Multiple sequence alignment - TraesCS4D01G266200

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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 TraesCS4D01G266200 chr4D 100.000 3171 0 0 1 3171 436696821 436699991 0.000000e+00 5856.0
1 TraesCS4D01G266200 chr4D 95.731 937 38 2 2237 3171 311743494 311742558 0.000000e+00 1507.0
2 TraesCS4D01G266200 chr4D 95.503 934 39 3 2240 3171 311756285 311755353 0.000000e+00 1489.0
3 TraesCS4D01G266200 chr4D 88.157 1047 109 5 234 1269 436379167 436378125 0.000000e+00 1232.0
4 TraesCS4D01G266200 chr4D 88.711 1001 108 3 271 1269 436836758 436837755 0.000000e+00 1218.0
5 TraesCS4D01G266200 chr4D 82.480 879 94 30 1384 2235 436377998 436377153 0.000000e+00 715.0
6 TraesCS4D01G266200 chr4D 81.758 603 81 16 1384 1974 436837882 436838467 7.960000e-131 477.0
7 TraesCS4D01G266200 chr4D 79.521 459 65 11 1666 2117 455319656 455320092 1.850000e-77 300.0
8 TraesCS4D01G266200 chr4B 93.597 1265 54 4 233 1471 538384997 538386260 0.000000e+00 1862.0
9 TraesCS4D01G266200 chr4B 94.465 813 39 5 472 1284 538370641 538371447 0.000000e+00 1247.0
10 TraesCS4D01G266200 chr4B 88.004 1042 115 4 234 1268 538270397 538269359 0.000000e+00 1223.0
11 TraesCS4D01G266200 chr4B 87.644 1044 119 3 233 1269 538673167 538674207 0.000000e+00 1205.0
12 TraesCS4D01G266200 chr4B 95.080 691 31 3 1546 2236 538386260 538386947 0.000000e+00 1085.0
13 TraesCS4D01G266200 chr4B 94.561 570 27 2 1670 2236 538372061 538372629 0.000000e+00 878.0
14 TraesCS4D01G266200 chr4B 81.995 872 106 25 1385 2235 538674335 538675176 0.000000e+00 693.0
15 TraesCS4D01G266200 chr4B 90.672 461 40 2 1 461 538350473 538350930 7.520000e-171 610.0
16 TraesCS4D01G266200 chr4B 80.552 869 103 31 1384 2235 538269231 538268412 2.700000e-170 608.0
17 TraesCS4D01G266200 chr4B 87.812 361 19 7 1283 1623 538371704 538372059 1.770000e-107 399.0
18 TraesCS4D01G266200 chr4B 80.260 461 67 12 1666 2121 568411064 568411505 3.050000e-85 326.0
19 TraesCS4D01G266200 chr2D 96.261 936 33 2 2237 3171 85513976 85513042 0.000000e+00 1533.0
20 TraesCS4D01G266200 chr2D 95.838 937 36 3 2237 3171 85526681 85525746 0.000000e+00 1511.0
21 TraesCS4D01G266200 chr2D 95.731 937 37 3 2237 3171 499656532 499657467 0.000000e+00 1506.0
22 TraesCS4D01G266200 chr5D 96.051 937 34 3 2237 3171 515624118 515623183 0.000000e+00 1522.0
23 TraesCS4D01G266200 chr5D 95.624 937 37 4 2237 3171 515617116 515616182 0.000000e+00 1500.0
24 TraesCS4D01G266200 chr5D 95.329 942 41 3 2232 3171 195180538 195181478 0.000000e+00 1493.0
25 TraesCS4D01G266200 chr6D 95.736 938 39 1 2235 3171 129809808 129810745 0.000000e+00 1509.0
26 TraesCS4D01G266200 chr6D 86.735 196 22 3 1923 2115 137154304 137154498 6.890000e-52 215.0
27 TraesCS4D01G266200 chr4A 88.269 1057 111 6 221 1269 31621462 31622513 0.000000e+00 1253.0
28 TraesCS4D01G266200 chr4A 88.669 962 105 2 309 1269 31596495 31595537 0.000000e+00 1170.0
29 TraesCS4D01G266200 chr4A 80.693 953 170 10 312 1254 12678780 12677832 0.000000e+00 728.0
30 TraesCS4D01G266200 chr4A 82.594 879 93 30 1384 2235 31622640 31623485 0.000000e+00 721.0
31 TraesCS4D01G266200 chr4A 81.086 571 79 16 1384 1944 31595409 31594858 2.260000e-116 429.0
32 TraesCS4D01G266200 chr4A 81.855 496 70 13 797 1284 12658681 12658198 1.770000e-107 399.0
33 TraesCS4D01G266200 chr4A 79.684 507 79 14 1673 2174 12677820 12677333 8.420000e-91 344.0
34 TraesCS4D01G266200 chr4A 80.176 454 64 15 1673 2117 12626322 12625886 1.840000e-82 316.0
35 TraesCS4D01G266200 chr4A 87.624 202 22 1 2037 2235 31594519 31594318 6.840000e-57 231.0
36 TraesCS4D01G266200 chr6B 75.462 379 66 16 1463 1831 236572813 236573174 3.270000e-35 159.0
37 TraesCS4D01G266200 chr6B 75.066 381 61 17 1494 1850 236478463 236478833 2.550000e-31 147.0
38 TraesCS4D01G266200 chr6B 87.500 64 6 1 1578 1641 236478237 236478298 4.390000e-09 73.1


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 TraesCS4D01G266200 chr4D 436696821 436699991 3170 False 5856.000000 5856 100.000000 1 3171 1 chr4D.!!$F1 3170
1 TraesCS4D01G266200 chr4D 311742558 311743494 936 True 1507.000000 1507 95.731000 2237 3171 1 chr4D.!!$R1 934
2 TraesCS4D01G266200 chr4D 311755353 311756285 932 True 1489.000000 1489 95.503000 2240 3171 1 chr4D.!!$R2 931
3 TraesCS4D01G266200 chr4D 436377153 436379167 2014 True 973.500000 1232 85.318500 234 2235 2 chr4D.!!$R3 2001
4 TraesCS4D01G266200 chr4D 436836758 436838467 1709 False 847.500000 1218 85.234500 271 1974 2 chr4D.!!$F3 1703
5 TraesCS4D01G266200 chr4B 538384997 538386947 1950 False 1473.500000 1862 94.338500 233 2236 2 chr4B.!!$F4 2003
6 TraesCS4D01G266200 chr4B 538673167 538675176 2009 False 949.000000 1205 84.819500 233 2235 2 chr4B.!!$F5 2002
