Multiple sequence alignment - TraesCS4A01G074300

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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 TraesCS4A01G074300 chr4A 100.000 3758 0 0 1 3758 73540626 73544383 0.000000e+00 6940.0
1 TraesCS4A01G074300 chr4A 89.130 46 2 3 654 699 641245488 641245530 2.000000e-03 54.7
2 TraesCS4A01G074300 chr4D 92.754 3657 185 41 137 3758 392217730 392221341 0.000000e+00 5212.0
3 TraesCS4A01G074300 chr4D 94.203 138 8 0 1 138 24811214 24811351 1.060000e-50 211.0
4 TraesCS4A01G074300 chr4B 96.979 2516 66 7 1252 3758 481801117 481803631 0.000000e+00 4217.0
5 TraesCS4A01G074300 chr4B 89.535 430 34 8 663 1086 481800330 481800754 5.530000e-148 534.0
6 TraesCS4A01G074300 chr1A 94.928 138 7 0 1 138 506592759 506592896 2.270000e-52 217.0
7 TraesCS4A01G074300 chr1A 94.245 139 8 0 1 139 103400345 103400483 2.940000e-51 213.0
8 TraesCS4A01G074300 chr6D 90.244 164 15 1 1 164 403792255 403792093 2.940000e-51 213.0
9 TraesCS4A01G074300 chr6D 94.203 138 8 0 1 138 430990663 430990800 1.060000e-50 211.0
10 TraesCS4A01G074300 chr6D 75.542 323 75 4 166 485 461425324 461425003 5.030000e-34 156.0
11 TraesCS4A01G074300 chr6A 92.617 149 10 1 1 149 224142093 224142240 2.940000e-51 213.0
12 TraesCS4A01G074300 chr6A 94.203 138 8 0 1 138 220275350 220275487 1.060000e-50 211.0
13 TraesCS4A01G074300 chr5A 94.203 138 8 0 1 138 127975731 127975868 1.060000e-50 211.0
14 TraesCS4A01G074300 chr5A 85.057 87 11 1 620 704 430249895 430249981 1.860000e-13 87.9
15 TraesCS4A01G074300 chr2A 94.203 138 8 0 1 138 104335837 104335700 1.060000e-50 211.0
16 TraesCS4A01G074300 chr2B 74.583 480 108 12 137 607 514994888 514995362 8.230000e-47 198.0
17 TraesCS4A01G074300 chr3D 74.797 369 89 4 137 502 532694771 532695138 3.000000e-36 163.0
18 TraesCS4A01G074300 chr3D 84.211 114 16 2 184 296 346066257 346066145 3.970000e-20 110.0
19 TraesCS4A01G074300 chr6B 81.325 166 27 3 620 783 539273135 539272972 8.470000e-27 132.0
20 TraesCS4A01G074300 chr7D 70.833 624 137 32 192 779 37227900 37227286 6.640000e-18 102.0
21 TraesCS4A01G074300 chr7B 71.277 470 110 21 237 692 706121400 706121858 3.090000e-16 97.1


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 TraesCS4A01G074300 chr4A 73540626 73544383 3757 False 6940.0 6940 100.000 1 3758 1 chr4A.!!$F1 3757
1 TraesCS4A01G074300 chr4D 392217730 392221341 3611 False 5212.0 5212 92.754 137 3758 1 chr4D.!!$F2 3621
2 TraesCS4A01G074300 chr4B 481800330 481803631 3301 False 2375.5 4217 93.257 663 3758 2 chr4B.!!$F1 3095

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
34 35 0.030235 AAACGCTTCCGCTTTTGGTC 59.970 50.0 0.0 0.0 36.41 4.02 F
958 989 0.031994 AAAGCGTGGCATTTGTGTCC 59.968 50.0 0.0 0.0 0.00 4.02 F
1455 1685 0.409092 TCTGGAATGCAATGGTGGGT 59.591 50.0 0.0 0.0 0.00 4.51 F
1733 1966 0.960364 ACCCGCCACATTCACATCAC 60.960 55.0 0.0 0.0 0.00 3.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1857 2090 0.250858 TTCTGGTGATGGTGCTGGTG 60.251 55.0 0.00 0.0 0.0 4.17 R
1858 2091 0.250901 GTTCTGGTGATGGTGCTGGT 60.251 55.0 0.00 0.0 0.0 4.00 R
2417 2656 1.804396 TTGTGTTCATTGGCAGCGGG 61.804 55.0 0.00 0.0 0.0 6.13 R
3096 3337 2.004583 TCAGCGCATAGTAACACCAC 57.995 50.0 11.47 0.0 0.0 4.16 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
20 21 3.668596 ATCAACCGCATTACTAAACGC 57.331 42.857 0.00 0.00 0.00 4.84
21 22 2.690786 TCAACCGCATTACTAAACGCT 58.309 42.857 0.00 0.00 0.00 5.07
22 23 3.068560 TCAACCGCATTACTAAACGCTT 58.931 40.909 0.00 0.00 0.00 4.68
23 24 3.123959 TCAACCGCATTACTAAACGCTTC 59.876 43.478 0.00 0.00 0.00 3.86
24 25 2.004733 ACCGCATTACTAAACGCTTCC 58.995 47.619 0.00 0.00 0.00 3.46
25 26 1.005347 CCGCATTACTAAACGCTTCCG 60.005 52.381 0.00 0.00 41.14 4.30
26 27 1.591394 CGCATTACTAAACGCTTCCGC 60.591 52.381 0.00 0.00 38.22 5.54
27 28 1.664151 GCATTACTAAACGCTTCCGCT 59.336 47.619 0.00 0.00 38.22 5.52
28 29 2.095372 GCATTACTAAACGCTTCCGCTT 59.905 45.455 0.00 0.00 38.22 4.68
29 30 3.425758 GCATTACTAAACGCTTCCGCTTT 60.426 43.478 0.00 0.00 38.22 3.51
30 31 4.719040 CATTACTAAACGCTTCCGCTTTT 58.281 39.130 0.00 0.00 40.25 2.27
31 32 2.681152 ACTAAACGCTTCCGCTTTTG 57.319 45.000 0.00 0.00 38.01 2.44
32 33 1.265905 ACTAAACGCTTCCGCTTTTGG 59.734 47.619 0.00 0.00 40.24 3.28
33 34 1.265905 CTAAACGCTTCCGCTTTTGGT 59.734 47.619 0.00 0.00 38.01 3.67
