2684 3835 3.555956 CGATACCACCATGTTGAAGTAGC 59.444 47.826 0.00 0.00 0.00 3.58
2685 3836 2.949177 ACCACCATGTTGAAGTAGCA 57.051 45.000 0.00 0.00 0.00 3.49
2686 3837 3.222173 ACCACCATGTTGAAGTAGCAA 57.778 42.857 0.00 0.00 0.00 3.91
2687 3838 3.766545 ACCACCATGTTGAAGTAGCAAT 58.233 40.909 0.00 0.00 0.00 3.56
2688 3839 4.151883 ACCACCATGTTGAAGTAGCAATT 58.848 39.130 0.00 0.00 0.00 2.32
2689 3840 4.588528 ACCACCATGTTGAAGTAGCAATTT 59.411 37.500 0.00 0.00 0.00 1.82
2690 3841 4.925054 CCACCATGTTGAAGTAGCAATTTG 59.075 41.667 0.00 0.00 0.00 2.32
2691 3842 4.386652 CACCATGTTGAAGTAGCAATTTGC 59.613 41.667 13.55 13.55 45.46 3.68
2720 3871 9.970553 AATTCATCCATGTAATATGATGCTAGT 57.029 29.630 3.32 0.00 35.74 2.57
2762 3919 3.740115 AGTGTATCTTTGGCGTCACTTT 58.260 40.909 0.00 0.00 33.26 2.66
2773 3930 3.749088 TGGCGTCACTTTACGAATCAATT 59.251 39.130 0.00 0.00 45.68 2.32
2807 3964 9.614792 ATGGATAGTTCTAGTAATTTGAACACC 57.385 33.333 0.00 0.00 41.91 4.16
2808 3965 8.598916 TGGATAGTTCTAGTAATTTGAACACCA 58.401 33.333 0.00 0.00 41.91 4.17
2809 3966 9.099454 GGATAGTTCTAGTAATTTGAACACCAG 57.901 37.037 0.00 0.00 41.91 4.00
2810 3967 9.654663 GATAGTTCTAGTAATTTGAACACCAGT 57.345 33.333 0.00 0.00 41.91 4.00
2812 3969 8.747538 AGTTCTAGTAATTTGAACACCAGTTT 57.252 30.769 0.00 0.00 41.91 2.66
2813 3970 8.621286 AGTTCTAGTAATTTGAACACCAGTTTG 58.379 33.333 0.00 0.00 41.91 2.93
2814 3971 6.966021 TCTAGTAATTTGAACACCAGTTTGC 58.034 36.000 0.00 0.00 38.30 3.68
2815 3972 5.590530 AGTAATTTGAACACCAGTTTGCA 57.409 34.783 0.00 0.00 38.30 4.08
2816 3973 5.971763 AGTAATTTGAACACCAGTTTGCAA 58.028 33.333 0.00 0.00 38.30 4.08
2817 3974 6.402222 AGTAATTTGAACACCAGTTTGCAAA 58.598 32.000 8.05 8.05 38.30 3.68
2818 3975 6.876257 AGTAATTTGAACACCAGTTTGCAAAA 59.124 30.769 14.67 0.00 38.30 2.44
2819 3976 4.999751 TTTGAACACCAGTTTGCAAAAC 57.000 36.364 14.67 8.45 38.30 2.43
2820 3977 3.667497 TGAACACCAGTTTGCAAAACA 57.333 38.095 14.67 2.10 38.30 2.83
2821 3978 3.321497 TGAACACCAGTTTGCAAAACAC 58.679 40.909 14.67 2.03 38.30 3.32
2822 3979 3.243873 TGAACACCAGTTTGCAAAACACA 60.244 39.130 14.67 3.60 38.30 3.72
2823 3980 3.393089 ACACCAGTTTGCAAAACACAA 57.607 38.095 14.67 0.00 0.00 3.33
2824 3981 3.063485 ACACCAGTTTGCAAAACACAAC 58.937 40.909 14.67 0.35 0.00 3.32
2825 3982 2.414825 CACCAGTTTGCAAAACACAACC 59.585 45.455 14.67 0.00 0.00 3.77
2826 3983 2.037772 ACCAGTTTGCAAAACACAACCA 59.962 40.909 14.67 0.00 0.00 3.67
2827 3984 3.269178 CCAGTTTGCAAAACACAACCAT 58.731 40.909 14.67 0.00 0.00 3.55
2828 3985 4.081420 ACCAGTTTGCAAAACACAACCATA 60.081 37.500 14.67 0.00 0.00 2.74
2829 3986 5.055812 CCAGTTTGCAAAACACAACCATAT 58.944 37.500 14.67 0.00 0.00 1.78