7 TraesCS4D01G266200 chr4B 538268412 538270397 1985 True 915.500000 1223 84.278000 234 2235 2 chr4B.!!$R1 2001
8 TraesCS4D01G266200 chr4B 538370641 538372629 1988 False 841.333333 1247 92.279333 472 2236 3 chr4B.!!$F3 1764
9 TraesCS4D01G266200 chr2D 85513042 85513976 934 True 1533.000000 1533 96.261000 2237 3171 1 chr2D.!!$R1 934
10 TraesCS4D01G266200 chr2D 85525746 85526681 935 True 1511.000000 1511 95.838000 2237 3171 1 chr2D.!!$R2 934
11 TraesCS4D01G266200 chr2D 499656532 499657467 935 False 1506.000000 1506 95.731000 2237 3171 1 chr2D.!!$F1 934
12 TraesCS4D01G266200 chr5D 515623183 515624118 935 True 1522.000000 1522 96.051000 2237 3171 1 chr5D.!!$R2 934
13 TraesCS4D01G266200 chr5D 515616182 515617116 934 True 1500.000000 1500 95.624000 2237 3171 1 chr5D.!!$R1 934
14 TraesCS4D01G266200 chr5D 195180538 195181478 940 False 1493.000000 1493 95.329000 2232 3171 1 chr5D.!!$F1 939
15 TraesCS4D01G266200 chr6D 129809808 129810745 937 False 1509.000000 1509 95.736000 2235 3171 1 chr6D.!!$F1 936
16 TraesCS4D01G266200 chr4A 31621462 31623485 2023 False 987.000000 1253 85.431500 221 2235 2 chr4A.!!$F1 2014
17 TraesCS4D01G266200 chr4A 31594318 31596495 2177 True 610.000000 1170 85.793000 309 2235 3 chr4A.!!$R4 1926
18 TraesCS4D01G266200 chr4A 12677333 12678780 1447 True 536.000000 728 80.188500 312 2174 2 chr4A.!!$R3 1862

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
202 203 0.036875 CGCCTTTCCCTCTCCACTTT 59.963 55.0 0.0 0.0 0.0 2.66 F
347 354 0.616111 AGCACGTCCTCTTCCTCCAT 60.616 55.0 0.0 0.0 0.0 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1875 2225 1.002430 CGGTGTATGCATCTAGGCCAT 59.998 52.381 5.01 0.0 0.00 4.40 R
2317 2941 3.202706 GGCCCCGTGCTTCGAATC 61.203 66.667 0.00 0.0 42.86 2.52 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 2.940994 AGTCTAGAGAGATAGCGGCA 57.059 50.000 1.45 0.00 33.14 5.69
21 22 2.500229 AGTCTAGAGAGATAGCGGCAC 58.500 52.381 1.45 0.00 33.14 5.01
22 23 2.105821 AGTCTAGAGAGATAGCGGCACT 59.894 50.000 1.45 0.00 33.14 4.40
23 24 2.225491 GTCTAGAGAGATAGCGGCACTG 59.775 54.545 1.45 0.00 33.14 3.66
24 25 2.158740 TCTAGAGAGATAGCGGCACTGT 60.159 50.000 1.45 0.00 0.00 3.55
25 26 1.479709 AGAGAGATAGCGGCACTGTT 58.520 50.000 1.45 0.00 0.00 3.16
26 27 1.827969 AGAGAGATAGCGGCACTGTTT 59.172 47.619 1.45 0.00 0.00 2.83
27 28 2.159170 AGAGAGATAGCGGCACTGTTTC 60.159 50.000 1.45 0.00 0.00 2.78
28 29 0.924090 GAGATAGCGGCACTGTTTCG 59.076 55.000 1.45 0.00 0.00 3.46
29 30 0.246635 AGATAGCGGCACTGTTTCGT 59.753 50.000 1.45 0.00 0.00 3.85
30 31 1.076332 GATAGCGGCACTGTTTCGTT 58.924 50.000 1.45 0.00 0.00 3.85
31 32 1.060698 GATAGCGGCACTGTTTCGTTC 59.939 52.381 1.45 0.00 0.00 3.95
32 33 0.947180 TAGCGGCACTGTTTCGTTCC 60.947 55.000 1.45 0.00 0.00 3.62
33 34 2.539338 GCGGCACTGTTTCGTTCCA 61.539 57.895 0.00 0.00 0.00 3.53
34 35 2.018544 CGGCACTGTTTCGTTCCAA 58.981 52.632 0.00 0.00 0.00 3.53
35 36 0.378962 CGGCACTGTTTCGTTCCAAA 59.621 50.000 0.00 0.00 0.00 3.28
36 37 1.596954 CGGCACTGTTTCGTTCCAAAG 60.597 52.381 0.00 0.00 0.00 2.77
37 38 1.477105 GCACTGTTTCGTTCCAAAGC 58.523 50.000 0.00 0.00 0.00 3.51
38 39 1.065551 GCACTGTTTCGTTCCAAAGCT 59.934 47.619 0.00 0.00 0.00 3.74
39 40 2.289547 GCACTGTTTCGTTCCAAAGCTA 59.710 45.455 0.00 0.00 0.00 3.32
40 41 3.058224 GCACTGTTTCGTTCCAAAGCTAT 60.058 43.478 0.00 0.00 0.00 2.97
41 42 4.466828 CACTGTTTCGTTCCAAAGCTATG 58.533 43.478 0.00 0.00 0.00 2.23
42 43 3.502211 ACTGTTTCGTTCCAAAGCTATGG 59.498 43.478 0.00 0.00 42.12 2.74
43 44 3.482436 TGTTTCGTTCCAAAGCTATGGT 58.518 40.909 0.00 0.00 41.46 3.55
44 45 3.886505 TGTTTCGTTCCAAAGCTATGGTT 59.113 39.130 0.00 0.00 41.46 3.67
45 46 4.339814 TGTTTCGTTCCAAAGCTATGGTTT 59.660 37.500 0.00 0.00 41.46 3.27
46 47 4.759516 TTCGTTCCAAAGCTATGGTTTC 57.240 40.909 0.00 0.00 41.46 2.78
47 48 4.015872 TCGTTCCAAAGCTATGGTTTCT 57.984 40.909 0.00 0.00 41.46 2.52
48 49 4.394729 TCGTTCCAAAGCTATGGTTTCTT 58.605 39.130 0.00 0.00 41.46 2.52
49 50 4.825085 TCGTTCCAAAGCTATGGTTTCTTT 59.175 37.500 0.00 0.00 41.46 2.52
50 51 5.300792 TCGTTCCAAAGCTATGGTTTCTTTT 59.699 36.000 0.00 0.00 41.46 2.27
51 52 5.983118 CGTTCCAAAGCTATGGTTTCTTTTT 59.017 36.000 0.00 0.00 41.46 1.94
52 53 6.143919 CGTTCCAAAGCTATGGTTTCTTTTTC 59.856 38.462 0.00 0.00 41.46 2.29
53 54 6.723298 TCCAAAGCTATGGTTTCTTTTTCA 57.277 33.333 0.00 0.00 41.46 2.69
54 55 7.301868 TCCAAAGCTATGGTTTCTTTTTCAT 57.698 32.000 0.00 0.00 41.46 2.57
55 56 7.734942 TCCAAAGCTATGGTTTCTTTTTCATT 58.265 30.769 0.00 0.00 41.46 2.57
56 57 7.872483 TCCAAAGCTATGGTTTCTTTTTCATTC 59.128 33.333 0.00 0.00 41.46 2.67
57 58 7.118245 CCAAAGCTATGGTTTCTTTTTCATTCC 59.882 37.037 0.00 0.00 35.65 3.01