34 35 0.030235 AAACGCTTCCGCTTTTGGTC 59.970 50.000 0.00 0.00 36.41 4.02
35 36 0.818040 AACGCTTCCGCTTTTGGTCT 60.818 50.000 0.00 0.00 38.22 3.85
36 37 0.034337 ACGCTTCCGCTTTTGGTCTA 59.966 50.000 0.00 0.00 38.22 2.59
37 38 1.338769 ACGCTTCCGCTTTTGGTCTAT 60.339 47.619 0.00 0.00 38.22 1.98
38 39 1.062587 CGCTTCCGCTTTTGGTCTATG 59.937 52.381 0.00 0.00 0.00 2.23
39 40 2.356135 GCTTCCGCTTTTGGTCTATGA 58.644 47.619 0.00 0.00 0.00 2.15
40 41 2.352960 GCTTCCGCTTTTGGTCTATGAG 59.647 50.000 0.00 0.00 0.00 2.90
41 42 2.691409 TCCGCTTTTGGTCTATGAGG 57.309 50.000 0.00 0.00 0.00 3.86
42 43 1.209504 TCCGCTTTTGGTCTATGAGGG 59.790 52.381 0.00 0.00 0.00 4.30
43 44 1.065418 CCGCTTTTGGTCTATGAGGGT 60.065 52.381 0.00 0.00 0.00 4.34
44 45 2.169769 CCGCTTTTGGTCTATGAGGGTA 59.830 50.000 0.00 0.00 0.00 3.69
45 46 3.195661 CGCTTTTGGTCTATGAGGGTAC 58.804 50.000 0.00 0.00 0.00 3.34
46 47 3.195661 GCTTTTGGTCTATGAGGGTACG 58.804 50.000 0.00 0.00 0.00 3.67
47 48 3.369157 GCTTTTGGTCTATGAGGGTACGT 60.369 47.826 0.00 0.00 0.00 3.57
48 49 4.142093 GCTTTTGGTCTATGAGGGTACGTA 60.142 45.833 0.00 0.00 0.00 3.57
49 50 5.452917 GCTTTTGGTCTATGAGGGTACGTAT 60.453 44.000 0.00 0.00 0.00 3.06
50 51 6.239120 GCTTTTGGTCTATGAGGGTACGTATA 60.239 42.308 0.00 0.00 0.00 1.47
51 52 6.639632 TTTGGTCTATGAGGGTACGTATAC 57.360 41.667 0.00 0.00 0.00 1.47
52 53 5.308976 TGGTCTATGAGGGTACGTATACA 57.691 43.478 0.00 0.00 32.40 2.29
53 54 5.065914 TGGTCTATGAGGGTACGTATACAC 58.934 45.833 0.00 0.00 34.60 2.90
54 55 5.065914 GGTCTATGAGGGTACGTATACACA 58.934 45.833 0.00 0.25 37.15 3.72
55 56 5.709164 GGTCTATGAGGGTACGTATACACAT 59.291 44.000 0.00 7.92 37.15 3.21
56 57 6.208204 GGTCTATGAGGGTACGTATACACATT 59.792 42.308 14.10 3.94 37.15 2.71
57 58 7.303998 GTCTATGAGGGTACGTATACACATTC 58.696 42.308 14.10 1.71 37.15 2.67
58 59 7.174599 GTCTATGAGGGTACGTATACACATTCT 59.825 40.741 14.10 0.00 37.15 2.40
59 60 5.762825 TGAGGGTACGTATACACATTCTC 57.237 43.478 0.00 4.93 37.15 2.87
60 61 4.581824 TGAGGGTACGTATACACATTCTCC 59.418 45.833 0.00 0.00 37.15 3.71
61 62 3.893813 AGGGTACGTATACACATTCTCCC 59.106 47.826 0.00 0.09 37.15 4.30
62 63 3.893813 GGGTACGTATACACATTCTCCCT 59.106 47.826 0.00 0.00 34.53 4.20
63 64 4.343239 GGGTACGTATACACATTCTCCCTT 59.657 45.833 0.00 0.00 34.53 3.95
64 65 5.287226 GGTACGTATACACATTCTCCCTTG 58.713 45.833 0.00 0.00 32.40 3.61
65 66 5.163478 GGTACGTATACACATTCTCCCTTGT 60.163 44.000 0.00 0.00 32.40 3.16
66 67 5.007385 ACGTATACACATTCTCCCTTGTC 57.993 43.478 3.32 0.00 0.00 3.18
67 68 4.464951 ACGTATACACATTCTCCCTTGTCA 59.535 41.667 3.32 0.00 0.00 3.58
68 69 5.128827 ACGTATACACATTCTCCCTTGTCAT 59.871 40.000 3.32 0.00 0.00 3.06
69 70 6.049149 CGTATACACATTCTCCCTTGTCATT 58.951 40.000 3.32 0.00 0.00 2.57
70 71 6.018751 CGTATACACATTCTCCCTTGTCATTG 60.019 42.308 3.32 0.00 0.00 2.82
71 72 2.821969 ACACATTCTCCCTTGTCATTGC 59.178 45.455 0.00 0.00 0.00 3.56
72 73 3.087031 CACATTCTCCCTTGTCATTGCT 58.913 45.455 0.00 0.00 0.00 3.91
73 74 4.263462 ACACATTCTCCCTTGTCATTGCTA 60.263 41.667 0.00 0.00 0.00 3.49
74 75 4.885907 CACATTCTCCCTTGTCATTGCTAT 59.114 41.667 0.00 0.00 0.00 2.97
75 76 4.885907 ACATTCTCCCTTGTCATTGCTATG 59.114 41.667 1.30 1.30 0.00 2.23
76 77 2.923121 TCTCCCTTGTCATTGCTATGC 58.077 47.619 3.00 0.03 0.00 3.14
77 78 2.239402 TCTCCCTTGTCATTGCTATGCA 59.761 45.455 3.00 0.00 36.47 3.96
78 79 3.117776 TCTCCCTTGTCATTGCTATGCAT 60.118 43.478 3.79 3.79 38.76 3.96
79 80 3.216800 TCCCTTGTCATTGCTATGCATC 58.783 45.455 0.19 0.00 38.76 3.91
80 81 3.117776 TCCCTTGTCATTGCTATGCATCT 60.118 43.478 0.19 0.00 38.76 2.90
81 82 3.252701 CCCTTGTCATTGCTATGCATCTC 59.747 47.826 0.19 0.00 38.76 2.75
82 83 3.252701 CCTTGTCATTGCTATGCATCTCC 59.747 47.826 0.19 0.00 38.76 3.71
83 84 3.851458 TGTCATTGCTATGCATCTCCT 57.149 42.857 0.19 0.00 38.76 3.69
84 85 4.961438 TGTCATTGCTATGCATCTCCTA 57.039 40.909 0.19 0.00 38.76 2.94
85 86 4.891260 TGTCATTGCTATGCATCTCCTAG 58.109 43.478 0.19 0.00 38.76 3.02
86 87 4.590222 TGTCATTGCTATGCATCTCCTAGA 59.410 41.667 0.19 0.00 38.76 2.43
87 88 5.247792 TGTCATTGCTATGCATCTCCTAGAT 59.752 40.000 0.19 0.00 38.76 1.98
88 89 6.438425 TGTCATTGCTATGCATCTCCTAGATA 59.562 38.462 0.19 0.00 38.76 1.98
89 90 6.979817 GTCATTGCTATGCATCTCCTAGATAG 59.020 42.308 0.19 0.00 38.76 2.08
90 91 6.894103 TCATTGCTATGCATCTCCTAGATAGA 59.106 38.462 0.19 0.00 38.76 1.98
