Multiple sequence alignment - TraesCS6D01G374000

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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 TraesCS6D01G374000 chr6D 100.000 3289 0 0 1 3289 458608778 458605490 0.000000e+00 6074.0
1 TraesCS6D01G374000 chr6D 87.133 1500 132 29 1635 3114 458722774 458721316 0.000000e+00 1644.0
2 TraesCS6D01G374000 chr6D 86.850 327 30 8 954 1276 458728158 458727841 1.450000e-93 353.0
3 TraesCS6D01G374000 chr6D 96.954 197 4 2 1 196 458686094 458685899 2.450000e-86 329.0
4 TraesCS6D01G374000 chr6D 82.632 380 54 9 314 686 458737949 458737575 3.160000e-85 326.0
5 TraesCS6D01G374000 chr6D 95.556 90 4 0 1339 1428 458722860 458722771 9.510000e-31 145.0
6 TraesCS6D01G374000 chr6D 89.041 73 6 1 206 276 458738335 458738263 4.520000e-14 89.8
7 TraesCS6D01G374000 chr6B 94.910 1729 71 6 1563 3289 697603929 697602216 0.000000e+00 2689.0
8 TraesCS6D01G374000 chr6B 93.742 751 32 8 194 934 697618782 697618037 0.000000e+00 1112.0
9 TraesCS6D01G374000 chr6B 85.806 930 87 22 1635 2557 697694278 697693387 0.000000e+00 944.0
10 TraesCS6D01G374000 chr6B 96.357 549 19 1 1023 1570 697617704 697617156 0.000000e+00 902.0
11 TraesCS6D01G374000 chr6B 89.130 644 57 4 2562 3194 697681790 697681149 0.000000e+00 789.0
12 TraesCS6D01G374000 chr6B 89.591 269 25 3 1010 1276 697695373 697695106 4.070000e-89 339.0
13 TraesCS6D01G374000 chr6B 94.444 90 5 0 1339 1428 697694364 697694275 4.430000e-29 139.0
14 TraesCS6D01G374000 chr6B 87.379 103 11 1 189 289 697696379 697696277 2.070000e-22 117.0
15 TraesCS6D01G374000 chr6B 98.182 55 1 0 3190 3244 697680985 697680931 2.700000e-16 97.1
16 TraesCS6D01G374000 chr6A 89.109 1010 91 8 2247 3244 605036871 605037873 0.000000e+00 1238.0
17 TraesCS6D01G374000 chr6A 83.022 642 79 17 314 938 605023549 605024177 3.710000e-154 555.0
18 TraesCS6D01G374000 chr6A 84.242 330 36 9 952 1276 605024223 605024541 1.150000e-79 307.0
19 TraesCS6D01G374000 chr7D 95.939 197 8 0 1 197 285080011 285080207 1.470000e-83 320.0
20 TraesCS6D01G374000 chr7D 95.431 197 9 0 1 197 134242741 134242937 6.850000e-82 315.0
21 TraesCS6D01G374000 chr2D 95.918 196 8 0 1 196 482159453 482159648 5.300000e-83 318.0
22 TraesCS6D01G374000 chr2D 94.472 199 11 0 1 199 551544356 551544554 1.150000e-79 307.0
23 TraesCS6D01G374000 chr3D 95.408 196 9 0 1 196 389253958 389254153 2.460000e-81 313.0
24 TraesCS6D01G374000 chr3D 95.408 196 9 0 1 196 429005648 429005843 2.460000e-81 313.0
25 TraesCS6D01G374000 chr3D 94.146 205 9 3 1 205 171618864 171619065 3.190000e-80 309.0
26 TraesCS6D01G374000 chr3D 82.805 221 30 5 1052 1269 24569708 24569493 1.200000e-44 191.0
27 TraesCS6D01G374000 chr3D 82.569 218 31 6 1052 1266 597288364 597288577 5.600000e-43 185.0
28 TraesCS6D01G374000 chr1D 95.408 196 9 0 1 196 355066465 355066660 2.460000e-81 313.0
29 TraesCS6D01G374000 chr5B 82.028 217 34 3 1052 1266 638783202 638783415 2.610000e-41 180.0
30 TraesCS6D01G374000 chr2A 82.028 217 34 3 1052 1266 138922382 138922595 2.610000e-41 180.0
31 TraesCS6D01G374000 chr1A 81.900 221 32 5 1052 1269 556086517 556086302 2.610000e-41 180.0
32 TraesCS6D01G374000 chr7B 98.113 53 1 0 2840 2892 703562015 703561963 3.490000e-15 93.5
33 TraesCS6D01G374000 chr3B 100.000 28 0 0 1810 1837 580066162 580066189 6.000000e-03 52.8


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 TraesCS6D01G374000 chr6D 458605490 458608778 3288 True 6074.00 6074 100.0000 1 3289 1 chr6D.!!$R1 3288
1 TraesCS6D01G374000 chr6D 458721316 458722860 1544 True 894.50 1644 91.3445 1339 3114 2 chr6D.!!$R4 1775
2 TraesCS6D01G374000 chr6D 458737575 458738335 760 True 207.90 326 85.8365 206 686 2 chr6D.!!$R5 480
3 TraesCS6D01G374000 chr6B 697602216 697603929 1713 True 2689.00 2689 94.9100 1563 3289 1 chr6B.!!$R1 1726
4 TraesCS6D01G374000 chr6B 697617156 697618782 1626 True 1007.00 1112 95.0495 194 1570 2 chr6B.!!$R2 1376
5 TraesCS6D01G374000 chr6B 697680931 697681790 859 True 443.05 789 93.6560 2562 3244 2 chr6B.!!$R3 682
6 TraesCS6D01G374000 chr6B 697693387 697696379 2992 True 384.75 944 89.3050 189 2557 4 chr6B.!!$R4 2368
7 TraesCS6D01G374000 chr6A 605036871 605037873 1002 False 1238.00 1238 89.1090 2247 3244 1 chr6A.!!$F1 997