58 59 6.916360 AGCTATGGTTTCTTTTTCATTCCA 57.084 33.333 0.00 0.00 0.00 3.53
59 60 6.928520 AGCTATGGTTTCTTTTTCATTCCAG 58.071 36.000 0.00 0.00 0.00 3.86
60 61 5.578336 GCTATGGTTTCTTTTTCATTCCAGC 59.422 40.000 0.00 0.00 0.00 4.85
61 62 3.976169 TGGTTTCTTTTTCATTCCAGCG 58.024 40.909 0.00 0.00 0.00 5.18
62 63 3.383185 TGGTTTCTTTTTCATTCCAGCGT 59.617 39.130 0.00 0.00 0.00 5.07
63 64 3.735746 GGTTTCTTTTTCATTCCAGCGTG 59.264 43.478 0.00 0.00 0.00 5.34
64 65 4.359706 GTTTCTTTTTCATTCCAGCGTGT 58.640 39.130 0.00 0.00 0.00 4.49
65 66 4.647424 TTCTTTTTCATTCCAGCGTGTT 57.353 36.364 0.00 0.00 0.00 3.32
66 67 4.647424 TCTTTTTCATTCCAGCGTGTTT 57.353 36.364 0.00 0.00 0.00 2.83
67 68 5.759506 TCTTTTTCATTCCAGCGTGTTTA 57.240 34.783 0.00 0.00 0.00 2.01
68 69 6.325919 TCTTTTTCATTCCAGCGTGTTTAT 57.674 33.333 0.00 0.00 0.00 1.40
69 70 6.148948 TCTTTTTCATTCCAGCGTGTTTATG 58.851 36.000 0.00 0.00 0.00 1.90
70 71 5.446143 TTTTCATTCCAGCGTGTTTATGT 57.554 34.783 0.00 0.00 0.00 2.29
71 72 6.561737 TTTTCATTCCAGCGTGTTTATGTA 57.438 33.333 0.00 0.00 0.00 2.29
72 73 6.751514 TTTCATTCCAGCGTGTTTATGTAT 57.248 33.333 0.00 0.00 0.00 2.29
73 74 5.733226 TCATTCCAGCGTGTTTATGTATG 57.267 39.130 0.00 0.00 0.00 2.39
74 75 5.182487 TCATTCCAGCGTGTTTATGTATGT 58.818 37.500 0.00 0.00 0.00 2.29
75 76 5.645929 TCATTCCAGCGTGTTTATGTATGTT 59.354 36.000 0.00 0.00 0.00 2.71
76 77 4.937696 TCCAGCGTGTTTATGTATGTTG 57.062 40.909 0.00 0.00 0.00 3.33
77 78 4.320023 TCCAGCGTGTTTATGTATGTTGT 58.680 39.130 0.00 0.00 0.00 3.32
78 79 5.480205 TCCAGCGTGTTTATGTATGTTGTA 58.520 37.500 0.00 0.00 0.00 2.41
79 80 5.579119 TCCAGCGTGTTTATGTATGTTGTAG 59.421 40.000 0.00 0.00 0.00 2.74
80 81 5.579119 CCAGCGTGTTTATGTATGTTGTAGA 59.421 40.000 0.00 0.00 0.00 2.59
81 82 6.091577 CCAGCGTGTTTATGTATGTTGTAGAA 59.908 38.462 0.00 0.00 0.00 2.10
82 83 7.201609 CCAGCGTGTTTATGTATGTTGTAGAAT 60.202 37.037 0.00 0.00 0.00 2.40
83 84 8.175069 CAGCGTGTTTATGTATGTTGTAGAATT 58.825 33.333 0.00 0.00 0.00 2.17
84 85 8.175069 AGCGTGTTTATGTATGTTGTAGAATTG 58.825 33.333 0.00 0.00 0.00 2.32
85 86 7.044966 GCGTGTTTATGTATGTTGTAGAATTGC 60.045 37.037 0.00 0.00 0.00 3.56
86 87 7.161900 CGTGTTTATGTATGTTGTAGAATTGCG 59.838 37.037 0.00 0.00 0.00 4.85
87 88 6.964370 TGTTTATGTATGTTGTAGAATTGCGC 59.036 34.615 0.00 0.00 0.00 6.09
88 89 4.552166 ATGTATGTTGTAGAATTGCGCC 57.448 40.909 4.18 0.00 0.00 6.53
89 90 3.605634 TGTATGTTGTAGAATTGCGCCT 58.394 40.909 4.18 0.00 0.00 5.52
90 91 4.006989 TGTATGTTGTAGAATTGCGCCTT 58.993 39.130 4.18 0.00 0.00 4.35
91 92 4.457603 TGTATGTTGTAGAATTGCGCCTTT 59.542 37.500 4.18 0.00 0.00 3.11
92 93 3.552604 TGTTGTAGAATTGCGCCTTTC 57.447 42.857 4.18 8.21 0.00 2.62
93 94 2.227865 TGTTGTAGAATTGCGCCTTTCC 59.772 45.455 4.18 0.00 0.00 3.13
94 95 1.459450 TGTAGAATTGCGCCTTTCCC 58.541 50.000 4.18 2.63 0.00 3.97
95 96 1.271652 TGTAGAATTGCGCCTTTCCCA 60.272 47.619 4.18 5.23 0.00 4.37
96 97 1.132453 GTAGAATTGCGCCTTTCCCAC 59.868 52.381 4.18 5.58 0.00 4.61
97 98 0.251341 AGAATTGCGCCTTTCCCACT 60.251 50.000 4.18 0.00 0.00 4.00
98 99 0.171231 GAATTGCGCCTTTCCCACTC 59.829 55.000 4.18 0.00 0.00 3.51
99 100 1.250840 AATTGCGCCTTTCCCACTCC 61.251 55.000 4.18 0.00 0.00 3.85
100 101 2.424842 ATTGCGCCTTTCCCACTCCA 62.425 55.000 4.18 0.00 0.00 3.86
101 102 2.747855 GCGCCTTTCCCACTCCAG 60.748 66.667 0.00 0.00 0.00 3.86
102 103 3.068881 CGCCTTTCCCACTCCAGA 58.931 61.111 0.00 0.00 0.00 3.86
103 104 1.376037 CGCCTTTCCCACTCCAGAC 60.376 63.158 0.00 0.00 0.00 3.51
104 105 1.761174 GCCTTTCCCACTCCAGACA 59.239 57.895 0.00 0.00 0.00 3.41
105 106 0.329596 GCCTTTCCCACTCCAGACAT 59.670 55.000 0.00 0.00 0.00 3.06
106 107 1.680249 GCCTTTCCCACTCCAGACATC 60.680 57.143 0.00 0.00 0.00 3.06
107 108 1.912043 CCTTTCCCACTCCAGACATCT 59.088 52.381 0.00 0.00 0.00 2.90
108 109 2.307098 CCTTTCCCACTCCAGACATCTT 59.693 50.000 0.00 0.00 0.00 2.40
109 110 3.519510 CCTTTCCCACTCCAGACATCTTA 59.480 47.826 0.00 0.00 0.00 2.10
110 111 4.164988 CCTTTCCCACTCCAGACATCTTAT 59.835 45.833 0.00 0.00 0.00 1.73
111 112 5.339530 CCTTTCCCACTCCAGACATCTTATT 60.340 44.000 0.00 0.00 0.00 1.40
112 113 6.126768 CCTTTCCCACTCCAGACATCTTATTA 60.127 42.308 0.00 0.00 0.00 0.98
113 114 7.420680 CCTTTCCCACTCCAGACATCTTATTAT 60.421 40.741 0.00 0.00 0.00 1.28
114 115 7.451731 TTCCCACTCCAGACATCTTATTATT 57.548 36.000 0.00 0.00 0.00 1.40
115 116 8.561536 TTCCCACTCCAGACATCTTATTATTA 57.438 34.615 0.00 0.00 0.00 0.98
116 117 8.742125 TCCCACTCCAGACATCTTATTATTAT 57.258 34.615 0.00 0.00 0.00 1.28
117 118 9.837681 TCCCACTCCAGACATCTTATTATTATA 57.162 33.333 0.00 0.00 0.00 0.98
144 145 9.762933 TCAAGAAAACAAATTTAATTCTGAGGG 57.237 29.630 11.04 4.94 31.14 4.30
145 146 8.498358 CAAGAAAACAAATTTAATTCTGAGGGC 58.502 33.333 11.04 0.00 31.14 5.19