2830 3987 5.177327 CCAGTTTGCAAAACACAACCATATC 59.823 40.000 14.67 0.00 0.00 1.63
2831 3988 4.981674 AGTTTGCAAAACACAACCATATCG 59.018 37.500 14.67 0.00 0.00 2.92
2832 3989 3.567576 TGCAAAACACAACCATATCGG 57.432 42.857 0.00 0.00 42.50 4.18
2833 3990 2.230025 TGCAAAACACAACCATATCGGG 59.770 45.455 0.00 0.00 40.22 5.14
2834 3991 2.416701 GCAAAACACAACCATATCGGGG 60.417 50.000 0.00 0.00 40.22 5.73
2835 3992 2.137810 AAACACAACCATATCGGGGG 57.862 50.000 0.00 0.00 40.22 5.40
2836 3993 1.291109 AACACAACCATATCGGGGGA 58.709 50.000 0.00 0.00 40.22 4.81
2837 3994 1.291109 ACACAACCATATCGGGGGAA 58.709 50.000 0.00 0.00 40.22 3.97
2838 3995 1.850345 ACACAACCATATCGGGGGAAT 59.150 47.619 0.00 0.00 40.22 3.01
2839 3996 2.158667 ACACAACCATATCGGGGGAATC 60.159 50.000 0.00 0.00 40.22 2.52
2840 3997 1.071699 ACAACCATATCGGGGGAATCG 59.928 52.381 0.00 0.00 40.22 3.34
2841 3998 0.690762 AACCATATCGGGGGAATCGG 59.309 55.000 0.00 0.00 40.22 4.18
2842 3999 1.198759 ACCATATCGGGGGAATCGGG 61.199 60.000 0.00 0.00 40.22 5.14
2843 4000 1.602237 CATATCGGGGGAATCGGGG 59.398 63.158 0.00 0.00 0.00 5.73
2844 4001 0.907704 CATATCGGGGGAATCGGGGA 60.908 60.000 0.00 0.00 0.00 4.81
2845 4002 0.178885 ATATCGGGGGAATCGGGGAA 60.179 55.000 0.00 0.00 0.00 3.97
2846 4003 0.400237 TATCGGGGGAATCGGGGAAA 60.400 55.000 0.00 0.00 0.00 3.13
2847 4004 1.065997 ATCGGGGGAATCGGGGAAAT 61.066 55.000 0.00 0.00 0.00 2.17
2848 4005 0.400237 TCGGGGGAATCGGGGAAATA 60.400 55.000 0.00 0.00 0.00 1.40
2849 4006 0.696501 CGGGGGAATCGGGGAAATAT 59.303 55.000 0.00 0.00 0.00 1.28
2850 4007 1.613255 CGGGGGAATCGGGGAAATATG 60.613 57.143 0.00 0.00 0.00 1.78
2854 4011 3.344515 GGGAATCGGGGAAATATGCTAC 58.655 50.000 0.00 0.00 0.00 3.58
2930 4090 0.382873 ACAGCAATACGGCGATACGA 59.617 50.000 16.62 0.00 39.27 3.43
3114 4297 6.314648 TCATCATCAATTTACTCAGCAGTGAC 59.685 38.462 0.00 0.00 33.62 3.67
3115 4298 4.937620 TCATCAATTTACTCAGCAGTGACC 59.062 41.667 0.00 0.00 33.62 4.02
3116 4299 4.350368 TCAATTTACTCAGCAGTGACCA 57.650 40.909 0.00 0.00 33.62 4.02
3117 4300 4.318332 TCAATTTACTCAGCAGTGACCAG 58.682 43.478 0.00 0.00 33.62 4.00
3118 4301 4.067896 CAATTTACTCAGCAGTGACCAGT 58.932 43.478 0.00 0.00 33.62 4.00
3119 4302 5.011635 TCAATTTACTCAGCAGTGACCAGTA 59.988 40.000 0.00 0.00 33.62 2.74
3120 4303 4.521130 TTTACTCAGCAGTGACCAGTAG 57.479 45.455 0.00 0.00 33.62 2.57
3121 4304 2.002505 ACTCAGCAGTGACCAGTAGT 57.997 50.000 0.00 0.00 0.00 2.73
3122 4305 1.889829 ACTCAGCAGTGACCAGTAGTC 59.110 52.381 0.00 0.00 46.51 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.203994 GACTGGACCGAAATTCCTCGA 59.796 52.381 1.10 0.00 41.44 4.04