91 92 7.564292 TCATTGCTATGCATCTCCTAGATAGAT 59.436 37.037 0.19 0.00 38.76 1.98
92 93 6.957920 TGCTATGCATCTCCTAGATAGATC 57.042 41.667 0.19 0.00 32.12 2.75
93 94 6.671605 TGCTATGCATCTCCTAGATAGATCT 58.328 40.000 0.19 0.00 32.12 2.75
94 95 7.124721 TGCTATGCATCTCCTAGATAGATCTT 58.875 38.462 0.19 0.00 32.12 2.40
95 96 7.068470 TGCTATGCATCTCCTAGATAGATCTTG 59.932 40.741 0.19 0.00 32.12 3.02
96 97 5.657826 TGCATCTCCTAGATAGATCTTGC 57.342 43.478 0.00 0.69 38.32 4.01
97 98 4.157472 TGCATCTCCTAGATAGATCTTGCG 59.843 45.833 0.00 0.00 36.48 4.85
98 99 4.157656 GCATCTCCTAGATAGATCTTGCGT 59.842 45.833 0.00 0.00 38.32 5.24
99 100 5.639757 CATCTCCTAGATAGATCTTGCGTG 58.360 45.833 0.00 0.00 38.32 5.34
100 101 4.974399 TCTCCTAGATAGATCTTGCGTGA 58.026 43.478 0.00 0.00 38.32 4.35
101 102 5.565509 TCTCCTAGATAGATCTTGCGTGAT 58.434 41.667 0.00 0.00 38.32 3.06
102 103 5.645929 TCTCCTAGATAGATCTTGCGTGATC 59.354 44.000 0.00 9.82 42.18 2.92
103 104 4.393371 TCCTAGATAGATCTTGCGTGATCG 59.607 45.833 0.00 0.00 45.35 3.69
104 105 4.155099 CCTAGATAGATCTTGCGTGATCGT 59.845 45.833 0.00 6.35 45.35 3.73
105 106 5.351740 CCTAGATAGATCTTGCGTGATCGTA 59.648 44.000 0.00 6.70 45.35 3.43
106 107 5.289917 AGATAGATCTTGCGTGATCGTAG 57.710 43.478 0.00 0.00 45.35 3.51
107 108 2.783828 AGATCTTGCGTGATCGTAGG 57.216 50.000 11.44 0.00 45.35 3.18
108 109 2.298610 AGATCTTGCGTGATCGTAGGA 58.701 47.619 11.44 0.00 45.35 2.94
109 110 2.887783 AGATCTTGCGTGATCGTAGGAT 59.112 45.455 11.44 0.00 46.54 3.24
110 111 3.319405 AGATCTTGCGTGATCGTAGGATT 59.681 43.478 11.44 0.00 44.79 3.01
111 112 3.520290 TCTTGCGTGATCGTAGGATTT 57.480 42.857 0.00 0.00 39.49 2.17
112 113 3.857052 TCTTGCGTGATCGTAGGATTTT 58.143 40.909 0.00 0.00 39.49 1.82
113 114 4.250464 TCTTGCGTGATCGTAGGATTTTT 58.750 39.130 0.00 0.00 39.49 1.94
133 134 3.926821 TTTTGAAATACTGCGTTCCCC 57.073 42.857 0.00 0.00 0.00 4.81
134 135 2.570415 TTGAAATACTGCGTTCCCCA 57.430 45.000 0.00 0.00 0.00 4.96
135 136 2.570415 TGAAATACTGCGTTCCCCAA 57.430 45.000 0.00 0.00 0.00 4.12
162 163 3.094062 GCCATAGCCTCAGCGGACA 62.094 63.158 0.00 0.00 46.67 4.02
163 164 1.522092 CCATAGCCTCAGCGGACAA 59.478 57.895 0.00 0.00 46.67 3.18
169 171 2.031012 CTCAGCGGACAAGCCACA 59.969 61.111 0.00 0.00 38.01 4.17
170 172 1.376424 CTCAGCGGACAAGCCACAT 60.376 57.895 0.00 0.00 38.01 3.21
182 185 4.462394 CCACATATGGCCTCGTGG 57.538 61.111 15.75 15.75 42.72 4.94
208 211 3.659092 CAACGAAGGGCTTGCGCA 61.659 61.111 5.66 5.66 38.10 6.09
209 212 2.672996 AACGAAGGGCTTGCGCAT 60.673 55.556 12.75 0.00 38.10 4.73
210 213 2.268076 AACGAAGGGCTTGCGCATT 61.268 52.632 12.75 0.49 38.10 3.56
213 216 2.672996 AAGGGCTTGCGCATTCGT 60.673 55.556 12.75 2.47 38.10 3.85
215 218 4.520846 GGGCTTGCGCATTCGTCG 62.521 66.667 12.75 0.00 38.10 5.12
223 226 4.845824 GCATTCGTCGCGGCGTTC 62.846 66.667 33.52 16.04 0.00 3.95
224 227 4.204891 CATTCGTCGCGGCGTTCC 62.205 66.667 33.52 10.47 0.00 3.62
250 253 4.101448 ATGGAGTGCACCGCCTCC 62.101 66.667 22.48 18.66 42.32 4.30
296 299 2.124193 TGGATCCAGGCGCCATTG 60.124 61.111 31.54 19.47 0.00 2.82
308 311 2.194056 CCATTGGGCTGAGGCGAT 59.806 61.111 0.00 0.00 39.81 4.58
309 312 2.191513 CCATTGGGCTGAGGCGATG 61.192 63.158 12.08 12.08 39.81 3.84
310 313 2.191513 CATTGGGCTGAGGCGATGG 61.192 63.158 11.45 0.00 39.81 3.51
311 314 4.802051 TTGGGCTGAGGCGATGGC 62.802 66.667 0.00 0.00 39.81 4.40
315 319 2.188994 GCTGAGGCGATGGCTTCT 59.811 61.111 12.84 0.00 44.92 2.85
353 357 1.823295 GCTGTCGGGCATTCTCCTA 59.177 57.895 0.00 0.00 0.00 2.94
354 358 0.178068 GCTGTCGGGCATTCTCCTAA 59.822 55.000 0.00 0.00 0.00 2.69
357 361 0.175073 GTCGGGCATTCTCCTAACGT 59.825 55.000 0.00 0.00 0.00 3.99
358 362 1.406539 GTCGGGCATTCTCCTAACGTA 59.593 52.381 0.00 0.00 0.00 3.57
364 368 0.248784 ATTCTCCTAACGTACGCGGC 60.249 55.000 16.72 1.19 43.45 6.53
402 406 3.767268 ATCTCCTCCTCGGGCCCA 61.767 66.667 24.92 8.28 0.00 5.36
404 408 3.787001 CTCCTCCTCGGGCCCAAC 61.787 72.222 24.92 0.00 0.00 3.77
433 437 4.673061 CGATGTCCTAGTTCATAGATCGGC 60.673 50.000 0.00 0.00 34.49 5.54
438 442 3.570125 CCTAGTTCATAGATCGGCTGACA 59.430 47.826 0.00 0.00 32.76 3.58
439 443 4.038042 CCTAGTTCATAGATCGGCTGACAA 59.962 45.833 0.00 0.00 32.76 3.18
440 444 3.786635 AGTTCATAGATCGGCTGACAAC 58.213 45.455 0.00 0.00 0.00 3.32
441 445 3.195610 AGTTCATAGATCGGCTGACAACA 59.804 43.478 0.00 0.00 0.00 3.33