146 147 7.734942 AGAAAACAAATTTAATTCTGAGGGCA 58.265 30.769 10.01 0.00 0.00 5.36
147 148 8.377799 AGAAAACAAATTTAATTCTGAGGGCAT 58.622 29.630 10.01 0.00 0.00 4.40
148 149 7.910441 AAACAAATTTAATTCTGAGGGCATG 57.090 32.000 0.00 0.00 0.00 4.06
149 150 5.981174 ACAAATTTAATTCTGAGGGCATGG 58.019 37.500 0.00 0.00 0.00 3.66
150 151 5.721000 ACAAATTTAATTCTGAGGGCATGGA 59.279 36.000 0.00 0.00 0.00 3.41
151 152 6.127253 ACAAATTTAATTCTGAGGGCATGGAG 60.127 38.462 0.00 0.00 0.00 3.86
152 153 3.582998 TTAATTCTGAGGGCATGGAGG 57.417 47.619 0.00 0.00 0.00 4.30
153 154 0.554792 AATTCTGAGGGCATGGAGGG 59.445 55.000 0.00 0.00 0.00 4.30
154 155 0.625683 ATTCTGAGGGCATGGAGGGT 60.626 55.000 0.00 0.00 0.00 4.34
155 156 0.846427 TTCTGAGGGCATGGAGGGTT 60.846 55.000 0.00 0.00 0.00 4.11
156 157 1.225704 CTGAGGGCATGGAGGGTTC 59.774 63.158 0.00 0.00 0.00 3.62
157 158 2.276309 CTGAGGGCATGGAGGGTTCC 62.276 65.000 0.00 0.00 44.31 3.62
158 159 3.023735 AGGGCATGGAGGGTTCCC 61.024 66.667 0.00 0.00 43.33 3.97
159 160 4.506255 GGGCATGGAGGGTTCCCG 62.506 72.222 1.91 0.00 43.33 5.14
160 161 3.728373 GGCATGGAGGGTTCCCGT 61.728 66.667 1.91 0.00 43.33 5.28
161 162 2.372074 GGCATGGAGGGTTCCCGTA 61.372 63.158 1.91 0.00 43.33 4.02
162 163 1.705997 GGCATGGAGGGTTCCCGTAT 61.706 60.000 1.91 0.00 43.33 3.06
163 164 0.182775 GCATGGAGGGTTCCCGTATT 59.817 55.000 1.91 0.00 43.33 1.89
164 165 1.409661 GCATGGAGGGTTCCCGTATTT 60.410 52.381 1.91 0.00 43.33 1.40
165 166 2.158726 GCATGGAGGGTTCCCGTATTTA 60.159 50.000 1.91 0.00 43.33 1.40
166 167 3.740115 CATGGAGGGTTCCCGTATTTAG 58.260 50.000 1.91 0.00 43.33 1.85
167 168 2.836667 TGGAGGGTTCCCGTATTTAGT 58.163 47.619 1.91 0.00 43.33 2.24
168 169 3.992999 TGGAGGGTTCCCGTATTTAGTA 58.007 45.455 1.91 0.00 43.33 1.82
169 170 3.962718 TGGAGGGTTCCCGTATTTAGTAG 59.037 47.826 1.91 0.00 43.33 2.57
170 171 4.218312 GGAGGGTTCCCGTATTTAGTAGA 58.782 47.826 1.91 0.00 37.53 2.59
171 172 4.651045 GGAGGGTTCCCGTATTTAGTAGAA 59.349 45.833 1.91 0.00 37.53 2.10
172 173 5.129320 GGAGGGTTCCCGTATTTAGTAGAAA 59.871 44.000 1.91 0.00 37.53 2.52
173 174 6.231258 AGGGTTCCCGTATTTAGTAGAAAG 57.769 41.667 1.91 0.00 0.00 2.62
174 175 5.723405 AGGGTTCCCGTATTTAGTAGAAAGT 59.277 40.000 1.91 0.00 0.00 2.66
175 176 6.045318 GGGTTCCCGTATTTAGTAGAAAGTC 58.955 44.000 0.00 0.00 0.00 3.01
176 177 6.127225 GGGTTCCCGTATTTAGTAGAAAGTCT 60.127 42.308 0.00 0.00 0.00 3.24
177 178 6.755607 GGTTCCCGTATTTAGTAGAAAGTCTG 59.244 42.308 0.00 0.00 0.00 3.51
178 179 7.363268 GGTTCCCGTATTTAGTAGAAAGTCTGA 60.363 40.741 0.00 0.00 0.00 3.27
179 180 7.330900 TCCCGTATTTAGTAGAAAGTCTGAG 57.669 40.000 0.00 0.00 0.00 3.35
180 181 6.320672 TCCCGTATTTAGTAGAAAGTCTGAGG 59.679 42.308 0.00 0.00 0.00 3.86
181 182 6.096564 CCCGTATTTAGTAGAAAGTCTGAGGT 59.903 42.308 0.00 0.00 0.00 3.85
182 183 7.363617 CCCGTATTTAGTAGAAAGTCTGAGGTT 60.364 40.741 0.00 0.00 0.00 3.50
183 184 7.701501 CCGTATTTAGTAGAAAGTCTGAGGTTC 59.298 40.741 0.00 0.00 0.00 3.62
184 185 7.428761 CGTATTTAGTAGAAAGTCTGAGGTTCG 59.571 40.741 0.00 0.00 0.00 3.95
185 186 3.579335 AGTAGAAAGTCTGAGGTTCGC 57.421 47.619 0.00 0.00 0.00 4.70
186 187 2.231721 AGTAGAAAGTCTGAGGTTCGCC 59.768 50.000 0.00 0.00 37.60 5.54
196 197 4.619852 GGTTCGCCTTTCCCTCTC 57.380 61.111 0.00 0.00 0.00 3.20
197 198 1.078356 GGTTCGCCTTTCCCTCTCC 60.078 63.158 0.00 0.00 0.00 3.71
198 199 1.677552 GTTCGCCTTTCCCTCTCCA 59.322 57.895 0.00 0.00 0.00 3.86
199 200 0.673956 GTTCGCCTTTCCCTCTCCAC 60.674 60.000 0.00 0.00 0.00 4.02
200 201 0.836400 TTCGCCTTTCCCTCTCCACT 60.836 55.000 0.00 0.00 0.00 4.00
201 202 0.836400 TCGCCTTTCCCTCTCCACTT 60.836 55.000 0.00 0.00 0.00 3.16
202 203 0.036875 CGCCTTTCCCTCTCCACTTT 59.963 55.000 0.00 0.00 0.00 2.66
203 204 1.278127 CGCCTTTCCCTCTCCACTTTA 59.722 52.381 0.00 0.00 0.00 1.85
204 205 2.678190 CGCCTTTCCCTCTCCACTTTAG 60.678 54.545 0.00 0.00 0.00 1.85
205 206 2.572104 GCCTTTCCCTCTCCACTTTAGA 59.428 50.000 0.00 0.00 0.00 2.10
206 207 3.620226 GCCTTTCCCTCTCCACTTTAGAC 60.620 52.174 0.00 0.00 0.00 2.59
207 208 3.841255 CCTTTCCCTCTCCACTTTAGACT 59.159 47.826 0.00 0.00 0.00 3.24
208 209 4.287326 CCTTTCCCTCTCCACTTTAGACTT 59.713 45.833 0.00 0.00 0.00 3.01
209 210 5.483811 CTTTCCCTCTCCACTTTAGACTTC 58.516 45.833 0.00 0.00 0.00 3.01
210 211 4.127918 TCCCTCTCCACTTTAGACTTCA 57.872 45.455 0.00 0.00 0.00 3.02
211 212 4.090090 TCCCTCTCCACTTTAGACTTCAG 58.910 47.826 0.00 0.00 0.00 3.02
212 213 3.368948 CCCTCTCCACTTTAGACTTCAGC 60.369 52.174 0.00 0.00 0.00 4.26
213 214 3.506810 CTCTCCACTTTAGACTTCAGCG 58.493 50.000 0.00 0.00 0.00 5.18
214 215 2.891580 TCTCCACTTTAGACTTCAGCGT 59.108 45.455 0.00 0.00 0.00 5.07
215 216 3.321111 TCTCCACTTTAGACTTCAGCGTT 59.679 43.478 0.00 0.00 0.00 4.84