1 2 1.204941 AGACTGGACCGAAATTCCTCG 59.795 52.381 0.00 0.00 38.58 4.63
2 3 2.498078 AGAGACTGGACCGAAATTCCTC 59.502 50.000 0.00 0.00 33.84 3.71
3 4 2.234908 CAGAGACTGGACCGAAATTCCT 59.765 50.000 0.00 0.00 33.84 3.36
4 5 2.622436 CAGAGACTGGACCGAAATTCC 58.378 52.381 0.00 0.00 0.00 3.01
5 6 2.003301 GCAGAGACTGGACCGAAATTC 58.997 52.381 0.00 0.00 31.21 2.17
6 7 1.673033 CGCAGAGACTGGACCGAAATT 60.673 52.381 0.00 0.00 31.21 1.82
7 8 0.108615 CGCAGAGACTGGACCGAAAT 60.109 55.000 0.00 0.00 31.21 2.17
8 9 1.289066 CGCAGAGACTGGACCGAAA 59.711 57.895 0.00 0.00 31.21 3.46
9 10 1.863662 GACGCAGAGACTGGACCGAA 61.864 60.000 0.00 0.00 31.21 4.30
10 11 2.282251 ACGCAGAGACTGGACCGA 60.282 61.111 0.00 0.00 31.21 4.69
11 12 2.179517 GACGCAGAGACTGGACCG 59.820 66.667 0.00 0.00 31.21 4.79
12 13 1.214062 CTGACGCAGAGACTGGACC 59.786 63.158 1.18 0.00 32.44 4.46
13 14 1.445238 GCTGACGCAGAGACTGGAC 60.445 63.158 10.46 0.00 32.44 4.02
14 15 1.903404 TGCTGACGCAGAGACTGGA 60.903 57.895 10.46 0.00 42.25 3.86
15 16 2.653115 TGCTGACGCAGAGACTGG 59.347 61.111 10.46 0.00 42.25 4.00
23 24 2.316867 CGACACCATTGCTGACGCA 61.317 57.895 0.00 0.00 46.24 5.24
24 25 2.476051 CGACACCATTGCTGACGC 59.524 61.111 0.00 0.00 0.00 5.19
25 26 2.476051 GCGACACCATTGCTGACG 59.524 61.111 0.00 0.46 34.45 4.35
30 31 3.561429 TCGAAGCGACACCATTGC 58.439 55.556 0.00 0.00 38.10 3.56
53 54 7.012989 GTGTTAAATACATATCTCAACACCCCC 59.987 40.741 0.00 0.00 38.73 5.40
54 55 7.554835 TGTGTTAAATACATATCTCAACACCCC 59.445 37.037 11.00 0.00 42.09 4.95
55 56 8.500753 TGTGTTAAATACATATCTCAACACCC 57.499 34.615 11.00 0.00 42.09 4.61
56 57 9.935682 CATGTGTTAAATACATATCTCAACACC 57.064 33.333 11.00 0.00 42.09 4.16
71 72 9.733556 TGGAGTACAAGAATACATGTGTTAAAT 57.266 29.630 9.11 0.00 0.00 1.40
72 73 9.562408 TTGGAGTACAAGAATACATGTGTTAAA 57.438 29.630 9.11 0.00 33.18 1.52
73 74 9.562408 TTTGGAGTACAAGAATACATGTGTTAA 57.438 29.630 9.11 0.00 40.82 2.01
74 75 9.733556 ATTTGGAGTACAAGAATACATGTGTTA 57.266 29.630 9.11 0.00 40.82 2.41
75 76 8.635765 ATTTGGAGTACAAGAATACATGTGTT 57.364 30.769 9.11 8.33 40.82 3.32
76 77 8.103305 AGATTTGGAGTACAAGAATACATGTGT 58.897 33.333 9.11 0.00 40.82 3.72
77 78 8.498054 AGATTTGGAGTACAAGAATACATGTG 57.502 34.615 9.11 0.00 40.82 3.21
78 79 7.770897 GGAGATTTGGAGTACAAGAATACATGT 59.229 37.037 2.69 2.69 40.82 3.21
79 80 7.989741 AGGAGATTTGGAGTACAAGAATACATG 59.010 37.037 0.00 0.00 40.82 3.21
80 81 8.095452 AGGAGATTTGGAGTACAAGAATACAT 57.905 34.615 0.00 0.00 40.82 2.29
81 82 7.364762 GGAGGAGATTTGGAGTACAAGAATACA 60.365 40.741 0.00 0.00 40.82 2.29
82 83 6.987404 GGAGGAGATTTGGAGTACAAGAATAC 59.013 42.308 0.00 0.00 40.82 1.89
83 84 6.903534 AGGAGGAGATTTGGAGTACAAGAATA 59.096 38.462 0.00 0.00 40.82 1.75