453 457 1.688735 CTGACAACAGACTCAGACCCA 59.311 52.381 0.00 0.00 46.03 4.51
454 458 2.301296 CTGACAACAGACTCAGACCCAT 59.699 50.000 0.00 0.00 46.03 4.00
458 462 0.326264 ACAGACTCAGACCCATTGCC 59.674 55.000 0.00 0.00 0.00 4.52
459 463 0.742281 CAGACTCAGACCCATTGCCG 60.742 60.000 0.00 0.00 0.00 5.69
461 465 2.825836 CTCAGACCCATTGCCGGC 60.826 66.667 22.73 22.73 0.00 6.13
486 491 0.882474 CAGAGAAGGTCGGAGTTCGT 59.118 55.000 0.00 0.00 40.32 3.85
487 492 0.882474 AGAGAAGGTCGGAGTTCGTG 59.118 55.000 0.00 0.00 40.32 4.35
501 506 1.264288 GTTCGTGGAAAGTGAGCTTGG 59.736 52.381 0.00 0.00 34.71 3.61
502 507 0.756294 TCGTGGAAAGTGAGCTTGGA 59.244 50.000 0.00 0.00 34.71 3.53
509 514 2.045536 GTGAGCTTGGAGGCAGGG 60.046 66.667 0.00 0.00 34.17 4.45
513 518 4.748144 GCTTGGAGGCAGGGGGTG 62.748 72.222 0.00 0.00 0.00 4.61
514 519 2.935481 CTTGGAGGCAGGGGGTGA 60.935 66.667 0.00 0.00 0.00 4.02
528 552 0.691078 GGGTGATGGAGTGGCTAGGA 60.691 60.000 0.00 0.00 0.00 2.94
533 557 3.114606 TGATGGAGTGGCTAGGATTTGA 58.885 45.455 0.00 0.00 0.00 2.69
536 560 3.387962 TGGAGTGGCTAGGATTTGATCT 58.612 45.455 0.00 0.00 0.00 2.75
537 561 3.389329 TGGAGTGGCTAGGATTTGATCTC 59.611 47.826 0.00 0.00 0.00 2.75
540 564 2.365617 GTGGCTAGGATTTGATCTCGGA 59.634 50.000 0.00 0.00 0.00 4.55
541 565 2.630098 TGGCTAGGATTTGATCTCGGAG 59.370 50.000 0.00 0.00 0.00 4.63
542 566 2.611722 GGCTAGGATTTGATCTCGGAGC 60.612 54.545 0.00 0.00 0.00 4.70
543 567 2.036475 GCTAGGATTTGATCTCGGAGCA 59.964 50.000 0.00 0.00 0.00 4.26
552 577 2.702478 TGATCTCGGAGCAAATGAGGAT 59.298 45.455 0.00 0.00 0.00 3.24
558 583 4.380531 TCGGAGCAAATGAGGATGAATAC 58.619 43.478 0.00 0.00 0.00 1.89
562 587 5.449107 AGCAAATGAGGATGAATACATGC 57.551 39.130 0.00 0.00 43.55 4.06
563 588 4.891168 AGCAAATGAGGATGAATACATGCA 59.109 37.500 0.00 0.00 45.19 3.96
569 594 2.779430 AGGATGAATACATGCAGGGTCA 59.221 45.455 2.31 3.63 45.19 4.02
570 595 3.144506 GGATGAATACATGCAGGGTCAG 58.855 50.000 2.31 0.00 42.90 3.51
581 606 4.678743 GGGTCAGGGTGGGCCAAC 62.679 72.222 14.87 14.87 36.17 3.77
601 626 4.356979 GGTCCAGATCCGACCTGA 57.643 61.111 18.28 0.00 45.41 3.86
631 656 4.035102 GGCCTCCCATATCCGCCC 62.035 72.222 0.00 0.00 33.30 6.13
639 664 4.030913 CTCCCATATCCGCCCTAGAATTA 58.969 47.826 0.00 0.00 0.00 1.40
644 669 1.048601 TCCGCCCTAGAATTAGGCTG 58.951 55.000 0.00 0.00 44.44 4.85
645 670 0.603975 CCGCCCTAGAATTAGGCTGC 60.604 60.000 0.00 0.00 44.44 5.25
665 690 1.069204 CATATGAGGGGTGTCGGTCAG 59.931 57.143 0.00 0.00 0.00 3.51
717 744 2.574450 GGTTGGGTCGTACTTTTTGGA 58.426 47.619 0.00 0.00 0.00 3.53
750 781 1.682849 CCATCCGGGTGTTTGAGGA 59.317 57.895 15.03 0.00 37.17 3.71
759 790 2.230660 GGTGTTTGAGGAGGGTTTGAG 58.769 52.381 0.00 0.00 0.00 3.02
760 791 2.158667 GGTGTTTGAGGAGGGTTTGAGA 60.159 50.000 0.00 0.00 0.00 3.27
765 796 0.246910 GAGGAGGGTTTGAGACGTCC 59.753 60.000 13.01 4.42 33.99 4.79
768 799 0.388263 GAGGGTTTGAGACGTCCGAC 60.388 60.000 13.01 5.83 0.00 4.79
771 802 1.282930 GGTTTGAGACGTCCGACTGC 61.283 60.000 13.01 0.00 0.00 4.40
779 810 1.446792 CGTCCGACTGCAGATGCTT 60.447 57.895 23.35 0.00 42.66 3.91
786 817 4.458989 TCCGACTGCAGATGCTTTAATTTT 59.541 37.500 23.35 0.00 42.66 1.82
787 818 4.795278 CCGACTGCAGATGCTTTAATTTTC 59.205 41.667 23.35 1.03 42.66 2.29
789 820 5.619757 CGACTGCAGATGCTTTAATTTTCCA 60.620 40.000 23.35 0.00 42.66 3.53
888 919 0.036732 TGGAGATGCTCGGCAGTTTT 59.963 50.000 4.90 0.00 43.65 2.43
931 962 4.692475 GCCGCTTACACGTGGGGT 62.692 66.667 21.57 0.74 38.37 4.95
941 972 1.700739 ACACGTGGGGTCTTATCCAAA 59.299 47.619 21.57 0.00 34.47 3.28
958 989 0.031994 AAAGCGTGGCATTTGTGTCC 59.968 50.000 0.00 0.00 0.00 4.02
961 992 0.664166 GCGTGGCATTTGTGTCCAAG 60.664 55.000 0.00 0.00 33.46 3.61
995 1026 7.577303 AGAAATATGCCATTTTCTCTAGACCA 58.423 34.615 8.24 0.00 37.58 4.02
1089 1120 3.181438 GGCTCCATCTCTCCTAGACTGTA 60.181 52.174 0.00 0.00 36.93 2.74
1095 1126 1.671845 CTCTCCTAGACTGTACCACGC 59.328 57.143 0.00 0.00 0.00 5.34
1165 1197 3.897122 GCACCCCCACTCCCACAA 61.897 66.667 0.00 0.00 0.00 3.33
1217 1249 4.772687 GCCGTCCCCGTTCTTCCC 62.773 72.222 0.00 0.00 0.00 3.97
1218 1250 3.001406 CCGTCCCCGTTCTTCCCT 61.001 66.667 0.00 0.00 0.00 4.20
1347 1576 2.752354 CCAATCGCAATTTCTGGGTGTA 59.248 45.455 0.00 0.00 39.04 2.90
1388 1617 2.829592 CCCCTGCTTACGGATCCC 59.170 66.667 6.06 0.00 0.00 3.85