8 TraesCS6D01G374000 chr6A 605023549 605024541 992 False 431.00 555 83.6320 314 1276 2 chr6A.!!$F2 962

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
106 107 0.093705 CGCTGCAAGTAGTTCTTCGC 59.906 55.000 0.00 0.00 35.30 4.70 F
139 140 1.003118 TCACCCTGAAATTCCTCGGTG 59.997 52.381 13.71 13.71 41.73 4.94 F
1425 2686 0.531532 CTAGCGCTCACCATCTTGGG 60.532 60.000 16.34 0.00 43.37 4.12 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1182 1740 0.322816 GGGTGATGATGGCAGTGTGT 60.323 55.000 0.00 0.0 0.00 3.72 R
1887 3157 0.398696 TTCCACCGTGGTGCAACTAT 59.601 50.000 17.32 0.0 44.16 2.12 R
2469 3746 2.022195 CCAGAATCCTAACTCGTCGGA 58.978 52.381 0.00 0.0 0.00 4.55 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
22 23 5.909621 TTACGCTTCCTGTACTCTATGTT 57.090 39.130 0.00 0.00 0.00 2.71
23 24 4.803098 ACGCTTCCTGTACTCTATGTTT 57.197 40.909 0.00 0.00 0.00 2.83
24 25 4.495422 ACGCTTCCTGTACTCTATGTTTG 58.505 43.478 0.00 0.00 0.00 2.93
25 26 4.021368 ACGCTTCCTGTACTCTATGTTTGT 60.021 41.667 0.00 0.00 0.00 2.83
26 27 4.929808 CGCTTCCTGTACTCTATGTTTGTT 59.070 41.667 0.00 0.00 0.00 2.83
27 28 5.408604 CGCTTCCTGTACTCTATGTTTGTTT 59.591 40.000 0.00 0.00 0.00 2.83
28 29 6.073222 CGCTTCCTGTACTCTATGTTTGTTTT 60.073 38.462 0.00 0.00 0.00 2.43
29 30 7.298854 GCTTCCTGTACTCTATGTTTGTTTTC 58.701 38.462 0.00 0.00 0.00 2.29
30 31 7.573283 GCTTCCTGTACTCTATGTTTGTTTTCC 60.573 40.741 0.00 0.00 0.00 3.13
31 32 7.074653 TCCTGTACTCTATGTTTGTTTTCCT 57.925 36.000 0.00 0.00 0.00 3.36
32 33 7.514721 TCCTGTACTCTATGTTTGTTTTCCTT 58.485 34.615 0.00 0.00 0.00 3.36
33 34 7.996644 TCCTGTACTCTATGTTTGTTTTCCTTT 59.003 33.333 0.00 0.00 0.00 3.11
34 35 8.290325 CCTGTACTCTATGTTTGTTTTCCTTTC 58.710 37.037 0.00 0.00 0.00 2.62
35 36 8.740123 TGTACTCTATGTTTGTTTTCCTTTCA 57.260 30.769 0.00 0.00 0.00 2.69
36 37 9.349713 TGTACTCTATGTTTGTTTTCCTTTCAT 57.650 29.630 0.00 0.00 0.00 2.57
37 38 9.827411 GTACTCTATGTTTGTTTTCCTTTCATC 57.173 33.333 0.00 0.00 0.00 2.92
38 39 8.463930 ACTCTATGTTTGTTTTCCTTTCATCA 57.536 30.769 0.00 0.00 0.00 3.07
39 40 9.082313 ACTCTATGTTTGTTTTCCTTTCATCAT 57.918 29.630 0.00 0.00 0.00 2.45
40 41 9.350357 CTCTATGTTTGTTTTCCTTTCATCATG 57.650 33.333 0.00 0.00 0.00 3.07
41 42 9.076781 TCTATGTTTGTTTTCCTTTCATCATGA 57.923 29.630 0.00 0.00 0.00 3.07
42 43 9.865321 CTATGTTTGTTTTCCTTTCATCATGAT 57.135 29.630 1.18 1.18 0.00 2.45
43 44 7.949903 TGTTTGTTTTCCTTTCATCATGATG 57.050 32.000 26.79 26.79 40.09 3.07
44 45 7.499292 TGTTTGTTTTCCTTTCATCATGATGT 58.501 30.769 30.01 0.00 39.72 3.06
45 46 7.652909 TGTTTGTTTTCCTTTCATCATGATGTC 59.347 33.333 30.01 13.39 39.72 3.06
46 47 7.528996 TTGTTTTCCTTTCATCATGATGTCT 57.471 32.000 30.01 0.00 39.72 3.41
47 48 8.634335 TTGTTTTCCTTTCATCATGATGTCTA 57.366 30.769 30.01 16.72 39.72 2.59
48 49 8.812513 TGTTTTCCTTTCATCATGATGTCTAT 57.187 30.769 30.01 0.00 39.72 1.98
49 50 8.680001 TGTTTTCCTTTCATCATGATGTCTATG 58.320 33.333 30.01 18.83 39.72 2.23
50 51 6.872628 TTCCTTTCATCATGATGTCTATGC 57.127 37.500 30.01 0.00 39.72 3.14
51 52 6.183810 TCCTTTCATCATGATGTCTATGCT 57.816 37.500 30.01 0.00 39.72 3.79
52 53 6.598503 TCCTTTCATCATGATGTCTATGCTT 58.401 36.000 30.01 0.00 39.72 3.91
53 54 6.485648 TCCTTTCATCATGATGTCTATGCTTG 59.514 38.462 30.01 13.25 39.72 4.01
54 55 6.262496 CCTTTCATCATGATGTCTATGCTTGT 59.738 38.462 30.01 0.00 39.72 3.16
55 56 6.613755 TTCATCATGATGTCTATGCTTGTG 57.386 37.500 30.01 6.67 39.72 3.33
56 57 5.677567 TCATCATGATGTCTATGCTTGTGT 58.322 37.500 30.01 0.00 39.72 3.72
57 58 6.117488 TCATCATGATGTCTATGCTTGTGTT 58.883 36.000 30.01 0.00 39.72 3.32
58 59 7.274447 TCATCATGATGTCTATGCTTGTGTTA 58.726 34.615 30.01 6.98 39.72 2.41
59 60 7.440255 TCATCATGATGTCTATGCTTGTGTTAG 59.560 37.037 30.01 3.51 39.72 2.34
60 61 6.051074 TCATGATGTCTATGCTTGTGTTAGG 58.949 40.000 0.00 0.00 0.00 2.69
61 62 5.420725 TGATGTCTATGCTTGTGTTAGGT 57.579 39.130 0.00 0.00 0.00 3.08
62 63 5.804639 TGATGTCTATGCTTGTGTTAGGTT 58.195 37.500 0.00 0.00 0.00 3.50
63 64 6.941857 TGATGTCTATGCTTGTGTTAGGTTA 58.058 36.000 0.00 0.00 0.00 2.85
64 65 7.564793 TGATGTCTATGCTTGTGTTAGGTTAT 58.435 34.615 0.00 0.00 0.00 1.89
65 66 7.495606 TGATGTCTATGCTTGTGTTAGGTTATG 59.504 37.037 0.00 0.00 0.00 1.90
66 67 6.941857 TGTCTATGCTTGTGTTAGGTTATGA 58.058 36.000 0.00 0.00 0.00 2.15
67 68 6.816640 TGTCTATGCTTGTGTTAGGTTATGAC 59.183 38.462 0.00 0.00 0.00 3.06