84 85 5.728741 AGGAGGAGATTTGGAGTACAAGAAT 59.271 40.000 0.00 0.00 40.82 2.40
85 86 5.094387 AGGAGGAGATTTGGAGTACAAGAA 58.906 41.667 0.00 0.00 40.82 2.52
86 87 4.689062 AGGAGGAGATTTGGAGTACAAGA 58.311 43.478 0.00 0.00 40.82 3.02
87 88 5.181748 CAAGGAGGAGATTTGGAGTACAAG 58.818 45.833 0.00 0.00 40.82 3.16
88 89 4.597507 ACAAGGAGGAGATTTGGAGTACAA 59.402 41.667 0.00 0.00 37.28 2.41
89 90 4.168101 ACAAGGAGGAGATTTGGAGTACA 58.832 43.478 0.00 0.00 0.00 2.90
90 91 4.828072 ACAAGGAGGAGATTTGGAGTAC 57.172 45.455 0.00 0.00 0.00 2.73
91 92 9.535170 CTATATACAAGGAGGAGATTTGGAGTA 57.465 37.037 0.00 0.00 0.00 2.59
92 93 8.013667 ACTATATACAAGGAGGAGATTTGGAGT 58.986 37.037 0.00 0.00 0.00 3.85
93 94 8.429237 ACTATATACAAGGAGGAGATTTGGAG 57.571 38.462 0.00 0.00 0.00 3.86
94 95 8.651389 CAACTATATACAAGGAGGAGATTTGGA 58.349 37.037 0.00 0.00 0.00 3.53
95 96 8.651389 TCAACTATATACAAGGAGGAGATTTGG 58.349 37.037 0.00 0.00 0.00 3.28
96 97 9.703892 CTCAACTATATACAAGGAGGAGATTTG 57.296 37.037 0.00 0.00 0.00 2.32
97 98 8.875168 CCTCAACTATATACAAGGAGGAGATTT 58.125 37.037 0.00 0.00 42.32 2.17
98 99 8.235230 TCCTCAACTATATACAAGGAGGAGATT 58.765 37.037 0.00 0.00 43.19 2.40
99 100 7.770662 TCCTCAACTATATACAAGGAGGAGAT 58.229 38.462 0.00 0.00 43.19 2.75
100 101 7.162973 TCCTCAACTATATACAAGGAGGAGA 57.837 40.000 0.00 0.00 43.19 3.71
110 111 9.819267 GGGCAAGTTATATCCTCAACTATATAC 57.181 37.037 0.00 0.00 33.92 1.47
111 112 9.784376 AGGGCAAGTTATATCCTCAACTATATA 57.216 33.333 0.00 0.00 33.92 0.86
112 113 8.686739 AGGGCAAGTTATATCCTCAACTATAT 57.313 34.615 0.00 0.00 33.92 0.86
113 114 9.784376 ATAGGGCAAGTTATATCCTCAACTATA 57.216 33.333 0.00 0.00 33.92 1.31
114 115 8.543774 CATAGGGCAAGTTATATCCTCAACTAT 58.456 37.037 0.00 0.00 33.92 2.12
115 116 7.512746 ACATAGGGCAAGTTATATCCTCAACTA 59.487 37.037 0.00 0.00 33.92 2.24
116 117 6.330250 ACATAGGGCAAGTTATATCCTCAACT 59.670 38.462 0.00 0.00 36.56 3.16
117 118 6.534634 ACATAGGGCAAGTTATATCCTCAAC 58.465 40.000 0.00 0.00 0.00 3.18
118 119 6.763715 ACATAGGGCAAGTTATATCCTCAA 57.236 37.500 0.00 0.00 0.00 3.02
119 120 7.016914 AGTACATAGGGCAAGTTATATCCTCA 58.983 38.462 0.00 0.00 0.00 3.86
120 121 7.483580 AGTACATAGGGCAAGTTATATCCTC 57.516 40.000 0.00 0.00 0.00 3.71
132 133 8.692710 GCACAAGTATATATAGTACATAGGGCA 58.307 37.037 0.38 0.00 0.00 5.36
133 134 8.692710 TGCACAAGTATATATAGTACATAGGGC 58.307 37.037 0.38 3.32 0.00 5.19
156 157 6.941436 TCAATGTATTGATAGGTGCATATGCA 59.059 34.615 26.32 26.32 44.18 3.96
157 158 7.335171 TCTCAATGTATTGATAGGTGCATATGC 59.665 37.037 21.09 21.09 44.92 3.14
158 159 8.782339 TCTCAATGTATTGATAGGTGCATATG 57.218 34.615 7.67 0.00 44.92 1.78