1455 1685 0.409092 TCTGGAATGCAATGGTGGGT 59.591 50.000 0.00 0.00 0.00 4.51
1733 1966 0.960364 ACCCGCCACATTCACATCAC 60.960 55.000 0.00 0.00 0.00 3.06
1853 2086 1.356979 GCAGCATCAGCATCAGCAG 59.643 57.895 0.00 0.00 45.49 4.24
1854 2087 1.356979 CAGCATCAGCATCAGCAGC 59.643 57.895 0.00 0.00 45.49 5.25
1855 2088 1.077716 AGCATCAGCATCAGCAGCA 60.078 52.632 0.00 0.00 45.49 4.41
1856 2089 1.098129 AGCATCAGCATCAGCAGCAG 61.098 55.000 0.00 0.00 45.49 4.24
1857 2090 1.356979 CATCAGCATCAGCAGCAGC 59.643 57.895 0.00 0.00 45.49 5.25
1858 2091 1.077716 ATCAGCATCAGCAGCAGCA 60.078 52.632 3.17 0.00 45.49 4.41
1868 2107 2.675423 CAGCAGCACCAGCACCAT 60.675 61.111 0.00 0.00 45.49 3.55
2126 2365 3.072330 TGGTTGAAGAGCATTCTGTGGTA 59.928 43.478 3.70 0.00 39.00 3.25
2417 2656 6.403333 TGCACAACTTCTATTTCGACATAC 57.597 37.500 0.00 0.00 0.00 2.39
2685 2924 2.286872 CTGCTCTTGCCAATCTGTAGG 58.713 52.381 0.00 0.00 38.71 3.18
2723 2962 2.790433 TGTAGCCATGTTCAGTTTCCC 58.210 47.619 0.00 0.00 0.00 3.97
2772 3011 2.751166 TCAGCTGTGAAGTAGGAAGC 57.249 50.000 14.67 0.00 0.00 3.86
2960 3199 7.290110 AGGGCTAGTTATCATTTAATTTGGC 57.710 36.000 0.00 0.00 0.00 4.52
3074 3315 6.658849 TGGATCTAAGCAAGTAAAATGCCTA 58.341 36.000 0.00 0.00 44.91 3.93
3096 3337 7.519008 GCCTAATAGTTTCTCATTGTTCCGATG 60.519 40.741 0.00 0.00 0.00 3.84
3148 3389 5.957842 TTTATTTGTGTGCCTCTACCTTG 57.042 39.130 0.00 0.00 0.00 3.61
3158 3399 2.104963 GCCTCTACCTTGATACCTTGGG 59.895 54.545 0.00 0.00 0.00 4.12
3159 3400 3.654273 CCTCTACCTTGATACCTTGGGA 58.346 50.000 0.00 0.00 0.00 4.37
3186 3428 2.647297 GCAACTGCTCACCAAGGC 59.353 61.111 0.00 0.00 38.21 4.35
3262 3504 6.930731 ACTTTAACTTGTGTGGTGTTTGATT 58.069 32.000 0.00 0.00 0.00 2.57
3333 3577 9.134734 TGTGTAAAAGTCTTGCAAGTTAAAAAG 57.865 29.630 25.19 0.00 0.00 2.27
3605 3851 1.134280 CCTATCCTCTTGCCACCAGTG 60.134 57.143 0.00 0.00 0.00 3.66
3661 3907 6.681729 TTAAGACCAGTCCATCTGTAGTTT 57.318 37.500 0.00 0.00 42.19 2.66
3722 3968 6.878923 TCCGAGTTGTTGAAATCTGATTACAT 59.121 34.615 2.85 0.00 0.00 2.29
3752 3998 7.704578 TCTGTCAACATCTTACTAGCTTAGT 57.295 36.000 0.00 0.00 42.68 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.668596 GCGTTTAGTAATGCGGTTGAT 57.331 42.857 8.71 0.00 36.62 2.57
20 21 2.939103 CCTCATAGACCAAAAGCGGAAG 59.061 50.000 0.00 0.00 0.00 3.46
21 22 2.355716 CCCTCATAGACCAAAAGCGGAA 60.356 50.000 0.00 0.00 0.00 4.30
22 23 1.209504 CCCTCATAGACCAAAAGCGGA 59.790 52.381 0.00 0.00 0.00 5.54
23 24 1.065418 ACCCTCATAGACCAAAAGCGG 60.065 52.381 0.00 0.00 0.00 5.52
24 25 2.403252 ACCCTCATAGACCAAAAGCG 57.597 50.000 0.00 0.00 0.00 4.68
25 26 3.195661 CGTACCCTCATAGACCAAAAGC 58.804 50.000 0.00 0.00 0.00 3.51
26 27 4.467198 ACGTACCCTCATAGACCAAAAG 57.533 45.455 0.00 0.00 0.00 2.27
27 28 6.606796 TGTATACGTACCCTCATAGACCAAAA 59.393 38.462 0.00 0.00 0.00 2.44
28 29 6.039717 GTGTATACGTACCCTCATAGACCAAA 59.960 42.308 0.00 0.00 0.00 3.28
29 30 5.532406 GTGTATACGTACCCTCATAGACCAA 59.468 44.000 0.00 0.00 0.00 3.67
30 31 5.065914 GTGTATACGTACCCTCATAGACCA 58.934 45.833 0.00 0.00 0.00 4.02
31 32 5.065914 TGTGTATACGTACCCTCATAGACC 58.934 45.833 0.00 0.00 0.00 3.85
32 33 6.814506 ATGTGTATACGTACCCTCATAGAC 57.185 41.667 0.00 0.00 0.00 2.59
33 34 7.229308 AGAATGTGTATACGTACCCTCATAGA 58.771 38.462 0.00 0.00 0.00 1.98
34 35 7.361885 GGAGAATGTGTATACGTACCCTCATAG 60.362 44.444 0.00 0.00 0.00 2.23
35 36 6.432162 GGAGAATGTGTATACGTACCCTCATA 59.568 42.308 0.00 0.00 0.00 2.15
36 37 5.243283 GGAGAATGTGTATACGTACCCTCAT 59.757 44.000 0.00 1.39 0.00 2.90
37 38 4.581824 GGAGAATGTGTATACGTACCCTCA 59.418 45.833 0.00 0.00 0.00 3.86
38 39 4.022503 GGGAGAATGTGTATACGTACCCTC 60.023 50.000 0.00 2.71 34.18 4.30
39 40 3.893813 GGGAGAATGTGTATACGTACCCT 59.106 47.826 0.00 0.00 34.18 4.34
40 41 3.893813 AGGGAGAATGTGTATACGTACCC 59.106 47.826 0.00 0.00 35.70 3.69
41 42 5.163478 ACAAGGGAGAATGTGTATACGTACC 60.163 44.000 0.00 0.00 0.00 3.34
42 43 5.899299 ACAAGGGAGAATGTGTATACGTAC 58.101 41.667 0.00 0.00 0.00 3.67
43 44 5.653330 TGACAAGGGAGAATGTGTATACGTA 59.347 40.000 0.00 0.00 0.00 3.57
44 45 4.464951 TGACAAGGGAGAATGTGTATACGT 59.535 41.667 0.00 0.00 0.00 3.57
45 46 5.006153 TGACAAGGGAGAATGTGTATACG 57.994 43.478 0.00 0.00 0.00 3.06
46 47 6.238484 GCAATGACAAGGGAGAATGTGTATAC 60.238 42.308 0.00 0.00 0.00 1.47
47 48 5.822519 GCAATGACAAGGGAGAATGTGTATA 59.177 40.000 0.00 0.00 0.00 1.47