68 69 7.042335 GTCTATGCTTGTGTTAGGTTATGACT 58.958 38.462 0.00 0.00 0.00 3.41
69 70 7.010552 GTCTATGCTTGTGTTAGGTTATGACTG 59.989 40.741 0.00 0.00 0.00 3.51
70 71 3.751175 TGCTTGTGTTAGGTTATGACTGC 59.249 43.478 0.00 0.00 0.00 4.40
71 72 3.751175 GCTTGTGTTAGGTTATGACTGCA 59.249 43.478 0.00 0.00 0.00 4.41
72 73 4.396166 GCTTGTGTTAGGTTATGACTGCAT 59.604 41.667 0.00 0.00 38.54 3.96
73 74 5.447818 GCTTGTGTTAGGTTATGACTGCATC 60.448 44.000 0.00 0.00 35.94 3.91
74 75 5.420725 TGTGTTAGGTTATGACTGCATCT 57.579 39.130 0.00 0.00 35.94 2.90
75 76 5.178061 TGTGTTAGGTTATGACTGCATCTG 58.822 41.667 0.00 0.00 35.94 2.90
76 77 5.046663 TGTGTTAGGTTATGACTGCATCTGA 60.047 40.000 0.00 0.00 35.94 3.27
77 78 5.521735 GTGTTAGGTTATGACTGCATCTGAG 59.478 44.000 0.00 0.00 35.94 3.35
78 79 5.187772 TGTTAGGTTATGACTGCATCTGAGT 59.812 40.000 0.00 0.00 35.94 3.41
79 80 6.379988 TGTTAGGTTATGACTGCATCTGAGTA 59.620 38.462 0.00 0.00 35.94 2.59
80 81 5.269505 AGGTTATGACTGCATCTGAGTAC 57.730 43.478 0.00 0.00 35.94 2.73
81 82 4.959210 AGGTTATGACTGCATCTGAGTACT 59.041 41.667 0.00 0.00 35.94 2.73
82 83 5.423610 AGGTTATGACTGCATCTGAGTACTT 59.576 40.000 0.00 0.00 35.94 2.24
83 84 6.607600 AGGTTATGACTGCATCTGAGTACTTA 59.392 38.462 0.00 0.00 35.94 2.24
84 85 7.288852 AGGTTATGACTGCATCTGAGTACTTAT 59.711 37.037 0.00 0.00 35.94 1.73
85 86 7.928706 GGTTATGACTGCATCTGAGTACTTATT 59.071 37.037 0.00 0.00 35.94 1.40
86 87 8.973378 GTTATGACTGCATCTGAGTACTTATTC 58.027 37.037 0.00 0.00 35.94 1.75
87 88 5.907207 TGACTGCATCTGAGTACTTATTCC 58.093 41.667 0.00 0.00 0.00 3.01
88 89 4.938080 ACTGCATCTGAGTACTTATTCCG 58.062 43.478 0.00 0.00 0.00 4.30
89 90 3.717707 TGCATCTGAGTACTTATTCCGC 58.282 45.455 0.00 0.00 0.00 5.54
90 91 3.384789 TGCATCTGAGTACTTATTCCGCT 59.615 43.478 0.00 0.00 0.00 5.52
91 92 3.738282 GCATCTGAGTACTTATTCCGCTG 59.262 47.826 0.00 0.00 0.00 5.18
92 93 3.438297 TCTGAGTACTTATTCCGCTGC 57.562 47.619 0.00 0.00 0.00 5.25
93 94 2.758423 TCTGAGTACTTATTCCGCTGCA 59.242 45.455 0.00 0.00 0.00 4.41
94 95 3.194755 TCTGAGTACTTATTCCGCTGCAA 59.805 43.478 0.00 0.00 0.00 4.08
95 96 3.521560 TGAGTACTTATTCCGCTGCAAG 58.478 45.455 0.00 0.00 0.00 4.01
96 97 3.056107 TGAGTACTTATTCCGCTGCAAGT 60.056 43.478 0.00 4.02 35.30 3.16
97 98 4.158949 TGAGTACTTATTCCGCTGCAAGTA 59.841 41.667 0.00 3.00 35.30 2.24
98 99 4.683832 AGTACTTATTCCGCTGCAAGTAG 58.316 43.478 9.07 0.00 34.93 2.57
99 100 3.611766 ACTTATTCCGCTGCAAGTAGT 57.388 42.857 0.00 0.00 35.30 2.73
100 101 3.939066 ACTTATTCCGCTGCAAGTAGTT 58.061 40.909 0.00 0.00 35.30 2.24
101 102 3.933332 ACTTATTCCGCTGCAAGTAGTTC 59.067 43.478 0.00 0.00 35.30 3.01
102 103 2.770164 ATTCCGCTGCAAGTAGTTCT 57.230 45.000 0.00 0.00 35.30 3.01
103 104 2.543777 TTCCGCTGCAAGTAGTTCTT 57.456 45.000 0.00 0.00 35.30 2.52
104 105 2.080286 TCCGCTGCAAGTAGTTCTTC 57.920 50.000 0.00 0.00 35.30 2.87
105 106 0.716108 CCGCTGCAAGTAGTTCTTCG 59.284 55.000 0.00 0.00 35.30 3.79
106 107 0.093705 CGCTGCAAGTAGTTCTTCGC 59.906 55.000 0.00 0.00 35.30 4.70
107 108 1.433534 GCTGCAAGTAGTTCTTCGCT 58.566 50.000 0.00 0.00 35.30 4.93
108 109 1.801178 GCTGCAAGTAGTTCTTCGCTT 59.199 47.619 0.00 0.00 35.30 4.68
109 110 2.993899 GCTGCAAGTAGTTCTTCGCTTA 59.006 45.455 0.00 0.00 35.30 3.09
110 111 3.061429 GCTGCAAGTAGTTCTTCGCTTAG 59.939 47.826 0.00 0.00 35.30 2.18
111 112 3.585862 TGCAAGTAGTTCTTCGCTTAGG 58.414 45.455 0.00 0.00 33.63 2.69
112 113 3.257375 TGCAAGTAGTTCTTCGCTTAGGA 59.743 43.478 0.00 0.00 33.63 2.94
113 114 4.243270 GCAAGTAGTTCTTCGCTTAGGAA 58.757 43.478 0.00 0.00 33.63 3.36
114 115 4.870991 GCAAGTAGTTCTTCGCTTAGGAAT 59.129 41.667 0.00 0.00 33.63 3.01
115 116 5.351740 GCAAGTAGTTCTTCGCTTAGGAATT 59.648 40.000 0.00 0.00 33.63 2.17
116 117 6.128254 GCAAGTAGTTCTTCGCTTAGGAATTT 60.128 38.462 0.00 0.00 33.63 1.82
117 118 7.457060 CAAGTAGTTCTTCGCTTAGGAATTTC 58.543 38.462 0.00 0.00 33.63 2.17
118 119 6.107343 AGTAGTTCTTCGCTTAGGAATTTCC 58.893 40.000 7.39 7.39 36.58 3.13
120 121 5.179533 AGTTCTTCGCTTAGGAATTTCCTC 58.820 41.667 21.20 6.87 45.66 3.71
121 122 4.819105 TCTTCGCTTAGGAATTTCCTCA 57.181 40.909 21.20 10.08 45.66 3.86
122 123 4.504858 TCTTCGCTTAGGAATTTCCTCAC 58.495 43.478 21.20 10.94 45.66 3.51
123 124 3.261981 TCGCTTAGGAATTTCCTCACC 57.738 47.619 21.20 9.58 45.66 4.02
124 125 2.093128 TCGCTTAGGAATTTCCTCACCC 60.093 50.000 21.20 7.96 45.66 4.61