159 160 8.600668 ACTCTCAATGTATTGATAGGTGCATAT 58.399 33.333 18.38 0.00 44.92 1.78
160 161 7.966812 ACTCTCAATGTATTGATAGGTGCATA 58.033 34.615 18.38 0.00 44.92 3.14
161 162 6.835174 ACTCTCAATGTATTGATAGGTGCAT 58.165 36.000 18.38 1.69 44.92 3.96
162 163 6.239217 ACTCTCAATGTATTGATAGGTGCA 57.761 37.500 18.38 0.00 44.92 4.57
163 164 6.952743 CAACTCTCAATGTATTGATAGGTGC 58.047 40.000 18.81 0.00 45.38 5.01
165 166 6.058183 GGCAACTCTCAATGTATTGATAGGT 58.942 40.000 18.38 12.45 44.92 3.08
166 167 6.551385 GGCAACTCTCAATGTATTGATAGG 57.449 41.667 18.38 10.39 44.92 2.57
184 185 4.443621 GGTGTAGAGGAATAAGAGGCAAC 58.556 47.826 0.00 0.00 0.00 4.17
185 186 3.132289 CGGTGTAGAGGAATAAGAGGCAA 59.868 47.826 0.00 0.00 0.00 4.52
186 187 2.693591 CGGTGTAGAGGAATAAGAGGCA 59.306 50.000 0.00 0.00 0.00 4.75
187 188 2.957006 TCGGTGTAGAGGAATAAGAGGC 59.043 50.000 0.00 0.00 0.00 4.70
188 189 4.839668 CTCGGTGTAGAGGAATAAGAGG 57.160 50.000 0.00 0.00 34.74 3.69
198 199 3.810941 GTGATCTAGTCCTCGGTGTAGAG 59.189 52.174 0.00 0.00 37.97 2.43
199 200 3.455177 AGTGATCTAGTCCTCGGTGTAGA 59.545 47.826 0.00 0.00 0.00 2.59
200 201 3.562141 CAGTGATCTAGTCCTCGGTGTAG 59.438 52.174 0.00 0.00 0.00 2.74
201 202 3.542648 CAGTGATCTAGTCCTCGGTGTA 58.457 50.000 0.00 0.00 0.00 2.90
202 203 2.370349 CAGTGATCTAGTCCTCGGTGT 58.630 52.381 0.00 0.00 0.00 4.16
203 204 1.678627 CCAGTGATCTAGTCCTCGGTG 59.321 57.143 0.00 0.00 0.00 4.94
204 205 1.564818 TCCAGTGATCTAGTCCTCGGT 59.435 52.381 0.00 0.00 0.00 4.69
222 223 1.474330 ATTTTGCGAATGGAGGGTCC 58.526 50.000 0.00 0.00 36.96 4.46
241 246 4.961438 GGTCCCGTACCCTCATATTTTA 57.039 45.455 0.00 0.00 43.16 1.52
257 263 3.400054 CCGGTCCAAGAGGGTCCC 61.400 72.222 0.00 0.00 41.37 4.46
261 267 4.148825 CGAGCCGGTCCAAGAGGG 62.149 72.222 1.90 0.00 34.83 4.30
266 272 3.296836 TCGTTCGAGCCGGTCCAA 61.297 61.111 1.90 0.00 0.00 3.53
438 574 1.728179 CGTCACGATACGAAGCTGTGT 60.728 52.381 8.28 0.00 45.68 3.72
448 584 2.649975 CGCCGGTCGTCACGATAC 60.650 66.667 1.61 0.00 38.42 2.24
475 613 0.177141 GCAGATGTTACCCCAGCGTA 59.823 55.000 0.00 0.00 0.00 4.42
481 619 0.743345 GTGGACGCAGATGTTACCCC 60.743 60.000 0.00 0.00 0.00 4.95
483 621 0.389426 ACGTGGACGCAGATGTTACC 60.389 55.000 0.00 0.00 44.43 2.85
530 668 4.280494 ACGTGAGCTGCCGAACGT 62.280 61.111 16.15 16.15 43.87 3.99
565 703 1.145819 GTCTGCTCCTGGCCATCTC 59.854 63.158 5.51 0.00 40.92 2.75
593 731 1.444212 CGTGGGGTTACCGTACACG 60.444 63.158 22.65 22.65 46.82 4.49
646 787 3.354678 GCCAAGCGAAAGGAAGCA 58.645 55.556 0.00 0.00 35.48 3.91
678 819 3.368323 GGAGGAGAGAAGTTGAGAAGCTG 60.368 52.174 0.00 0.00 0.00 4.24
699 842 1.064758 TGAAATTGTCCATCGGGAGGG 60.065 52.381 0.00 0.00 46.12 4.30