48 49 4.641989 GCAATGACAAGGGAGAATGTGTAT 59.358 41.667 0.00 0.00 0.00 2.29
49 50 4.009675 GCAATGACAAGGGAGAATGTGTA 58.990 43.478 0.00 0.00 0.00 2.90
50 51 2.821969 GCAATGACAAGGGAGAATGTGT 59.178 45.455 0.00 0.00 0.00 3.72
51 52 3.087031 AGCAATGACAAGGGAGAATGTG 58.913 45.455 0.00 0.00 0.00 3.21
52 53 3.446442 AGCAATGACAAGGGAGAATGT 57.554 42.857 0.00 0.00 0.00 2.71
53 54 4.261489 GCATAGCAATGACAAGGGAGAATG 60.261 45.833 0.00 0.00 34.84 2.67
54 55 3.887716 GCATAGCAATGACAAGGGAGAAT 59.112 43.478 0.00 0.00 34.84 2.40
55 56 3.282021 GCATAGCAATGACAAGGGAGAA 58.718 45.455 0.00 0.00 34.84 2.87
56 57 2.239402 TGCATAGCAATGACAAGGGAGA 59.761 45.455 0.00 0.00 34.76 3.71
57 58 2.646930 TGCATAGCAATGACAAGGGAG 58.353 47.619 0.00 0.00 34.76 4.30
58 59 2.804986 TGCATAGCAATGACAAGGGA 57.195 45.000 0.00 0.00 34.76 4.20
59 60 3.220110 AGATGCATAGCAATGACAAGGG 58.780 45.455 0.00 0.00 43.62 3.95
60 61 3.252701 GGAGATGCATAGCAATGACAAGG 59.747 47.826 0.00 0.00 43.62 3.61
61 62 4.135306 AGGAGATGCATAGCAATGACAAG 58.865 43.478 0.00 0.00 43.62 3.16
62 63 4.160642 AGGAGATGCATAGCAATGACAA 57.839 40.909 0.00 0.00 43.62 3.18
63 64 3.851458 AGGAGATGCATAGCAATGACA 57.149 42.857 0.00 0.00 43.62 3.58
64 65 5.144692 TCTAGGAGATGCATAGCAATGAC 57.855 43.478 0.00 0.00 43.62 3.06
65 66 6.894103 TCTATCTAGGAGATGCATAGCAATGA 59.106 38.462 0.00 0.00 43.62 2.57
66 67 7.110043 TCTATCTAGGAGATGCATAGCAATG 57.890 40.000 0.00 0.00 43.62 2.82
67 68 7.785985 AGATCTATCTAGGAGATGCATAGCAAT 59.214 37.037 0.00 0.00 37.47 3.56
68 69 7.124721 AGATCTATCTAGGAGATGCATAGCAA 58.875 38.462 0.00 0.00 37.47 3.91
69 70 6.671605 AGATCTATCTAGGAGATGCATAGCA 58.328 40.000 0.00 0.00 38.03 3.49
70 71 7.428020 CAAGATCTATCTAGGAGATGCATAGC 58.572 42.308 0.00 0.00 35.37 2.97
71 72 7.428020 GCAAGATCTATCTAGGAGATGCATAG 58.572 42.308 0.00 0.00 35.37 2.23
72 73 6.039159 CGCAAGATCTATCTAGGAGATGCATA 59.961 42.308 0.00 0.00 35.65 3.14
73 74 5.163530 CGCAAGATCTATCTAGGAGATGCAT 60.164 44.000 0.00 0.00 35.65 3.96
74 75 4.157472 CGCAAGATCTATCTAGGAGATGCA 59.843 45.833 11.48 0.00 35.65 3.96
75 76 4.157656 ACGCAAGATCTATCTAGGAGATGC 59.842 45.833 11.48 9.81 36.70 3.91
76 77 5.414144 TCACGCAAGATCTATCTAGGAGATG 59.586 44.000 11.48 2.82 36.70 2.90
77 78 5.565509 TCACGCAAGATCTATCTAGGAGAT 58.434 41.667 0.00 7.55 38.77 2.75
78 79 4.974399 TCACGCAAGATCTATCTAGGAGA 58.026 43.478 0.00 0.00 43.62 3.71
79 80 5.447144 CGATCACGCAAGATCTATCTAGGAG 60.447 48.000 12.06 0.00 41.74 3.69
80 81 4.393371 CGATCACGCAAGATCTATCTAGGA 59.607 45.833 12.06 0.00 41.74 2.94
81 82 4.155099 ACGATCACGCAAGATCTATCTAGG 59.845 45.833 12.06 0.32 41.74 3.02
82 83 5.289917 ACGATCACGCAAGATCTATCTAG 57.710 43.478 12.06 0.00 41.74 2.43
83 84 5.351740 CCTACGATCACGCAAGATCTATCTA 59.648 44.000 12.06 0.00 41.74 1.98
84 85 4.155099 CCTACGATCACGCAAGATCTATCT 59.845 45.833 12.06 0.00 41.74 1.98
85 86 4.154375 TCCTACGATCACGCAAGATCTATC 59.846 45.833 12.06 0.00 41.74 2.08
86 87 4.072839 TCCTACGATCACGCAAGATCTAT 58.927 43.478 12.06 4.73 41.74 1.98
87 88 3.473625 TCCTACGATCACGCAAGATCTA 58.526 45.455 12.06 4.90 41.74 1.98
88 89 2.298610 TCCTACGATCACGCAAGATCT 58.701 47.619 12.06 0.00 41.74 2.75
89 90 2.776312 TCCTACGATCACGCAAGATC 57.224 50.000 5.52 5.52 43.96 2.75
90 91 3.735237 AATCCTACGATCACGCAAGAT 57.265 42.857 0.00 0.00 43.96 2.40
91 92 3.520290 AAATCCTACGATCACGCAAGA 57.480 42.857 0.00 0.00 43.96 3.02
92 93 4.600012 AAAAATCCTACGATCACGCAAG 57.400 40.909 0.00 0.00 43.96 4.01
112 113 4.245845 GGGGAACGCAGTATTTCAAAAA 57.754 40.909 0.00 0.00 45.00 1.94
113 114 3.926821 GGGGAACGCAGTATTTCAAAA 57.073 42.857 0.00 0.00 45.00 2.44
125 126 2.517402 TGGTGTGTTGGGGAACGC 60.517 61.111 0.00 0.00 43.69 4.84
126 127 2.539338 CGTGGTGTGTTGGGGAACG 61.539 63.158 0.00 0.00 0.00 3.95
127 128 2.841160 GCGTGGTGTGTTGGGGAAC 61.841 63.158 0.00 0.00 0.00 3.62
128 129 2.517402 GCGTGGTGTGTTGGGGAA 60.517 61.111 0.00 0.00 0.00 3.97
129 130 4.572571 GGCGTGGTGTGTTGGGGA 62.573 66.667 0.00 0.00 0.00 4.81
130 131 2.756321 TATGGCGTGGTGTGTTGGGG 62.756 60.000 0.00 0.00 0.00 4.96
131 132 1.302913 TATGGCGTGGTGTGTTGGG 60.303 57.895 0.00 0.00 0.00 4.12
132 133 1.922135 GCTATGGCGTGGTGTGTTGG 61.922 60.000 0.00 0.00 0.00 3.77
133 134 1.501741 GCTATGGCGTGGTGTGTTG 59.498 57.895 0.00 0.00 0.00 3.33
134 135 1.674322 GGCTATGGCGTGGTGTGTT 60.674 57.895 0.00 0.00 39.81 3.32