125 126 2.092914 CGCTTAGGAATTTCCTCACCCT 60.093 50.000 21.20 0.00 45.66 4.34
126 127 3.282885 GCTTAGGAATTTCCTCACCCTG 58.717 50.000 21.20 7.77 45.66 4.45
127 128 3.054361 GCTTAGGAATTTCCTCACCCTGA 60.054 47.826 21.20 0.00 45.66 3.86
128 129 4.567747 GCTTAGGAATTTCCTCACCCTGAA 60.568 45.833 21.20 7.67 45.66 3.02
129 130 5.570320 CTTAGGAATTTCCTCACCCTGAAA 58.430 41.667 21.20 6.99 45.66 2.69
130 131 4.682021 AGGAATTTCCTCACCCTGAAAT 57.318 40.909 12.37 0.00 45.66 2.17
131 132 5.015813 AGGAATTTCCTCACCCTGAAATT 57.984 39.130 12.37 9.29 45.66 1.82
132 133 5.019470 AGGAATTTCCTCACCCTGAAATTC 58.981 41.667 21.03 21.03 45.66 2.17
134 135 4.682021 ATTTCCTCACCCTGAAATTCCT 57.318 40.909 0.00 0.00 37.82 3.36
135 136 3.721087 TTCCTCACCCTGAAATTCCTC 57.279 47.619 0.00 0.00 0.00 3.71
136 137 1.555075 TCCTCACCCTGAAATTCCTCG 59.445 52.381 0.00 0.00 0.00 4.63
137 138 1.407437 CCTCACCCTGAAATTCCTCGG 60.407 57.143 0.00 0.00 0.00 4.63
138 139 1.279271 CTCACCCTGAAATTCCTCGGT 59.721 52.381 0.00 0.00 0.00 4.69
139 140 1.003118 TCACCCTGAAATTCCTCGGTG 59.997 52.381 13.71 13.71 41.73 4.94
140 141 1.003118 CACCCTGAAATTCCTCGGTGA 59.997 52.381 14.37 0.00 42.75 4.02
141 142 1.702957 ACCCTGAAATTCCTCGGTGAA 59.297 47.619 0.00 0.00 0.00 3.18
142 143 2.290323 ACCCTGAAATTCCTCGGTGAAG 60.290 50.000 0.00 0.00 0.00 3.02
143 144 2.027192 CCCTGAAATTCCTCGGTGAAGA 60.027 50.000 0.00 0.00 0.00 2.87
144 145 3.559171 CCCTGAAATTCCTCGGTGAAGAA 60.559 47.826 0.00 0.00 0.00 2.52
145 146 4.265073 CCTGAAATTCCTCGGTGAAGAAT 58.735 43.478 0.00 0.00 0.00 2.40
146 147 4.702131 CCTGAAATTCCTCGGTGAAGAATT 59.298 41.667 0.00 0.00 40.92 2.17
167 168 9.822185 AGAATTCATAAAAATTGCCTATTCACC 57.178 29.630 8.44 0.00 0.00 4.02
168 169 8.962884 AATTCATAAAAATTGCCTATTCACCC 57.037 30.769 0.00 0.00 0.00 4.61
169 170 6.478512 TCATAAAAATTGCCTATTCACCCC 57.521 37.500 0.00 0.00 0.00 4.95
170 171 5.365314 TCATAAAAATTGCCTATTCACCCCC 59.635 40.000 0.00 0.00 0.00 5.40
187 188 1.674962 CCCCCTCTAGTCGACTTAACG 59.325 57.143 25.44 10.17 0.00 3.18
192 193 3.119919 CCTCTAGTCGACTTAACGCACTT 60.120 47.826 25.44 0.00 0.00 3.16
201 202 4.049186 GACTTAACGCACTTTCACTCTCA 58.951 43.478 0.00 0.00 0.00 3.27
268 271 8.896722 TCTCCCCTTATTTATGTAGGTCTATC 57.103 38.462 0.00 0.00 0.00 2.08
312 592 4.608170 ATCTCTCTTTGTCCCTCTCTCT 57.392 45.455 0.00 0.00 0.00 3.10
345 625 4.106197 CCGTTCTCTTTTCGGTAGATCTG 58.894 47.826 5.18 0.00 39.51 2.90
373 657 6.041409 TCACTCTCACACTCTTGATTTCTCTT 59.959 38.462 0.00 0.00 0.00 2.85
381 665 6.016192 ACACTCTTGATTTCTCTTAGACACGA 60.016 38.462 0.00 0.00 0.00 4.35
401 685 3.351885 ACTCTCCTCCCCTCGCCT 61.352 66.667 0.00 0.00 0.00 5.52
508 806 3.433274 CCACACACACACACATGTCTATC 59.567 47.826 0.00 0.00 36.72 2.08
577 875 2.392816 CCTCCCGGTCCCTCTCCTA 61.393 68.421 0.00 0.00 0.00 2.94
697 1007 6.601613 CACACACTATTTAGGTCTCTCTCTCT 59.398 42.308 0.00 0.00 0.00 3.10
698 1008 6.826741 ACACACTATTTAGGTCTCTCTCTCTC 59.173 42.308 0.00 0.00 0.00 3.20
699 1009 6.826231 CACACTATTTAGGTCTCTCTCTCTCA 59.174 42.308 0.00 0.00 0.00 3.27
700 1010 6.826741 ACACTATTTAGGTCTCTCTCTCTCAC 59.173 42.308 0.00 0.00 0.00 3.51
733 1043 1.703411 CACACACCACCCCATCTTTT 58.297 50.000 0.00 0.00 0.00 2.27
747 1057 3.523564 CCATCTTTTTGGACCCCTCTCTA 59.476 47.826 0.00 0.00 39.25 2.43
769 1079 9.950680 CTCTATCTCACTCTCTTTTAAGACATC 57.049 37.037 0.00 0.00 0.00 3.06
774 1084 4.019321 CACTCTCTTTTAAGACATCCCCCA 60.019 45.833 0.00 0.00 0.00 4.96
775 1085 4.601857 ACTCTCTTTTAAGACATCCCCCAA 59.398 41.667 0.00 0.00 0.00 4.12
781 1091 7.475299 TCTTTTAAGACATCCCCCAATAGTTT 58.525 34.615 0.00 0.00 0.00 2.66
792 1102 3.937079 CCCCAATAGTTTTGTCCGTCTAC 59.063 47.826 0.00 0.00 0.00 2.59
819 1129 2.629617 TCTCTCTCACTCACATGCACAA 59.370 45.455 0.00 0.00 0.00 3.33
871 1183 2.110721 TCTCCCTCTCTGCATGCCTATA 59.889 50.000 16.68 0.00 0.00 1.31
874 1186 2.159128 CCCTCTCTGCATGCCTATATCG 60.159 54.545 16.68 0.00 0.00 2.92
938 1250 3.006967 ACAACACAAACTCCGCTAGATCT 59.993 43.478 0.00 0.00 0.00 2.75
940 1252 3.093057 ACACAAACTCCGCTAGATCTCT 58.907 45.455 0.00 0.00 0.00 3.10
947 1259 3.006967 ACTCCGCTAGATCTCTCTCTCTC 59.993 52.174 0.00 0.00 32.66 3.20
948 1260 3.239449 TCCGCTAGATCTCTCTCTCTCT 58.761 50.000 0.00 0.00 32.66 3.10
949 1261 3.258372 TCCGCTAGATCTCTCTCTCTCTC 59.742 52.174 0.00 0.00 32.66 3.20