216 217 4.058817 CTCCACTTTAGACTTCAGCGTTT 58.941 43.478 0.00 0.00 0.00 3.60
217 218 4.448210 TCCACTTTAGACTTCAGCGTTTT 58.552 39.130 0.00 0.00 0.00 2.43
218 219 4.879545 TCCACTTTAGACTTCAGCGTTTTT 59.120 37.500 0.00 0.00 0.00 1.94
259 260 4.974645 ACTAACCTTCTGACCATGTTCA 57.025 40.909 0.00 0.00 0.00 3.18
261 262 2.867109 ACCTTCTGACCATGTTCAGG 57.133 50.000 18.98 7.82 42.95 3.86
262 263 2.338809 ACCTTCTGACCATGTTCAGGA 58.661 47.619 18.98 10.63 42.95 3.86
263 264 2.304180 ACCTTCTGACCATGTTCAGGAG 59.696 50.000 19.27 19.27 45.70 3.69
265 266 3.332919 CTTCTGACCATGTTCAGGAGTG 58.667 50.000 18.23 4.84 42.40 3.51
266 267 2.608623 TCTGACCATGTTCAGGAGTGA 58.391 47.619 18.98 0.00 42.95 3.41
267 268 3.176411 TCTGACCATGTTCAGGAGTGAT 58.824 45.455 18.98 0.00 42.95 3.06
269 270 4.777366 TCTGACCATGTTCAGGAGTGATTA 59.223 41.667 18.98 0.00 42.95 1.75
271 272 4.192317 GACCATGTTCAGGAGTGATTACC 58.808 47.826 0.00 0.00 30.85 2.85
272 273 3.054361 ACCATGTTCAGGAGTGATTACCC 60.054 47.826 0.00 0.00 30.85 3.69
273 274 3.200825 CCATGTTCAGGAGTGATTACCCT 59.799 47.826 0.00 0.00 30.85 4.34
285 292 9.615660 AGGAGTGATTACCCTTATTATGATGTA 57.384 33.333 0.00 0.00 0.00 2.29
293 300 5.013183 ACCCTTATTATGATGTACCTGAGCC 59.987 44.000 0.00 0.00 0.00 4.70
316 323 1.696832 GAAAACGCCGCTGCTAGAGG 61.697 60.000 0.00 2.39 38.30 3.69
333 340 1.008538 GGCAAAGAACACCAGCACG 60.009 57.895 0.00 0.00 0.00 5.34
347 354 0.616111 AGCACGTCCTCTTCCTCCAT 60.616 55.000 0.00 0.00 0.00 3.41
378 385 2.223502 GGCGATAACTCGTGACATCTCA 60.224 50.000 0.00 0.00 46.71 3.27
461 468 9.102757 TCTACAGTTTTTCATCAGAATAGATGC 57.897 33.333 0.00 0.00 43.94 3.91
466 473 4.944619 TTCATCAGAATAGATGCCGAGT 57.055 40.909 0.00 0.00 43.94 4.18
479 486 1.202758 TGCCGAGTGTTCTTTCCACAT 60.203 47.619 0.00 0.00 35.24 3.21
719 731 2.134789 CCTTTACTGGCTTGATGGCT 57.865 50.000 0.00 0.00 42.34 4.75
1053 1072 3.512724 CCAAAGGAGAAGATGGTTTGCAT 59.487 43.478 0.00 0.00 0.00 3.96
1058 1077 3.065925 GGAGAAGATGGTTTGCATAGTGC 59.934 47.826 0.00 0.00 45.29 4.40
1201 1223 6.040278 TCAAGTTCTGTTCATACAATTTGGCA 59.960 34.615 0.78 0.00 32.92 4.92
1219 1241 3.700539 TGGCATCACATTTATCTGGTTGG 59.299 43.478 0.00 0.00 0.00 3.77
1419 1745 8.729756 TGTTCATATAGTTTGGAGTCACATTTG 58.270 33.333 0.00 0.00 0.00 2.32
1423 1749 9.912634 CATATAGTTTGGAGTCACATTTGTTTT 57.087 29.630 0.00 0.00 0.00 2.43
1431 1757 5.394115 GGAGTCACATTTGTTTTGGTTGACT 60.394 40.000 1.08 1.08 36.90 3.41
1467 1793 3.696281 TGTGTCATGTTCACAAGCTTG 57.304 42.857 24.84 24.84 41.83 4.01
1525 1864 6.294453 CCAGCCATATGTAGTGAGAGTCTAAG 60.294 46.154 1.24 0.00 0.00 2.18
1526 1865 5.772672 AGCCATATGTAGTGAGAGTCTAAGG 59.227 44.000 1.24 0.00 0.00 2.69
1567 1911 8.644374 AGTTGGCTATTTGGTAACTAAATGAA 57.356 30.769 0.00 0.00 34.25 2.57
1665 2010 6.071952 GGCCTTCATGTTATTCAGTCTTTCAA 60.072 38.462 0.00 0.00 0.00 2.69
1875 2225 8.471609 TCTTGATCTACGGTGTGATGTTATTAA 58.528 33.333 0.00 0.00 0.00 1.40
2165 2789 1.185618 ACCTGCTAGGCGTCTGTTGA 61.186 55.000 0.00 0.00 39.63 3.18
2171 2795 2.742053 GCTAGGCGTCTGTTGATTTGAA 59.258 45.455 0.00 0.00 0.00 2.69
2190 2814 6.877668 TTGAATACCCTGTCAGGTACATAA 57.122 37.500 17.85 3.32 45.08 1.90
2286 2910 2.285743 ACTCCCCCTGGCTTCTCC 60.286 66.667 0.00 0.00 0.00 3.71
2329 2953 1.394917 CCTTCAAGGATTCGAAGCACG 59.605 52.381 16.24 2.70 37.67 5.34
2481 3105 1.675641 GCCGGCCATGAAGAACACT 60.676 57.895 18.11 0.00 0.00 3.55
2719 3343 2.874780 CGACAGACGCCAGTACGC 60.875 66.667 0.00 0.00 36.19 4.42
2789 3414 2.279073 CTCCCTAGTCGGCCAGGA 59.721 66.667 1.94 0.00 33.42 3.86
2932 3558 2.224066 CCTCGATAAAGCCCTCGTCATT 60.224 50.000 0.00 0.00 36.33 2.57
2961 3587 1.594833 CTACAGTAACCAGCCGCCA 59.405 57.895 0.00 0.00 0.00 5.69
2972 3598 4.966787 GCCGCCAACAAGACCCCA 62.967 66.667 0.00 0.00 0.00 4.96
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 2.105821 AGTGCCGCTATCTCTCTAGACT 59.894 50.000 0.00 0.00 33.57 3.24
4 5 2.226330 ACAGTGCCGCTATCTCTCTAG 58.774 52.381 0.00 0.00 0.00 2.43
5 6 2.350057 ACAGTGCCGCTATCTCTCTA 57.650 50.000 0.00 0.00 0.00 2.43
6 7 1.479709 AACAGTGCCGCTATCTCTCT 58.520 50.000 0.00 0.00 0.00 3.10
7 8 2.197577 GAAACAGTGCCGCTATCTCTC 58.802 52.381 0.00 0.00 0.00 3.20
8 9 1.469940 CGAAACAGTGCCGCTATCTCT 60.470 52.381 0.00 0.00 0.00 3.10
9 10 0.924090 CGAAACAGTGCCGCTATCTC 59.076 55.000 0.00 0.00 0.00 2.75
10 11 0.246635 ACGAAACAGTGCCGCTATCT 59.753 50.000 0.00 0.00 0.00 1.98
11 12 1.060698 GAACGAAACAGTGCCGCTATC 59.939 52.381 0.00 0.00 0.00 2.08
12 13 1.076332 GAACGAAACAGTGCCGCTAT 58.924 50.000 0.00 0.00 0.00 2.97
13 14 0.947180 GGAACGAAACAGTGCCGCTA 60.947 55.000 0.00 0.00 28.57 4.26
14 15 2.251642 GGAACGAAACAGTGCCGCT 61.252 57.895 0.00 0.00 28.57 5.52