135 136 2.046314 GGCTATGGCGTGGTGTGT 60.046 61.111 0.00 0.00 39.81 3.72
223 226 2.202797 CACTCCATCTGGCGTCGG 60.203 66.667 0.00 0.00 29.21 4.79
224 227 2.887568 GCACTCCATCTGGCGTCG 60.888 66.667 0.00 0.00 29.21 5.12
278 281 2.191513 CAATGGCGCCTGGATCCAG 61.192 63.158 31.69 31.69 43.26 3.86
279 282 2.124193 CAATGGCGCCTGGATCCA 60.124 61.111 29.70 15.27 0.00 3.41
280 283 2.908940 CCAATGGCGCCTGGATCC 60.909 66.667 26.60 4.20 34.35 3.36
281 284 2.908940 CCCAATGGCGCCTGGATC 60.909 66.667 30.93 4.15 34.35 3.36
296 299 4.496336 AAGCCATCGCCTCAGCCC 62.496 66.667 0.00 0.00 34.57 5.19
299 302 1.591059 CGAGAAGCCATCGCCTCAG 60.591 63.158 0.00 0.00 34.57 3.35
300 303 2.496341 CGAGAAGCCATCGCCTCA 59.504 61.111 0.00 0.00 34.57 3.86
302 305 4.537433 GCCGAGAAGCCATCGCCT 62.537 66.667 0.00 0.00 38.84 5.52
303 306 4.838152 TGCCGAGAAGCCATCGCC 62.838 66.667 0.00 0.00 38.84 5.54
305 308 0.943359 GATCTGCCGAGAAGCCATCG 60.943 60.000 0.00 0.00 39.86 3.84
306 309 0.943359 CGATCTGCCGAGAAGCCATC 60.943 60.000 0.00 0.00 0.00 3.51
307 310 1.068753 CGATCTGCCGAGAAGCCAT 59.931 57.895 0.00 0.00 0.00 4.40
308 311 2.052104 TCGATCTGCCGAGAAGCCA 61.052 57.895 0.00 0.00 34.19 4.75
309 312 2.808315 TCGATCTGCCGAGAAGCC 59.192 61.111 0.00 0.00 34.19 4.35
336 340 1.802880 CGTTAGGAGAATGCCCGACAG 60.803 57.143 0.00 0.00 0.00 3.51
339 343 1.406539 GTACGTTAGGAGAATGCCCGA 59.593 52.381 0.00 0.00 0.00 5.14
344 348 1.474017 CCGCGTACGTTAGGAGAATG 58.526 55.000 17.90 0.00 37.70 2.67
373 377 0.103208 GAGGAGATGGTCGTTCGCAT 59.897 55.000 0.00 0.00 0.00 4.73
378 382 1.038130 CCGAGGAGGAGATGGTCGTT 61.038 60.000 0.00 0.00 45.00 3.85
410 414 4.673061 GCCGATCTATGAACTAGGACATCG 60.673 50.000 7.09 6.30 34.16 3.84
413 417 3.570125 CAGCCGATCTATGAACTAGGACA 59.430 47.826 0.00 0.00 0.00 4.02
418 422 4.401202 TGTTGTCAGCCGATCTATGAACTA 59.599 41.667 0.00 0.00 0.00 2.24
424 428 3.027412 AGTCTGTTGTCAGCCGATCTAT 58.973 45.455 0.00 0.00 41.10 1.98
430 434 0.315251 TCTGAGTCTGTTGTCAGCCG 59.685 55.000 0.00 0.00 40.13 5.52
433 437 1.688735 TGGGTCTGAGTCTGTTGTCAG 59.311 52.381 0.00 0.00 41.44 3.51
438 442 1.271597 GGCAATGGGTCTGAGTCTGTT 60.272 52.381 0.00 0.00 0.00 3.16
439 443 0.326264 GGCAATGGGTCTGAGTCTGT 59.674 55.000 0.00 0.00 0.00 3.41
440 444 0.742281 CGGCAATGGGTCTGAGTCTG 60.742 60.000 0.00 0.00 0.00 3.51
441 445 1.599047 CGGCAATGGGTCTGAGTCT 59.401 57.895 0.00 0.00 0.00 3.24
447 451 3.743017 ATGGCCGGCAATGGGTCT 61.743 61.111 30.85 0.00 0.00 3.85
461 465 1.153289 CCGACCTTCTCTGGCATGG 60.153 63.158 0.00 0.00 0.00 3.66
468 472 0.882474 CACGAACTCCGACCTTCTCT 59.118 55.000 0.00 0.00 41.76 3.10
474 479 0.033090 ACTTTCCACGAACTCCGACC 59.967 55.000 0.00 0.00 41.76 4.79
476 481 1.000607 CTCACTTTCCACGAACTCCGA 60.001 52.381 0.00 0.00 41.76 4.55
486 491 0.250901 GCCTCCAAGCTCACTTTCCA 60.251 55.000 0.00 0.00 32.29 3.53
487 492 0.250901 TGCCTCCAAGCTCACTTTCC 60.251 55.000 0.00 0.00 32.29 3.13
501 506 2.692368 TCCATCACCCCCTGCCTC 60.692 66.667 0.00 0.00 0.00 4.70
502 507 2.693864 CTCCATCACCCCCTGCCT 60.694 66.667 0.00 0.00 0.00 4.75
509 514 0.691078 TCCTAGCCACTCCATCACCC 60.691 60.000 0.00 0.00 0.00 4.61
512 517 3.114606 TCAAATCCTAGCCACTCCATCA 58.885 45.455 0.00 0.00 0.00 3.07
513 518 3.845781 TCAAATCCTAGCCACTCCATC 57.154 47.619 0.00 0.00 0.00 3.51
514 519 3.979347 AGATCAAATCCTAGCCACTCCAT 59.021 43.478 0.00 0.00 0.00 3.41
528 552 3.881688 CCTCATTTGCTCCGAGATCAAAT 59.118 43.478 0.00 4.10 38.40 2.32
533 557 2.702478 TCATCCTCATTTGCTCCGAGAT 59.298 45.455 0.00 0.00 0.00 2.75
536 560 3.565764 ATTCATCCTCATTTGCTCCGA 57.434 42.857 0.00 0.00 0.00 4.55
537 561 4.129380 TGTATTCATCCTCATTTGCTCCG 58.871 43.478 0.00 0.00 0.00 4.63
540 564 4.891168 TGCATGTATTCATCCTCATTTGCT 59.109 37.500 0.00 0.00 31.15 3.91
541 565 5.190992 TGCATGTATTCATCCTCATTTGC 57.809 39.130 0.00 0.00 31.15 3.68
542 566 5.278808 CCCTGCATGTATTCATCCTCATTTG 60.279 44.000 0.00 0.00 31.15 2.32
543 567 4.831155 CCCTGCATGTATTCATCCTCATTT 59.169 41.667 0.00 0.00 31.15 2.32
545 569 3.396946 ACCCTGCATGTATTCATCCTCAT 59.603 43.478 0.00 0.00 31.15 2.90
546 570 2.779430 ACCCTGCATGTATTCATCCTCA 59.221 45.455 0.00 0.00 31.15 3.86
547 571 3.181451 TGACCCTGCATGTATTCATCCTC 60.181 47.826 0.00 0.00 31.15 3.71
552 577 1.212688 CCCTGACCCTGCATGTATTCA 59.787 52.381 0.00 0.00 0.00 2.57
558 583 2.044650 CCACCCTGACCCTGCATG 60.045 66.667 0.00 0.00 0.00 4.06