950 1262 3.259374 CCGCTAGATCTCTCTCTCTCTCT 59.741 52.174 0.00 0.00 32.66 3.10
961 1307 2.881513 TCTCTCTCTCTCACACACACAC 59.118 50.000 0.00 0.00 0.00 3.82
963 1309 3.023832 TCTCTCTCTCACACACACACAA 58.976 45.455 0.00 0.00 0.00 3.33
990 1338 8.038351 ACTCTTTTATTTGCCTTAGTCTCTCTC 58.962 37.037 0.00 0.00 0.00 3.20
991 1339 8.140112 TCTTTTATTTGCCTTAGTCTCTCTCT 57.860 34.615 0.00 0.00 0.00 3.10
992 1340 8.254508 TCTTTTATTTGCCTTAGTCTCTCTCTC 58.745 37.037 0.00 0.00 0.00 3.20
993 1341 7.726033 TTTATTTGCCTTAGTCTCTCTCTCT 57.274 36.000 0.00 0.00 0.00 3.10
994 1342 8.824756 TTTATTTGCCTTAGTCTCTCTCTCTA 57.175 34.615 0.00 0.00 0.00 2.43
995 1343 9.427821 TTTATTTGCCTTAGTCTCTCTCTCTAT 57.572 33.333 0.00 0.00 0.00 1.98
1182 1740 2.676822 ACTGGAGCGAGCCGAAGA 60.677 61.111 0.00 0.00 0.00 2.87
1241 1799 5.050567 CGGAAAACCTTGTTGTAGTAGACAC 60.051 44.000 0.00 0.00 37.96 3.67
1344 2605 1.064003 ACCACAATCTAGGTGCACCA 58.936 50.000 36.39 21.17 36.60 4.17
1370 2631 3.276846 AGCCACGTGCACGGTTTC 61.277 61.111 39.21 24.97 44.83 2.78
1425 2686 0.531532 CTAGCGCTCACCATCTTGGG 60.532 60.000 16.34 0.00 43.37 4.12
1432 2693 2.357154 GCTCACCATCTTGGGGTACATT 60.357 50.000 0.00 0.00 42.97 2.71
1447 2708 4.251268 GGTACATTGACAAGGTCTACCAC 58.749 47.826 16.40 7.05 38.89 4.16
1455 2716 2.167900 ACAAGGTCTACCACGGAATAGC 59.832 50.000 1.26 0.00 38.89 2.97
1461 2722 1.485066 CTACCACGGAATAGCACCCTT 59.515 52.381 0.00 0.00 0.00 3.95
1468 2729 2.552031 GGAATAGCACCCTTCGTCTTC 58.448 52.381 0.00 0.00 0.00 2.87
1595 2856 5.180810 TCTCACTACTCTGTCCATGTAGT 57.819 43.478 0.00 0.00 45.08 2.73
1768 3029 9.801714 CAGAAGTATTAGCTTTTTGCAAAATTG 57.198 29.630 24.39 19.72 45.94 2.32
1887 3157 2.805671 CGTATGTTTGTGACCTTGCAGA 59.194 45.455 0.00 0.00 0.00 4.26
1953 3223 4.227073 AGAAGAAAGATGAAGGAAGGGAGG 59.773 45.833 0.00 0.00 0.00 4.30
1957 3227 3.723098 AGATGAAGGAAGGGAGGAGAT 57.277 47.619 0.00 0.00 0.00 2.75
1961 3231 5.254972 AGATGAAGGAAGGGAGGAGATTTTT 59.745 40.000 0.00 0.00 0.00 1.94
2072 3344 3.075283 TCATTTTGGGTGGTATGGTCAGT 59.925 43.478 0.00 0.00 0.00 3.41
2074 3346 3.706600 TTTGGGTGGTATGGTCAGTAC 57.293 47.619 0.00 0.00 0.00 2.73
2107 3380 0.191314 GGGGAGCTCTATGGTAGGGT 59.809 60.000 14.64 0.00 0.00 4.34
2141 3414 1.581447 CAAGACCCCGCTTTTGCTC 59.419 57.895 0.00 0.00 44.80 4.26
2156 3429 4.356405 TTTGCTCGTATGGATGATGGAT 57.644 40.909 0.00 0.00 0.00 3.41
2240 3517 1.180029 CCAAGATGAAACAGGCCCAG 58.820 55.000 0.00 0.00 0.00 4.45
2265 3542 8.497745 AGAAGGCTCTAAATTAAGATGGAATGA 58.502 33.333 0.00 0.00 0.00 2.57
2266 3543 8.688747 AAGGCTCTAAATTAAGATGGAATGAG 57.311 34.615 0.00 0.00 0.00 2.90
2469 3746 5.305644 CCCCAGTACAAATAGCTCACTATCT 59.694 44.000 0.00 0.00 38.18 1.98
2520 3797 4.963628 GGTGGGAGAGTAAGGAAGAGTAAT 59.036 45.833 0.00 0.00 0.00 1.89
2522 3799 6.070136 GGTGGGAGAGTAAGGAAGAGTAATTT 60.070 42.308 0.00 0.00 0.00 1.82
2568 3845 3.169908 GAGGGGAGACAGATTAGGGATC 58.830 54.545 0.00 0.00 34.83 3.36
2727 4004 7.735326 TTTAATCTTCTAGAAGTAGGCCTGT 57.265 36.000 27.59 0.00 39.38 4.00
2929 4208 4.991687 CACACTAAGTGGAGGAGTTTTCTC 59.008 45.833 0.00 0.00 44.69 2.87
3134 4422 3.653835 AGGGGCCTTACAAGAGAATTC 57.346 47.619 0.84 0.00 0.00 2.17
3283 4739 7.496529 TGTGAAAAATCTCGAGAAGAATGTT 57.503 32.000 20.91 4.94 37.61 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.909621 AACATAGAGTACAGGAAGCGTAA 57.090 39.130 0.00 0.00 0.00 3.18
1 2 5.184479 ACAAACATAGAGTACAGGAAGCGTA 59.816 40.000 0.00 0.00 0.00 4.42
2 3 4.021368 ACAAACATAGAGTACAGGAAGCGT 60.021 41.667 0.00 0.00 0.00 5.07
3 4 4.495422 ACAAACATAGAGTACAGGAAGCG 58.505 43.478 0.00 0.00 0.00 4.68
4 5 6.803154 AAACAAACATAGAGTACAGGAAGC 57.197 37.500 0.00 0.00 0.00 3.86
5 6 7.661847 AGGAAAACAAACATAGAGTACAGGAAG 59.338 37.037 0.00 0.00 0.00 3.46
6 7 7.514721 AGGAAAACAAACATAGAGTACAGGAA 58.485 34.615 0.00 0.00 0.00 3.36
7 8 7.074653 AGGAAAACAAACATAGAGTACAGGA 57.925 36.000 0.00 0.00 0.00 3.86
8 9 7.745620 AAGGAAAACAAACATAGAGTACAGG 57.254 36.000 0.00 0.00 0.00 4.00
9 10 8.836413 TGAAAGGAAAACAAACATAGAGTACAG 58.164 33.333 0.00 0.00 0.00 2.74
10 11 8.740123 TGAAAGGAAAACAAACATAGAGTACA 57.260 30.769 0.00 0.00 0.00 2.90
11 12 9.827411 GATGAAAGGAAAACAAACATAGAGTAC 57.173 33.333 0.00 0.00 0.00 2.73
12 13 9.567776 TGATGAAAGGAAAACAAACATAGAGTA 57.432 29.630 0.00 0.00 0.00 2.59