15 16 2.054140 TTGGAACGAAACAGTGCCGC 62.054 55.000 0.00 0.00 42.97 6.53
16 17 0.378962 TTTGGAACGAAACAGTGCCG 59.621 50.000 0.00 0.00 42.97 5.69
17 18 1.864029 GCTTTGGAACGAAACAGTGCC 60.864 52.381 0.00 0.00 40.37 5.01
18 19 1.065551 AGCTTTGGAACGAAACAGTGC 59.934 47.619 0.00 0.00 0.00 4.40
19 20 4.466828 CATAGCTTTGGAACGAAACAGTG 58.533 43.478 0.00 0.00 0.00 3.66
20 21 3.502211 CCATAGCTTTGGAACGAAACAGT 59.498 43.478 17.55 0.00 39.25 3.55
21 22 3.502211 ACCATAGCTTTGGAACGAAACAG 59.498 43.478 27.54 0.00 39.25 3.16
22 23 3.482436 ACCATAGCTTTGGAACGAAACA 58.518 40.909 27.54 0.00 39.25 2.83
23 24 4.499037 AACCATAGCTTTGGAACGAAAC 57.501 40.909 27.54 0.00 39.25 2.78
24 25 4.825085 AGAAACCATAGCTTTGGAACGAAA 59.175 37.500 27.54 0.00 39.25 3.46
25 26 4.394729 AGAAACCATAGCTTTGGAACGAA 58.605 39.130 27.54 0.00 39.25 3.85
26 27 4.015872 AGAAACCATAGCTTTGGAACGA 57.984 40.909 27.54 0.00 39.25 3.85
27 28 4.766404 AAGAAACCATAGCTTTGGAACG 57.234 40.909 27.54 3.61 39.25 3.95
28 29 6.983890 TGAAAAAGAAACCATAGCTTTGGAAC 59.016 34.615 27.54 17.08 39.25 3.62
29 30 7.118496 TGAAAAAGAAACCATAGCTTTGGAA 57.882 32.000 27.54 0.00 39.25 3.53
30 31 6.723298 TGAAAAAGAAACCATAGCTTTGGA 57.277 33.333 27.54 0.27 39.25 3.53
31 32 7.118245 GGAATGAAAAAGAAACCATAGCTTTGG 59.882 37.037 20.36 20.36 42.82 3.28
32 33 7.656948 TGGAATGAAAAAGAAACCATAGCTTTG 59.343 33.333 0.00 0.00 32.63 2.77
33 34 7.734942 TGGAATGAAAAAGAAACCATAGCTTT 58.265 30.769 0.00 0.00 33.59 3.51
34 35 7.301868 TGGAATGAAAAAGAAACCATAGCTT 57.698 32.000 0.00 0.00 0.00 3.74
35 36 6.573094 GCTGGAATGAAAAAGAAACCATAGCT 60.573 38.462 0.00 0.00 0.00 3.32
36 37 5.578336 GCTGGAATGAAAAAGAAACCATAGC 59.422 40.000 0.00 0.00 0.00 2.97
37 38 5.801947 CGCTGGAATGAAAAAGAAACCATAG 59.198 40.000 0.00 0.00 0.00 2.23
38 39 5.242838 ACGCTGGAATGAAAAAGAAACCATA 59.757 36.000 0.00 0.00 0.00 2.74
39 40 4.039124 ACGCTGGAATGAAAAAGAAACCAT 59.961 37.500 0.00 0.00 0.00 3.55
40 41 3.383185 ACGCTGGAATGAAAAAGAAACCA 59.617 39.130 0.00 0.00 0.00 3.67
41 42 3.735746 CACGCTGGAATGAAAAAGAAACC 59.264 43.478 0.00 0.00 0.00 3.27
42 43 4.359706 ACACGCTGGAATGAAAAAGAAAC 58.640 39.130 0.00 0.00 0.00 2.78
43 44 4.647424 ACACGCTGGAATGAAAAAGAAA 57.353 36.364 0.00 0.00 0.00 2.52
44 45 4.647424 AACACGCTGGAATGAAAAAGAA 57.353 36.364 0.00 0.00 0.00 2.52
45 46 4.647424 AAACACGCTGGAATGAAAAAGA 57.353 36.364 0.00 0.00 0.00 2.52
46 47 5.920273 ACATAAACACGCTGGAATGAAAAAG 59.080 36.000 0.00 0.00 0.00 2.27
47 48 5.837437 ACATAAACACGCTGGAATGAAAAA 58.163 33.333 0.00 0.00 0.00 1.94
48 49 5.446143 ACATAAACACGCTGGAATGAAAA 57.554 34.783 0.00 0.00 0.00 2.29
49 50 6.150307 ACATACATAAACACGCTGGAATGAAA 59.850 34.615 0.00 0.00 0.00 2.69
50 51 5.645929 ACATACATAAACACGCTGGAATGAA 59.354 36.000 0.00 0.00 0.00 2.57
51 52 5.182487 ACATACATAAACACGCTGGAATGA 58.818 37.500 0.00 0.00 0.00 2.57
52 53 5.484173 ACATACATAAACACGCTGGAATG 57.516 39.130 0.00 0.00 0.00 2.67
53 54 5.414454 ACAACATACATAAACACGCTGGAAT 59.586 36.000 0.00 0.00 0.00 3.01
54 55 4.757657 ACAACATACATAAACACGCTGGAA 59.242 37.500 0.00 0.00 0.00 3.53
55 56 4.320023 ACAACATACATAAACACGCTGGA 58.680 39.130 0.00 0.00 0.00 3.86
56 57 4.678509 ACAACATACATAAACACGCTGG 57.321 40.909 0.00 0.00 0.00 4.85
57 58 6.641176 TCTACAACATACATAAACACGCTG 57.359 37.500 0.00 0.00 0.00 5.18
58 59 7.843490 ATTCTACAACATACATAAACACGCT 57.157 32.000 0.00 0.00 0.00 5.07
59 60 7.044966 GCAATTCTACAACATACATAAACACGC 60.045 37.037 0.00 0.00 0.00 5.34
60 61 7.161900 CGCAATTCTACAACATACATAAACACG 59.838 37.037 0.00 0.00 0.00 4.49
61 62 7.044966 GCGCAATTCTACAACATACATAAACAC 60.045 37.037 0.30 0.00 0.00 3.32
62 63 6.964370 GCGCAATTCTACAACATACATAAACA 59.036 34.615 0.30 0.00 0.00 2.83
63 64 6.413818 GGCGCAATTCTACAACATACATAAAC 59.586 38.462 10.83 0.00 0.00 2.01
64 65 6.317642 AGGCGCAATTCTACAACATACATAAA 59.682 34.615 10.83 0.00 0.00 1.40
65 66 5.820423 AGGCGCAATTCTACAACATACATAA 59.180 36.000 10.83 0.00 0.00 1.90
66 67 5.364778 AGGCGCAATTCTACAACATACATA 58.635 37.500 10.83 0.00 0.00 2.29
67 68 4.199310 AGGCGCAATTCTACAACATACAT 58.801 39.130 10.83 0.00 0.00 2.29
68 69 3.605634 AGGCGCAATTCTACAACATACA 58.394 40.909 10.83 0.00 0.00 2.29
69 70 4.616181 AAGGCGCAATTCTACAACATAC 57.384 40.909 10.83 0.00 0.00 2.39
70 71 4.095782 GGAAAGGCGCAATTCTACAACATA 59.904 41.667 19.61 0.00 0.00 2.29
71 72 3.119495 GGAAAGGCGCAATTCTACAACAT 60.119 43.478 19.61 0.00 0.00 2.71
72 73 2.227865 GGAAAGGCGCAATTCTACAACA 59.772 45.455 19.61 0.00 0.00 3.33
73 74 2.415491 GGGAAAGGCGCAATTCTACAAC 60.415 50.000 19.61 6.69 0.00 3.32
74 75 1.816224 GGGAAAGGCGCAATTCTACAA 59.184 47.619 19.61 0.00 0.00 2.41
75 76 1.271652 TGGGAAAGGCGCAATTCTACA 60.272 47.619 19.61 16.38 36.40 2.74