563 588 4.938756 TTGGCCCACCCTGACCCT 62.939 66.667 0.00 0.00 33.59 4.34
585 610 1.433879 CGTCAGGTCGGATCTGGAC 59.566 63.158 17.76 12.92 33.36 4.02
586 611 3.920031 CGTCAGGTCGGATCTGGA 58.080 61.111 17.76 2.72 33.36 3.86
631 656 5.426504 CCCTCATATGCAGCCTAATTCTAG 58.573 45.833 0.00 0.00 0.00 2.43
639 664 0.990282 ACACCCCTCATATGCAGCCT 60.990 55.000 0.00 0.00 0.00 4.58
644 669 0.249911 GACCGACACCCCTCATATGC 60.250 60.000 0.00 0.00 0.00 3.14
645 670 1.069204 CTGACCGACACCCCTCATATG 59.931 57.143 0.00 0.00 0.00 1.78
665 690 4.056125 GGCCTCAAACGCTTGGGC 62.056 66.667 17.58 17.58 43.09 5.36
670 695 2.203294 AAACCGGCCTCAAACGCT 60.203 55.556 0.00 0.00 0.00 5.07
734 765 1.562672 CCCTCCTCAAACACCCGGAT 61.563 60.000 0.73 0.00 0.00 4.18
750 781 0.826672 AGTCGGACGTCTCAAACCCT 60.827 55.000 16.46 0.00 0.00 4.34
759 790 2.161486 GCATCTGCAGTCGGACGTC 61.161 63.158 14.67 7.13 41.59 4.34
760 791 2.125912 GCATCTGCAGTCGGACGT 60.126 61.111 14.67 0.00 41.59 4.34
765 796 4.795278 GGAAAATTAAAGCATCTGCAGTCG 59.205 41.667 14.67 7.19 45.16 4.18
768 799 7.709947 TCTATGGAAAATTAAAGCATCTGCAG 58.290 34.615 7.63 7.63 45.16 4.41
799 830 8.612619 CGGAATTACAGCAACAGTTAGATTTAT 58.387 33.333 0.00 0.00 0.00 1.40
800 831 7.604927 ACGGAATTACAGCAACAGTTAGATTTA 59.395 33.333 0.00 0.00 0.00 1.40
914 945 4.692475 ACCCCACGTGTAAGCGGC 62.692 66.667 15.65 0.00 35.98 6.53
941 972 1.106351 TTGGACACAAATGCCACGCT 61.106 50.000 0.00 0.00 33.45 5.07
958 989 5.472148 TGGCATATTTCTTTCTTGCACTTG 58.528 37.500 0.00 0.00 35.04 3.16
961 992 6.973229 AAATGGCATATTTCTTTCTTGCAC 57.027 33.333 0.00 0.00 35.04 4.57
995 1026 2.567615 AGACGAAAGCAAGGTACAGGAT 59.432 45.455 0.00 0.00 0.00 3.24
1148 1179 3.897122 TTGTGGGAGTGGGGGTGC 61.897 66.667 0.00 0.00 0.00 5.01
1298 1527 8.059798 AGTGGGATTTAACAAATCTCTGATTG 57.940 34.615 11.65 0.00 46.35 2.67
1402 1632 4.039852 TGGGACCTATTTCCAAAAACAAGC 59.960 41.667 0.00 0.00 37.40 4.01
1412 1642 2.158460 CCAATCCCTGGGACCTATTTCC 60.158 54.545 19.82 0.00 42.17 3.13
1455 1685 1.982660 CTCTGGACGGTCAGGCTATA 58.017 55.000 10.76 0.00 35.58 1.31
1708 1941 4.594854 AATGTGGCGGGTGGTGCA 62.595 61.111 0.00 0.00 0.00 4.57
1721 1954 1.378514 GCGGGGGTGATGTGAATGT 60.379 57.895 0.00 0.00 0.00 2.71
1733 1966 1.068585 GTTACCATAGTCGCGGGGG 59.931 63.158 6.13 3.45 0.00 5.40
1853 2086 2.674033 TGATGGTGCTGGTGCTGC 60.674 61.111 0.00 0.00 40.48 5.25
1854 2087 2.338015 GGTGATGGTGCTGGTGCTG 61.338 63.158 0.00 0.00 40.48 4.41
1855 2088 2.034687 GGTGATGGTGCTGGTGCT 59.965 61.111 0.00 0.00 40.48 4.40
1856 2089 2.282391 TGGTGATGGTGCTGGTGC 60.282 61.111 0.00 0.00 40.20 5.01
1857 2090 0.250858 TTCTGGTGATGGTGCTGGTG 60.251 55.000 0.00 0.00 0.00 4.17
1858 2091 0.250901 GTTCTGGTGATGGTGCTGGT 60.251 55.000 0.00 0.00 0.00 4.00
1868 2107 3.213506 CTGTTGATGTTGGTTCTGGTGA 58.786 45.455 0.00 0.00 0.00 4.02
2417 2656 1.804396 TTGTGTTCATTGGCAGCGGG 61.804 55.000 0.00 0.00 0.00 6.13
2634 2873 2.717639 AACTCAGACCAAACTGCAGT 57.282 45.000 15.25 15.25 37.75 4.40
2685 2924 4.265792 GCTACAAGCTACTTCTAAAGACGC 59.734 45.833 0.00 0.00 38.45 5.19
2723 2962 7.042321 TCGAAATAGGCATGTAAATTAAGTCCG 60.042 37.037 0.00 0.00 0.00 4.79
2772 3011 4.725790 TGACATGACAGATACAGACAGG 57.274 45.455 0.00 0.00 0.00 4.00
2924 3163 4.884887 AACTAGCCCTAGAAGAGGTAGT 57.115 45.455 9.20 0.00 45.03 2.73
3074 3315 6.094048 CCACATCGGAACAATGAGAAACTATT 59.906 38.462 0.00 0.00 36.56 1.73
3096 3337 2.004583 TCAGCGCATAGTAACACCAC 57.995 50.000 11.47 0.00 0.00 4.16
3148 3389 9.740710 AGTTGCTATAATAATTCCCAAGGTATC 57.259 33.333 0.00 0.00 0.00 2.24
3186 3428 8.151141 ACACATATTGAGTCAAGATATGCAAG 57.849 34.615 16.65 12.65 37.29 4.01
3262 3504 5.754782 TGCATAATTCTAAGAGAAAGGGCA 58.245 37.500 0.00 0.00 37.82 5.36
3321 3565 8.816144 TCATTTGTCATGTTCTTTTTAACTTGC 58.184 29.630 0.00 0.00 35.55 4.01
3333 3577 8.131100 TCTCTTCTGTTTTCATTTGTCATGTTC 58.869 33.333 0.00 0.00 0.00 3.18
3540 3786 5.591877 AGGAAAATGTATGGACAGCTTCATC 59.408 40.000 0.00 0.00 39.50 2.92
3605 3851 6.071278 ACCCTCTCTTGATAGTGAACTGTAAC 60.071 42.308 0.00 0.00 0.00 2.50
3699 3945 6.963242 CCATGTAATCAGATTTCAACAACTCG 59.037 38.462 6.55 0.00 0.00 4.18
3722 3968 4.973168 AGTAAGATGTTGACAGAAAGCCA 58.027 39.130 0.00 0.00 0.00 4.75


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

AutoCloner maintained by Alex Coulton.