13 14 8.463930 TGATGAAAGGAAAACAAACATAGAGT 57.536 30.769 0.00 0.00 0.00 3.24
14 15 9.350357 CATGATGAAAGGAAAACAAACATAGAG 57.650 33.333 0.00 0.00 0.00 2.43
15 16 9.076781 TCATGATGAAAGGAAAACAAACATAGA 57.923 29.630 0.00 0.00 0.00 1.98
16 17 9.865321 ATCATGATGAAAGGAAAACAAACATAG 57.135 29.630 7.59 0.00 0.00 2.23
17 18 9.642327 CATCATGATGAAAGGAAAACAAACATA 57.358 29.630 28.37 0.00 41.20 2.29
18 19 8.152246 ACATCATGATGAAAGGAAAACAAACAT 58.848 29.630 36.37 9.76 41.20 2.71
19 20 7.499292 ACATCATGATGAAAGGAAAACAAACA 58.501 30.769 36.37 0.00 41.20 2.83
20 21 7.869429 AGACATCATGATGAAAGGAAAACAAAC 59.131 33.333 36.37 12.33 41.20 2.93
21 22 7.954835 AGACATCATGATGAAAGGAAAACAAA 58.045 30.769 36.37 0.00 41.20 2.83
22 23 7.528996 AGACATCATGATGAAAGGAAAACAA 57.471 32.000 36.37 0.00 41.20 2.83
23 24 8.680001 CATAGACATCATGATGAAAGGAAAACA 58.320 33.333 36.37 12.80 41.20 2.83
24 25 7.646922 GCATAGACATCATGATGAAAGGAAAAC 59.353 37.037 36.37 15.94 41.20 2.43
25 26 7.558807 AGCATAGACATCATGATGAAAGGAAAA 59.441 33.333 36.37 15.62 41.20 2.29
26 27 7.058525 AGCATAGACATCATGATGAAAGGAAA 58.941 34.615 36.37 16.94 41.20 3.13
27 28 6.598503 AGCATAGACATCATGATGAAAGGAA 58.401 36.000 36.37 17.83 41.20 3.36
28 29 6.183810 AGCATAGACATCATGATGAAAGGA 57.816 37.500 36.37 18.92 41.20 3.36
29 30 6.262496 ACAAGCATAGACATCATGATGAAAGG 59.738 38.462 36.37 23.33 41.20 3.11
30 31 7.132863 CACAAGCATAGACATCATGATGAAAG 58.867 38.462 36.37 22.14 41.20 2.62
31 32 6.600427 ACACAAGCATAGACATCATGATGAAA 59.400 34.615 36.37 22.38 41.20 2.69
32 33 6.117488 ACACAAGCATAGACATCATGATGAA 58.883 36.000 36.37 22.69 41.20 2.57
33 34 5.677567 ACACAAGCATAGACATCATGATGA 58.322 37.500 36.37 18.65 41.20 2.92
34 35 6.373186 AACACAAGCATAGACATCATGATG 57.627 37.500 29.95 29.95 44.15 3.07
35 36 6.709397 CCTAACACAAGCATAGACATCATGAT 59.291 38.462 1.18 1.18 0.00 2.45
36 37 6.051074 CCTAACACAAGCATAGACATCATGA 58.949 40.000 0.00 0.00 0.00 3.07
37 38 5.819379 ACCTAACACAAGCATAGACATCATG 59.181 40.000 0.00 0.00 0.00 3.07
38 39 5.994250 ACCTAACACAAGCATAGACATCAT 58.006 37.500 0.00 0.00 0.00 2.45
39 40 5.420725 ACCTAACACAAGCATAGACATCA 57.579 39.130 0.00 0.00 0.00 3.07
40 41 7.710907 TCATAACCTAACACAAGCATAGACATC 59.289 37.037 0.00 0.00 0.00 3.06
41 42 7.495934 GTCATAACCTAACACAAGCATAGACAT 59.504 37.037 0.00 0.00 0.00 3.06
42 43 6.816640 GTCATAACCTAACACAAGCATAGACA 59.183 38.462 0.00 0.00 0.00 3.41
43 44 7.010552 CAGTCATAACCTAACACAAGCATAGAC 59.989 40.741 0.00 0.00 0.00 2.59
44 45 7.041721 CAGTCATAACCTAACACAAGCATAGA 58.958 38.462 0.00 0.00 0.00 1.98
45 46 6.238211 GCAGTCATAACCTAACACAAGCATAG 60.238 42.308 0.00 0.00 0.00 2.23
46 47 5.584649 GCAGTCATAACCTAACACAAGCATA 59.415 40.000 0.00 0.00 0.00 3.14
47 48 4.396166 GCAGTCATAACCTAACACAAGCAT 59.604 41.667 0.00 0.00 0.00 3.79
48 49 3.751175 GCAGTCATAACCTAACACAAGCA 59.249 43.478 0.00 0.00 0.00 3.91
49 50 3.751175 TGCAGTCATAACCTAACACAAGC 59.249 43.478 0.00 0.00 0.00 4.01
50 51 5.877012 AGATGCAGTCATAACCTAACACAAG 59.123 40.000 0.00 0.00 31.96 3.16
51 52 5.643348 CAGATGCAGTCATAACCTAACACAA 59.357 40.000 0.00 0.00 31.96 3.33
52 53 5.046663 TCAGATGCAGTCATAACCTAACACA 60.047 40.000 0.00 0.00 31.96 3.72
53 54 5.419542 TCAGATGCAGTCATAACCTAACAC 58.580 41.667 0.00 0.00 31.96 3.32
54 55 5.187772 ACTCAGATGCAGTCATAACCTAACA 59.812 40.000 0.00 0.00 31.96 2.41
55 56 5.665459 ACTCAGATGCAGTCATAACCTAAC 58.335 41.667 0.00 0.00 31.96 2.34
56 57 5.939764 ACTCAGATGCAGTCATAACCTAA 57.060 39.130 0.00 0.00 31.96 2.69
57 58 6.129874 AGTACTCAGATGCAGTCATAACCTA 58.870 40.000 0.00 0.00 31.96 3.08
58 59 4.959210 AGTACTCAGATGCAGTCATAACCT 59.041 41.667 0.00 0.00 31.96 3.50
59 60 5.269505 AGTACTCAGATGCAGTCATAACC 57.730 43.478 0.00 0.00 31.96 2.85
60 61 8.879342 AATAAGTACTCAGATGCAGTCATAAC 57.121 34.615 0.00 0.00 31.96 1.89
61 62 8.144478 GGAATAAGTACTCAGATGCAGTCATAA 58.856 37.037 0.00 0.00 31.96 1.90
62 63 7.522236 CGGAATAAGTACTCAGATGCAGTCATA 60.522 40.741 0.00 0.00 31.96 2.15
63 64 6.520272 GGAATAAGTACTCAGATGCAGTCAT 58.480 40.000 0.00 0.00 35.17 3.06
64 65 5.450550 CGGAATAAGTACTCAGATGCAGTCA 60.451 44.000 0.00 0.00 0.00 3.41
65 66 4.979197 CGGAATAAGTACTCAGATGCAGTC 59.021 45.833 0.00 0.00 0.00 3.51
66 67 4.737946 GCGGAATAAGTACTCAGATGCAGT 60.738 45.833 0.00 0.00 0.00 4.40
67 68 3.738282 GCGGAATAAGTACTCAGATGCAG 59.262 47.826 0.00 0.00 0.00 4.41