76 77 1.132453 GTGGGAAAGGCGCAATTCTAC 59.868 52.381 19.61 15.68 41.49 2.59
77 78 1.004277 AGTGGGAAAGGCGCAATTCTA 59.996 47.619 19.61 9.80 41.49 2.10
78 79 0.251341 AGTGGGAAAGGCGCAATTCT 60.251 50.000 19.61 1.46 41.49 2.40
79 80 0.171231 GAGTGGGAAAGGCGCAATTC 59.829 55.000 10.83 12.86 41.49 2.17
80 81 1.250840 GGAGTGGGAAAGGCGCAATT 61.251 55.000 10.83 2.44 41.49 2.32
81 82 1.678970 GGAGTGGGAAAGGCGCAAT 60.679 57.895 10.83 0.00 41.49 3.56
82 83 2.282180 GGAGTGGGAAAGGCGCAA 60.282 61.111 10.83 0.00 41.49 4.85
83 84 3.551496 CTGGAGTGGGAAAGGCGCA 62.551 63.158 10.83 0.00 37.07 6.09
84 85 2.747855 CTGGAGTGGGAAAGGCGC 60.748 66.667 0.00 0.00 0.00 6.53
85 86 1.376037 GTCTGGAGTGGGAAAGGCG 60.376 63.158 0.00 0.00 0.00 5.52
86 87 0.329596 ATGTCTGGAGTGGGAAAGGC 59.670 55.000 0.00 0.00 0.00 4.35
87 88 1.912043 AGATGTCTGGAGTGGGAAAGG 59.088 52.381 0.00 0.00 0.00 3.11
88 89 3.710209 AAGATGTCTGGAGTGGGAAAG 57.290 47.619 0.00 0.00 0.00 2.62
89 90 5.779241 AATAAGATGTCTGGAGTGGGAAA 57.221 39.130 0.00 0.00 0.00 3.13
90 91 7.451731 AATAATAAGATGTCTGGAGTGGGAA 57.548 36.000 0.00 0.00 0.00 3.97
91 92 8.742125 ATAATAATAAGATGTCTGGAGTGGGA 57.258 34.615 0.00 0.00 0.00 4.37
118 119 9.762933 CCCTCAGAATTAAATTTGTTTTCTTGA 57.237 29.630 0.00 6.36 0.00 3.02
119 120 8.498358 GCCCTCAGAATTAAATTTGTTTTCTTG 58.502 33.333 0.00 2.87 0.00 3.02
120 121 8.210265 TGCCCTCAGAATTAAATTTGTTTTCTT 58.790 29.630 0.00 0.00 0.00 2.52
121 122 7.734942 TGCCCTCAGAATTAAATTTGTTTTCT 58.265 30.769 0.00 3.92 0.00 2.52
122 123 7.961325 TGCCCTCAGAATTAAATTTGTTTTC 57.039 32.000 0.00 1.68 0.00 2.29
123 124 7.391275 CCATGCCCTCAGAATTAAATTTGTTTT 59.609 33.333 0.00 0.00 0.00 2.43
124 125 6.880529 CCATGCCCTCAGAATTAAATTTGTTT 59.119 34.615 0.00 0.00 0.00 2.83
125 126 6.213195 TCCATGCCCTCAGAATTAAATTTGTT 59.787 34.615 0.00 0.00 0.00 2.83
126 127 5.721000 TCCATGCCCTCAGAATTAAATTTGT 59.279 36.000 0.00 0.00 0.00 2.83
127 128 6.224665 TCCATGCCCTCAGAATTAAATTTG 57.775 37.500 0.00 0.00 0.00 2.32
128 129 5.364735 CCTCCATGCCCTCAGAATTAAATTT 59.635 40.000 0.00 0.00 0.00 1.82
129 130 4.897670 CCTCCATGCCCTCAGAATTAAATT 59.102 41.667 0.00 0.00 0.00 1.82
130 131 4.477249 CCTCCATGCCCTCAGAATTAAAT 58.523 43.478 0.00 0.00 0.00 1.40
131 132 3.373001 CCCTCCATGCCCTCAGAATTAAA 60.373 47.826 0.00 0.00 0.00 1.52
132 133 2.175499 CCCTCCATGCCCTCAGAATTAA 59.825 50.000 0.00 0.00 0.00 1.40
133 134 1.776667 CCCTCCATGCCCTCAGAATTA 59.223 52.381 0.00 0.00 0.00 1.40
134 135 0.554792 CCCTCCATGCCCTCAGAATT 59.445 55.000 0.00 0.00 0.00 2.17
135 136 0.625683 ACCCTCCATGCCCTCAGAAT 60.626 55.000 0.00 0.00 0.00 2.40
136 137 0.846427 AACCCTCCATGCCCTCAGAA 60.846 55.000 0.00 0.00 0.00 3.02
137 138 1.229951 AACCCTCCATGCCCTCAGA 60.230 57.895 0.00 0.00 0.00 3.27
138 139 1.225704 GAACCCTCCATGCCCTCAG 59.774 63.158 0.00 0.00 0.00 3.35
139 140 2.308722 GGAACCCTCCATGCCCTCA 61.309 63.158 0.00 0.00 41.96 3.86
140 141 2.597903 GGAACCCTCCATGCCCTC 59.402 66.667 0.00 0.00 41.96 4.30
153 154 7.542025 TCAGACTTTCTACTAAATACGGGAAC 58.458 38.462 0.00 0.00 0.00 3.62
154 155 7.147949 CCTCAGACTTTCTACTAAATACGGGAA 60.148 40.741 0.00 0.00 0.00 3.97
155 156 6.320672 CCTCAGACTTTCTACTAAATACGGGA 59.679 42.308 0.00 0.00 0.00 5.14
156 157 6.096564 ACCTCAGACTTTCTACTAAATACGGG 59.903 42.308 0.00 0.00 0.00 5.28
157 158 7.098074 ACCTCAGACTTTCTACTAAATACGG 57.902 40.000 0.00 0.00 0.00 4.02
158 159 7.428761 CGAACCTCAGACTTTCTACTAAATACG 59.571 40.741 0.00 0.00 0.00 3.06
159 160 7.220491 GCGAACCTCAGACTTTCTACTAAATAC 59.780 40.741 0.00 0.00 0.00 1.89
160 161 7.256286 GCGAACCTCAGACTTTCTACTAAATA 58.744 38.462 0.00 0.00 0.00 1.40
161 162 6.100668 GCGAACCTCAGACTTTCTACTAAAT 58.899 40.000 0.00 0.00 0.00 1.40
162 163 5.467705 GCGAACCTCAGACTTTCTACTAAA 58.532 41.667 0.00 0.00 0.00 1.85
163 164 4.082354 GGCGAACCTCAGACTTTCTACTAA 60.082 45.833 0.00 0.00 0.00 2.24
164 165 3.442977 GGCGAACCTCAGACTTTCTACTA 59.557 47.826 0.00 0.00 0.00 1.82
165 166 2.231721 GGCGAACCTCAGACTTTCTACT 59.768 50.000 0.00 0.00 0.00 2.57
166 167 2.231721 AGGCGAACCTCAGACTTTCTAC 59.768 50.000 0.00 0.00 46.34 2.59
167 168 2.526432 AGGCGAACCTCAGACTTTCTA 58.474 47.619 0.00 0.00 46.34 2.10
168 169 1.343069 AGGCGAACCTCAGACTTTCT 58.657 50.000 0.00 0.00 46.34 2.52
169 170 3.917072 AGGCGAACCTCAGACTTTC 57.083 52.632 0.00 0.00 46.34 2.62
179 180 1.078356 GGAGAGGGAAAGGCGAACC 60.078 63.158 0.00 0.00 0.00 3.62
180 181 0.673956 GTGGAGAGGGAAAGGCGAAC 60.674 60.000 0.00 0.00 0.00 3.95
181 182 0.836400 AGTGGAGAGGGAAAGGCGAA 60.836 55.000 0.00 0.00 0.00 4.70
182 183 0.836400 AAGTGGAGAGGGAAAGGCGA 60.836 55.000 0.00 0.00 0.00 5.54
183 184 0.036875 AAAGTGGAGAGGGAAAGGCG 59.963 55.000 0.00 0.00 0.00 5.52
184 185 2.572104 TCTAAAGTGGAGAGGGAAAGGC 59.428 50.000 0.00 0.00 0.00 4.35