769 939 2.173669 GGCTTCGCGCTATGCTGAA 61.174 57.895 17.37 6.40 43.27 3.02
782 952 1.566018 CGTTTCCACCACGAGGCTTC 61.566 60.000 0.00 0.00 40.20 3.86
785 955 2.029964 TCGTTTCCACCACGAGGC 59.970 61.111 0.00 0.00 41.66 4.70
788 958 0.677288 ATGTCTCGTTTCCACCACGA 59.323 50.000 0.00 0.00 44.25 4.35
789 959 1.068474 GATGTCTCGTTTCCACCACG 58.932 55.000 0.00 0.00 39.08 4.94
790 960 1.068474 CGATGTCTCGTTTCCACCAC 58.932 55.000 0.00 0.00 40.07 4.16
791 961 0.037697 CCGATGTCTCGTTTCCACCA 60.038 55.000 0.00 0.00 43.49 4.17
792 962 0.037605 ACCGATGTCTCGTTTCCACC 60.038 55.000 0.00 0.00 43.49 4.61
794 964 0.109458 CGACCGATGTCTCGTTTCCA 60.109 55.000 0.00 0.00 43.49 3.53
795 965 0.109412 ACGACCGATGTCTCGTTTCC 60.109 55.000 0.00 0.00 40.16 3.13
799 969 1.505353 GGAACGACCGATGTCTCGT 59.495 57.895 0.00 0.00 44.89 4.18
800 970 4.379221 GGAACGACCGATGTCTCG 57.621 61.111 0.00 0.00 44.62 4.04
831 1001 1.369692 GACATGGTCACGGTGGTCA 59.630 57.895 8.50 7.47 32.09 4.02
832 1002 0.036388 ATGACATGGTCACGGTGGTC 60.036 55.000 8.50 7.79 45.65 4.02
835 1005 1.207089 ACCTATGACATGGTCACGGTG 59.793 52.381 16.63 0.56 45.65 4.94
836 1006 1.207089 CACCTATGACATGGTCACGGT 59.793 52.381 13.36 13.36 45.65 4.83
837 1007 1.207089 ACACCTATGACATGGTCACGG 59.793 52.381 0.49 7.89 45.65 4.94
839 1009 3.195610 TGAGACACCTATGACATGGTCAC 59.804 47.826 0.49 1.03 45.65 3.67
840 1010 3.195610 GTGAGACACCTATGACATGGTCA 59.804 47.826 1.05 1.05 46.90 4.02
845 1035 2.169352 GGCTGTGAGACACCTATGACAT 59.831 50.000 0.00 0.00 32.73 3.06
918 1108 2.416431 GGCTATATAGTGGTAACGGCGG 60.416 54.545 13.24 0.00 42.51 6.13
945 1149 4.687215 TTGCTCGCTTGCTCCGCT 62.687 61.111 0.00 0.00 0.00 5.52
966 1170 2.726351 CCTGCTTCTCTCCGGGTCC 61.726 68.421 0.00 0.00 0.00 4.46
970 1174 1.380515 TCTCCCTGCTTCTCTCCGG 60.381 63.158 0.00 0.00 0.00 5.14
1411 1632 2.273449 CATGACCAGCCTGGGGAC 59.727 66.667 16.70 6.79 43.37 4.46
1678 1904 1.296722 CGTAGGCGTCGACGAAGAG 60.297 63.158 39.74 21.57 43.10 2.85
2013 3164 2.936032 AGGCCCCTGTCCTTGACC 60.936 66.667 0.00 0.00 0.00 4.02
2350 3501 2.759795 GAGCTTCTTGGCCCTGGT 59.240 61.111 0.00 0.00 0.00 4.00
2411 3562 2.660064 ATGTCCTCCAGGTCGGTGC 61.660 63.158 0.00 0.00 36.34 5.01
2478 3629 4.148825 GTCGAGCTCGTGCCCCAT 62.149 66.667 33.33 0.00 40.80 4.00
2684 3835 4.519213 ACATGGATGAATTGGGCAAATTG 58.481 39.130 4.15 0.00 38.64 2.32
2685 3836 4.847990 ACATGGATGAATTGGGCAAATT 57.152 36.364 0.00 0.00 41.33 1.82
2686 3837 5.954153 TTACATGGATGAATTGGGCAAAT 57.046 34.783 0.00 0.00 0.00 2.32
2687 3838 5.954153 ATTACATGGATGAATTGGGCAAA 57.046 34.783 0.00 0.00 0.00 3.68
2688 3839 6.781507 TCATATTACATGGATGAATTGGGCAA 59.218 34.615 0.00 0.00 0.00 4.52