68 69 3.384789 AGCGGAATAAGTACTCAGATGCA 59.615 43.478 0.00 0.00 0.00 3.96
69 70 3.738282 CAGCGGAATAAGTACTCAGATGC 59.262 47.826 0.00 0.00 0.00 3.91
70 71 3.738282 GCAGCGGAATAAGTACTCAGATG 59.262 47.826 0.00 0.00 0.00 2.90
71 72 3.384789 TGCAGCGGAATAAGTACTCAGAT 59.615 43.478 0.00 0.00 0.00 2.90
72 73 2.758423 TGCAGCGGAATAAGTACTCAGA 59.242 45.455 0.00 0.00 0.00 3.27
73 74 3.165058 TGCAGCGGAATAAGTACTCAG 57.835 47.619 0.00 0.00 0.00 3.35
74 75 3.056107 ACTTGCAGCGGAATAAGTACTCA 60.056 43.478 0.00 0.00 32.05 3.41
75 76 3.522553 ACTTGCAGCGGAATAAGTACTC 58.477 45.455 0.00 0.00 32.05 2.59
76 77 3.611766 ACTTGCAGCGGAATAAGTACT 57.388 42.857 0.00 0.00 32.05 2.73
77 78 4.430908 ACTACTTGCAGCGGAATAAGTAC 58.569 43.478 0.00 0.00 35.26 2.73
78 79 4.730949 ACTACTTGCAGCGGAATAAGTA 57.269 40.909 3.08 3.08 35.26 2.24
79 80 3.611766 ACTACTTGCAGCGGAATAAGT 57.388 42.857 1.12 1.12 37.21 2.24
80 81 4.184629 AGAACTACTTGCAGCGGAATAAG 58.815 43.478 0.00 0.00 0.00 1.73
81 82 4.202245 AGAACTACTTGCAGCGGAATAA 57.798 40.909 0.00 0.00 0.00 1.40
82 83 3.887621 AGAACTACTTGCAGCGGAATA 57.112 42.857 0.00 0.00 0.00 1.75
83 84 2.770164 AGAACTACTTGCAGCGGAAT 57.230 45.000 0.00 0.00 0.00 3.01
84 85 2.413837 GAAGAACTACTTGCAGCGGAA 58.586 47.619 0.00 0.00 39.13 4.30
85 86 1.668919 CGAAGAACTACTTGCAGCGGA 60.669 52.381 0.00 0.00 39.13 5.54
86 87 0.716108 CGAAGAACTACTTGCAGCGG 59.284 55.000 0.00 0.00 39.13 5.52
87 88 0.093705 GCGAAGAACTACTTGCAGCG 59.906 55.000 0.00 0.00 39.13 5.18
88 89 1.433534 AGCGAAGAACTACTTGCAGC 58.566 50.000 0.00 0.00 39.13 5.25
89 90 3.614616 CCTAAGCGAAGAACTACTTGCAG 59.385 47.826 0.00 0.00 39.13 4.41
90 91 3.257375 TCCTAAGCGAAGAACTACTTGCA 59.743 43.478 0.00 0.00 39.13 4.08
91 92 3.846360 TCCTAAGCGAAGAACTACTTGC 58.154 45.455 0.00 0.00 39.13 4.01
92 93 6.969828 AATTCCTAAGCGAAGAACTACTTG 57.030 37.500 0.00 0.00 39.13 3.16
93 94 6.594547 GGAAATTCCTAAGCGAAGAACTACTT 59.405 38.462 4.46 0.00 36.06 2.24
94 95 6.107343 GGAAATTCCTAAGCGAAGAACTACT 58.893 40.000 4.46 0.00 32.53 2.57
95 96 6.347270 GGAAATTCCTAAGCGAAGAACTAC 57.653 41.667 4.46 0.00 32.53 2.73
113 114 4.604156 GAGGAATTTCAGGGTGAGGAAAT 58.396 43.478 0.00 0.00 43.54 2.17
114 115 3.559171 CGAGGAATTTCAGGGTGAGGAAA 60.559 47.826 0.00 0.00 37.41 3.13
115 116 2.027192 CGAGGAATTTCAGGGTGAGGAA 60.027 50.000 0.00 0.00 0.00 3.36
116 117 1.555075 CGAGGAATTTCAGGGTGAGGA 59.445 52.381 0.00 0.00 0.00 3.71
117 118 1.407437 CCGAGGAATTTCAGGGTGAGG 60.407 57.143 0.00 0.00 0.00 3.86
118 119 1.279271 ACCGAGGAATTTCAGGGTGAG 59.721 52.381 0.00 0.00 0.00 3.51
119 120 1.003118 CACCGAGGAATTTCAGGGTGA 59.997 52.381 17.21 0.00 45.96 4.02
120 121 1.003118 TCACCGAGGAATTTCAGGGTG 59.997 52.381 16.38 16.38 44.78 4.61
121 122 1.358152 TCACCGAGGAATTTCAGGGT 58.642 50.000 0.00 0.00 0.00 4.34
122 123 2.027192 TCTTCACCGAGGAATTTCAGGG 60.027 50.000 0.00 0.00 0.00 4.45
123 124 3.334583 TCTTCACCGAGGAATTTCAGG 57.665 47.619 0.00 1.51 0.00 3.86
124 125 5.412594 TGAATTCTTCACCGAGGAATTTCAG 59.587 40.000 13.29 0.00 44.41 3.02
125 126 5.312895 TGAATTCTTCACCGAGGAATTTCA 58.687 37.500 13.29 10.47 44.41 2.69
126 127 5.880054 TGAATTCTTCACCGAGGAATTTC 57.120 39.130 13.29 8.69 44.41 2.17
127 128 7.938140 TTATGAATTCTTCACCGAGGAATTT 57.062 32.000 13.29 4.15 44.41 1.82
128 129 7.938140 TTTATGAATTCTTCACCGAGGAATT 57.062 32.000 12.28 12.28 46.10 2.17
129 130 7.938140 TTTTATGAATTCTTCACCGAGGAAT 57.062 32.000 7.05 0.00 43.48 3.01
130 131 7.753309 TTTTTATGAATTCTTCACCGAGGAA 57.247 32.000 7.05 0.00 43.48 3.36
131 132 7.938140 ATTTTTATGAATTCTTCACCGAGGA 57.062 32.000 7.05 0.00 43.48 3.71
132 133 7.009540 GCAATTTTTATGAATTCTTCACCGAGG 59.990 37.037 7.05 0.00 43.48 4.63
133 134 7.009540 GGCAATTTTTATGAATTCTTCACCGAG 59.990 37.037 7.05 0.00 43.48 4.63
134 135 6.811170 GGCAATTTTTATGAATTCTTCACCGA 59.189 34.615 7.05 0.00 43.48 4.69
135 136 6.813152 AGGCAATTTTTATGAATTCTTCACCG 59.187 34.615 7.05 0.00 43.48 4.94
136 137 9.822185 ATAGGCAATTTTTATGAATTCTTCACC 57.178 29.630 7.05 0.00 43.48 4.02
141 142 9.822185 GGTGAATAGGCAATTTTTATGAATTCT 57.178 29.630 7.05 0.00 0.00 2.40
142 143 9.045223 GGGTGAATAGGCAATTTTTATGAATTC 57.955 33.333 0.00 0.00 0.00 2.17
143 144 7.992608 GGGGTGAATAGGCAATTTTTATGAATT 59.007 33.333 0.00 0.00 0.00 2.17
144 145 7.420097 GGGGGTGAATAGGCAATTTTTATGAAT 60.420 37.037 0.00 0.00 0.00 2.57