185 186 3.841255 AGTCTAAAGTGGAGAGGGAAAGG 59.159 47.826 0.00 0.00 0.00 3.11
186 187 5.012148 TGAAGTCTAAAGTGGAGAGGGAAAG 59.988 44.000 0.00 0.00 0.00 2.62
187 188 4.905456 TGAAGTCTAAAGTGGAGAGGGAAA 59.095 41.667 0.00 0.00 0.00 3.13
188 189 4.489737 TGAAGTCTAAAGTGGAGAGGGAA 58.510 43.478 0.00 0.00 0.00 3.97
189 190 4.090090 CTGAAGTCTAAAGTGGAGAGGGA 58.910 47.826 0.00 0.00 0.00 4.20
190 191 3.368948 GCTGAAGTCTAAAGTGGAGAGGG 60.369 52.174 0.00 0.00 0.00 4.30
191 192 3.674682 CGCTGAAGTCTAAAGTGGAGAGG 60.675 52.174 0.00 0.00 0.00 3.69
192 193 3.057174 ACGCTGAAGTCTAAAGTGGAGAG 60.057 47.826 0.00 0.00 0.00 3.20
193 194 2.891580 ACGCTGAAGTCTAAAGTGGAGA 59.108 45.455 0.00 0.00 0.00 3.71
194 195 3.305398 ACGCTGAAGTCTAAAGTGGAG 57.695 47.619 0.00 0.00 0.00 3.86
195 196 3.746045 AACGCTGAAGTCTAAAGTGGA 57.254 42.857 0.00 0.00 0.00 4.02
196 197 4.813296 AAAACGCTGAAGTCTAAAGTGG 57.187 40.909 0.00 0.00 0.00 4.00
226 227 6.651225 GTCAGAAGGTTAGTAGACAGCAAAAT 59.349 38.462 0.00 0.00 0.00 1.82
231 232 3.510360 TGGTCAGAAGGTTAGTAGACAGC 59.490 47.826 0.00 0.00 0.00 4.40
259 260 8.511748 ACATCATAATAAGGGTAATCACTCCT 57.488 34.615 0.00 0.00 0.00 3.69
261 262 9.654663 GGTACATCATAATAAGGGTAATCACTC 57.345 37.037 0.00 0.00 0.00 3.51
262 263 9.393786 AGGTACATCATAATAAGGGTAATCACT 57.606 33.333 0.00 0.00 0.00 3.41
263 264 9.436957 CAGGTACATCATAATAAGGGTAATCAC 57.563 37.037 0.00 0.00 0.00 3.06
265 266 9.877178 CTCAGGTACATCATAATAAGGGTAATC 57.123 37.037 0.00 0.00 0.00 1.75
266 267 8.322091 GCTCAGGTACATCATAATAAGGGTAAT 58.678 37.037 0.00 0.00 0.00 1.89
267 268 7.256547 GGCTCAGGTACATCATAATAAGGGTAA 60.257 40.741 0.00 0.00 0.00 2.85
269 270 5.013183 GGCTCAGGTACATCATAATAAGGGT 59.987 44.000 0.00 0.00 0.00 4.34
271 272 5.171476 CGGCTCAGGTACATCATAATAAGG 58.829 45.833 0.00 0.00 0.00 2.69
272 273 5.784177 ACGGCTCAGGTACATCATAATAAG 58.216 41.667 0.00 0.00 0.00 1.73
273 274 5.801531 ACGGCTCAGGTACATCATAATAA 57.198 39.130 0.00 0.00 0.00 1.40
316 323 0.317020 GACGTGCTGGTGTTCTTTGC 60.317 55.000 0.00 0.00 0.00 3.68
333 340 0.463474 GCTGCATGGAGGAAGAGGAC 60.463 60.000 16.65 0.00 0.00 3.85
378 385 2.040813 AGATGATTGCCTTGACACTGGT 59.959 45.455 0.00 0.00 0.00 4.00
461 468 2.494059 ACATGTGGAAAGAACACTCGG 58.506 47.619 0.00 0.00 39.52 4.63
466 473 6.013725 ACACTAGGATACATGTGGAAAGAACA 60.014 38.462 9.11 0.00 43.36 3.18
479 486 1.046472 CCCGCCCACACTAGGATACA 61.046 60.000 0.00 0.00 41.41 2.29
587 594 7.263100 TCGGTTATGATGAAAATCCATGAAG 57.737 36.000 0.00 0.00 0.00 3.02
719 731 3.580458 CCTTCAGGAGAACTCTTCCTTGA 59.420 47.826 1.86 0.00 37.39 3.02
906 919 1.340405 GGAGGCATGGACTGTGTCAAT 60.340 52.381 0.00 0.00 33.68 2.57
1053 1072 6.811253 AAAAATAGATTGTTGACGGCACTA 57.189 33.333 0.00 0.00 0.00 2.74
1201 1223 3.378112 CACGCCAACCAGATAAATGTGAT 59.622 43.478 0.00 0.00 0.00 3.06
1219 1241 1.140804 AAGTGGCAACCAAACACGC 59.859 52.632 0.00 0.00 39.95 5.34
1419 1745 3.586100 ACCACACAAGTCAACCAAAAC 57.414 42.857 0.00 0.00 0.00 2.43
1423 1749 2.645802 GGTAACCACACAAGTCAACCA 58.354 47.619 0.00 0.00 0.00 3.67
1499 1838 2.968574 ACTCTCACTACATATGGCTGGG 59.031 50.000 7.80 0.00 0.00 4.45
1696 2044 3.898482 AGTCAGTAAATATGGTTGGGCC 58.102 45.455 0.00 0.00 37.90 5.80
1728 2078 3.580039 CATTGGCCTTATGGGGAAGAAT 58.420 45.455 3.32 0.00 35.12 2.40
1731 2081 1.043022 GCATTGGCCTTATGGGGAAG 58.957 55.000 16.81 0.00 35.12 3.46
1850 2200 8.642908 TTAATAACATCACACCGTAGATCAAG 57.357 34.615 0.00 0.00 0.00 3.02
1875 2225 1.002430 CGGTGTATGCATCTAGGCCAT 59.998 52.381 5.01 0.00 0.00 4.40
2165 2789 5.772393 TGTACCTGACAGGGTATTCAAAT 57.228 39.130 25.34 3.64 42.84 2.32
2202 2826 8.216423 AGTGAGATCAAGCATTACCTAAATCAT 58.784 33.333 0.00 0.00 0.00 2.45
2286 2910 5.287226 GCTCAAATGGCCTGATAATTTCTG 58.713 41.667 3.32 0.00 0.00 3.02
2317 2941 3.202706 GGCCCCGTGCTTCGAATC 61.203 66.667 0.00 0.00 42.86 2.52
2481 3105 2.282180 GCCGGCTTTTGGGAGTCA 60.282 61.111 22.15 0.00 0.00 3.41
2630 3254 4.185059 GACCCGTACGGCGTCCTC 62.185 72.222 30.22 16.78 39.32 3.71
2681 3305 1.517257 GATGACGTCGAGGCCAGTG 60.517 63.158 11.62 0.00 0.00 3.66
2682 3306 2.711922 GGATGACGTCGAGGCCAGT 61.712 63.158 11.62 0.00 0.00 4.00
2683 3307 2.105128 GGATGACGTCGAGGCCAG 59.895 66.667 11.62 0.00 0.00 4.85
2738 3362 0.793250 GAGCGTCTCTCTGGCAAAAC 59.207 55.000 0.00 0.00 38.78 2.43
2742 3366 1.927608 CTTCGAGCGTCTCTCTGGCA 61.928 60.000 5.53 0.00 39.70 4.92
2932 3558 0.259647 TTACTGTAGCCTCGCCCCTA 59.740 55.000 0.00 0.00 0.00 3.53
2961 3587 1.106944 CACCGCTTTGGGGTCTTGTT 61.107 55.000 3.25 0.00 45.92 2.83
3096 3722 3.644738 CAGGGGTACAATAGTAATCCGGT 59.355 47.826 0.00 0.00 32.80 5.28


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

AutoCloner maintained by Alex Coulton.