2689 3840 6.313324 TCATATTACATGGATGAATTGGGCA 58.687 36.000 0.00 0.00 0.00 5.36
2690 3841 6.839124 TCATATTACATGGATGAATTGGGC 57.161 37.500 0.00 0.00 0.00 5.36
2691 3842 7.123697 AGCATCATATTACATGGATGAATTGGG 59.876 37.037 10.45 0.70 39.52 4.12
2736 3893 3.932710 TGACGCCAAAGATACACTTCATC 59.067 43.478 0.00 0.00 37.93 2.92
2792 3949 6.701145 TGCAAACTGGTGTTCAAATTACTA 57.299 33.333 0.00 0.00 34.96 1.82
2793 3950 5.590530 TGCAAACTGGTGTTCAAATTACT 57.409 34.783 0.00 0.00 34.96 2.24
2794 3951 6.654793 TTTGCAAACTGGTGTTCAAATTAC 57.345 33.333 8.05 0.00 34.96 1.89
2795 3952 6.650807 TGTTTTGCAAACTGGTGTTCAAATTA 59.349 30.769 12.39 0.00 33.17 1.40
2796 3953 5.471456 TGTTTTGCAAACTGGTGTTCAAATT 59.529 32.000 12.39 0.00 33.17 1.82
2797 3954 4.999950 TGTTTTGCAAACTGGTGTTCAAAT 59.000 33.333 12.39 0.00 33.17 2.32
2798 3955 4.212214 GTGTTTTGCAAACTGGTGTTCAAA 59.788 37.500 12.39 0.00 34.96 2.69
2799 3956 3.743396 GTGTTTTGCAAACTGGTGTTCAA 59.257 39.130 12.39 0.00 34.96 2.69
2800 3957 3.243873 TGTGTTTTGCAAACTGGTGTTCA 60.244 39.130 12.39 0.74 34.96 3.18
2801 3958 3.321497 TGTGTTTTGCAAACTGGTGTTC 58.679 40.909 12.39 0.00 34.96 3.18
2802 3959 3.393089 TGTGTTTTGCAAACTGGTGTT 57.607 38.095 12.39 0.00 38.16 3.32
2803 3960 3.063485 GTTGTGTTTTGCAAACTGGTGT 58.937 40.909 12.39 0.00 0.00 4.16
2804 3961 2.414825 GGTTGTGTTTTGCAAACTGGTG 59.585 45.455 12.39 0.00 31.36 4.17
2805 3962 2.037772 TGGTTGTGTTTTGCAAACTGGT 59.962 40.909 12.39 0.00 34.84 4.00
2806 3963 2.693069 TGGTTGTGTTTTGCAAACTGG 58.307 42.857 12.39 0.00 34.84 4.00
2807 3964 5.107913 CGATATGGTTGTGTTTTGCAAACTG 60.108 40.000 12.39 0.00 34.84 3.16
2808 3965 4.981674 CGATATGGTTGTGTTTTGCAAACT 59.018 37.500 12.39 0.00 34.84 2.66
2809 3966 4.149747 CCGATATGGTTGTGTTTTGCAAAC 59.850 41.667 12.39 8.01 34.38 2.93
2810 3967 4.302455 CCGATATGGTTGTGTTTTGCAAA 58.698 39.130 8.05 8.05 0.00 3.68
2811 3968 3.305676 CCCGATATGGTTGTGTTTTGCAA 60.306 43.478 0.00 0.00 35.15 4.08
2812 3969 2.230025 CCCGATATGGTTGTGTTTTGCA 59.770 45.455 0.00 0.00 35.15 4.08
2813 3970 2.416701 CCCCGATATGGTTGTGTTTTGC 60.417 50.000 0.00 0.00 35.15 3.68
2814 3971 2.165437 CCCCCGATATGGTTGTGTTTTG 59.835 50.000 0.00 0.00 35.15 2.44
2815 3972 2.041891 TCCCCCGATATGGTTGTGTTTT 59.958 45.455 0.00 0.00 35.15 2.43
2816 3973 1.636519 TCCCCCGATATGGTTGTGTTT 59.363 47.619 0.00 0.00 35.15 2.83
2817 3974 1.291109 TCCCCCGATATGGTTGTGTT 58.709 50.000 0.00 0.00 35.15 3.32
2818 3975 1.291109 TTCCCCCGATATGGTTGTGT 58.709 50.000 0.00 0.00 35.15 3.72
2819 3976 2.504367 GATTCCCCCGATATGGTTGTG 58.496 52.381 0.00 0.00 35.15 3.33
2820 3977 1.071699 CGATTCCCCCGATATGGTTGT 59.928 52.381 0.00 0.00 35.15 3.32
2821 3978 1.610624 CCGATTCCCCCGATATGGTTG 60.611 57.143 0.00 0.00 35.15 3.77
2822 3979 0.690762 CCGATTCCCCCGATATGGTT 59.309 55.000 0.00 0.00 35.15 3.67
2823 3980 1.198759 CCCGATTCCCCCGATATGGT 61.199 60.000 0.00 0.00 35.15 3.55
2824 3981 1.602237 CCCGATTCCCCCGATATGG 59.398 63.158 0.00 0.00 37.55 2.74
2825 3982 0.907704 TCCCCGATTCCCCCGATATG 60.908 60.000 0.00 0.00 0.00 1.78
2826 3983 0.178885 TTCCCCGATTCCCCCGATAT 60.179 55.000 0.00 0.00 0.00 1.63
2827 3984 0.400237 TTTCCCCGATTCCCCCGATA 60.400 55.000 0.00 0.00 0.00 2.92
2828 3985 1.065997 ATTTCCCCGATTCCCCCGAT 61.066 55.000 0.00 0.00 0.00 4.18
2829 3986 0.400237 TATTTCCCCGATTCCCCCGA 60.400 55.000 0.00 0.00 0.00 5.14
2830 3987 0.696501 ATATTTCCCCGATTCCCCCG 59.303 55.000 0.00 0.00 0.00 5.73
2831 3988 1.891011 GCATATTTCCCCGATTCCCCC 60.891 57.143 0.00 0.00 0.00 5.40
2832 3989 1.075536 AGCATATTTCCCCGATTCCCC 59.924 52.381 0.00 0.00 0.00 4.81
2833 3990 2.586648 AGCATATTTCCCCGATTCCC 57.413 50.000 0.00 0.00 0.00 3.97
2834 3991 3.000727 CGTAGCATATTTCCCCGATTCC 58.999 50.000 0.00 0.00 0.00 3.01
2835 3992 3.921677 TCGTAGCATATTTCCCCGATTC 58.078 45.455 0.00 0.00 0.00 2.52
2836 3993 4.315803 CTTCGTAGCATATTTCCCCGATT 58.684 43.478 0.00 0.00 0.00 3.34
2837 3994 3.864921 GCTTCGTAGCATATTTCCCCGAT 60.865 47.826 9.38 0.00 46.95 4.18
2838 3995 2.547218 GCTTCGTAGCATATTTCCCCGA 60.547 50.000 9.38 0.00 46.95 5.14
2839 3996 1.798813 GCTTCGTAGCATATTTCCCCG 59.201 52.381 9.38 0.00 46.95 5.73
2854 4011 0.316772 ATCGTCGTATCGGTGCTTCG 60.317 55.000 0.00 0.00 0.00 3.79
2877 4037 2.449464 CGTATCCCGTATCCCCATGTA 58.551 52.381 0.00 0.00 0.00 2.29
2879 4039 0.535335 CCGTATCCCGTATCCCCATG 59.465 60.000 0.00 0.00 33.66 3.66
2881 4041 0.776810 TACCGTATCCCGTATCCCCA 59.223 55.000 0.00 0.00 33.66 4.96
3114 4297 1.630244 GCGTGCTTGCTGACTACTGG 61.630 60.000 0.00 0.00 0.00 4.00
3115 4298 0.945743 TGCGTGCTTGCTGACTACTG 60.946 55.000 2.56 0.00 35.36 2.74
3116 4299 0.946221 GTGCGTGCTTGCTGACTACT 60.946 55.000 2.56 0.00 35.36 2.57
3117 4300 1.221466 TGTGCGTGCTTGCTGACTAC 61.221 55.000 2.56 0.00 35.36 2.73
3118 4301 1.068921 TGTGCGTGCTTGCTGACTA 59.931 52.632 2.56 0.00 35.36 2.59
3119 4302 2.203056 TGTGCGTGCTTGCTGACT 60.203 55.556 2.56 0.00 35.36 3.41
3120 4303 2.051882 GTGTGCGTGCTTGCTGAC 60.052 61.111 2.56 0.00 35.36 3.51
3121 4304 0.602372 TATGTGTGCGTGCTTGCTGA 60.602 50.000 2.56 0.00 35.36 4.26
3122 4305 0.238025 TTATGTGTGCGTGCTTGCTG 59.762 50.000 2.56 0.00 35.36 4.41
3123 4306 0.950836 TTTATGTGTGCGTGCTTGCT 59.049 45.000 2.56 0.00 35.36 3.91


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

AutoCloner maintained by Alex Coulton.