145 146 6.126911 GGGGGTGAATAGGCAATTTTTATGAA 60.127 38.462 0.00 0.00 0.00 2.57
146 147 5.365314 GGGGGTGAATAGGCAATTTTTATGA 59.635 40.000 0.00 0.00 0.00 2.15
147 148 5.610398 GGGGGTGAATAGGCAATTTTTATG 58.390 41.667 0.00 0.00 0.00 1.90
148 149 5.887214 GGGGGTGAATAGGCAATTTTTAT 57.113 39.130 0.00 0.00 0.00 1.40
167 168 1.674962 CGTTAAGTCGACTAGAGGGGG 59.325 57.143 20.39 1.07 0.00 5.40
168 169 1.065251 GCGTTAAGTCGACTAGAGGGG 59.935 57.143 20.39 7.63 0.00 4.79
169 170 1.741706 TGCGTTAAGTCGACTAGAGGG 59.258 52.381 20.39 8.71 0.00 4.30
170 171 2.419324 AGTGCGTTAAGTCGACTAGAGG 59.581 50.000 20.39 16.03 0.00 3.69
171 172 3.743567 AGTGCGTTAAGTCGACTAGAG 57.256 47.619 20.39 11.75 0.00 2.43
172 173 4.023792 TGAAAGTGCGTTAAGTCGACTAGA 60.024 41.667 20.39 7.29 0.00 2.43
173 174 4.088213 GTGAAAGTGCGTTAAGTCGACTAG 59.912 45.833 20.39 11.75 0.00 2.57
174 175 3.976942 GTGAAAGTGCGTTAAGTCGACTA 59.023 43.478 20.39 0.04 0.00 2.59
175 176 2.793232 GTGAAAGTGCGTTAAGTCGACT 59.207 45.455 13.58 13.58 0.00 4.18
176 177 2.793232 AGTGAAAGTGCGTTAAGTCGAC 59.207 45.455 7.70 7.70 0.00 4.20
177 178 3.047796 GAGTGAAAGTGCGTTAAGTCGA 58.952 45.455 0.00 0.00 0.00 4.20
178 179 3.050619 AGAGTGAAAGTGCGTTAAGTCG 58.949 45.455 0.00 0.00 0.00 4.18
179 180 4.049186 TGAGAGTGAAAGTGCGTTAAGTC 58.951 43.478 0.00 0.00 0.00 3.01
180 181 3.802685 GTGAGAGTGAAAGTGCGTTAAGT 59.197 43.478 0.00 0.00 0.00 2.24
181 182 4.051922 AGTGAGAGTGAAAGTGCGTTAAG 58.948 43.478 0.00 0.00 0.00 1.85
182 183 4.049186 GAGTGAGAGTGAAAGTGCGTTAA 58.951 43.478 0.00 0.00 0.00 2.01
183 184 3.318275 AGAGTGAGAGTGAAAGTGCGTTA 59.682 43.478 0.00 0.00 0.00 3.18
184 185 2.101582 AGAGTGAGAGTGAAAGTGCGTT 59.898 45.455 0.00 0.00 0.00 4.84
185 186 1.683917 AGAGTGAGAGTGAAAGTGCGT 59.316 47.619 0.00 0.00 0.00 5.24
186 187 2.030363 AGAGAGTGAGAGTGAAAGTGCG 60.030 50.000 0.00 0.00 0.00 5.34
187 188 3.255642 AGAGAGAGTGAGAGTGAAAGTGC 59.744 47.826 0.00 0.00 0.00 4.40
192 193 4.323485 GGAGAGAGAGAGAGTGAGAGTGAA 60.323 50.000 0.00 0.00 0.00 3.18
201 202 4.473196 TGATACAGTGGAGAGAGAGAGAGT 59.527 45.833 0.00 0.00 0.00 3.24
299 303 1.964223 GTGTGTGAGAGAGAGGGACAA 59.036 52.381 0.00 0.00 0.00 3.18
312 592 0.828022 AGAGAACGGGTTGTGTGTGA 59.172 50.000 0.00 0.00 0.00 3.58
345 625 4.782019 ATCAAGAGTGTGAGAGTGAGAC 57.218 45.455 0.00 0.00 0.00 3.36
373 657 1.339824 GGAGGAGAGTGGTCGTGTCTA 60.340 57.143 0.00 0.00 0.00 2.59
381 665 2.360980 CGAGGGGAGGAGAGTGGT 59.639 66.667 0.00 0.00 0.00 4.16
401 685 6.901300 AGGGGTTTGTGTATCTAAGAGACATA 59.099 38.462 0.00 0.00 36.19 2.29
508 806 2.363683 GGCTTGATTTGGGAGAGACAG 58.636 52.381 0.00 0.00 0.00 3.51
577 875 9.713713 GGAAATAGAAAGTGACTTAAAGAGAGT 57.286 33.333 0.00 0.00 0.00 3.24
600 898 5.045651 TGTCTTTGAAGAGAGGCATATGGAA 60.046 40.000 4.56 0.00 35.32 3.53
697 1007 1.374758 TGCGTGTGTGTGTGTGTGA 60.375 52.632 0.00 0.00 0.00 3.58
698 1008 1.225991 GTGCGTGTGTGTGTGTGTG 60.226 57.895 0.00 0.00 0.00 3.82
699 1009 1.669437 TGTGCGTGTGTGTGTGTGT 60.669 52.632 0.00 0.00 0.00 3.72
700 1010 1.225991 GTGTGCGTGTGTGTGTGTG 60.226 57.895 0.00 0.00 0.00 3.82
733 1043 2.587777 AGTGAGATAGAGAGGGGTCCAA 59.412 50.000 0.00 0.00 0.00 3.53
747 1057 6.126911 GGGGATGTCTTAAAAGAGAGTGAGAT 60.127 42.308 0.00 0.00 35.32 2.75
769 1079 2.089201 GACGGACAAAACTATTGGGGG 58.911 52.381 0.00 0.00 0.00 5.40
774 1084 5.245526 AGACCTGTAGACGGACAAAACTATT 59.754 40.000 0.00 0.00 0.00 1.73
775 1085 4.771054 AGACCTGTAGACGGACAAAACTAT 59.229 41.667 0.00 0.00 0.00 2.12
781 1091 2.040012 AGAGAGACCTGTAGACGGACAA 59.960 50.000 0.00 0.00 0.00 3.18
792 1102 2.789213 TGTGAGTGAGAGAGAGACCTG 58.211 52.381 0.00 0.00 0.00 4.00
819 1129 7.382759 GTGTCTTACAGAGAGACGAGAAATTTT 59.617 37.037 0.00 0.00 45.05 1.82
871 1183 2.036475 AGTCAGAAAGTGAGTGTGCGAT 59.964 45.455 0.00 0.00 37.45 4.58
874 1186 3.243907 ACCTAGTCAGAAAGTGAGTGTGC 60.244 47.826 0.00 0.00 39.36 4.57
938 1250 3.181450 TGTGTGTGTGAGAGAGAGAGAGA 60.181 47.826 0.00 0.00 0.00 3.10
940 1252 2.881513 GTGTGTGTGTGAGAGAGAGAGA 59.118 50.000 0.00 0.00 0.00 3.10
947 1259 3.525537 AGAGTTTGTGTGTGTGTGAGAG 58.474 45.455 0.00 0.00 0.00 3.20
948 1260 3.610040 AGAGTTTGTGTGTGTGTGAGA 57.390 42.857 0.00 0.00 0.00 3.27
949 1261 4.685169 AAAGAGTTTGTGTGTGTGTGAG 57.315 40.909 0.00 0.00 0.00 3.51
950 1262 6.751514 ATAAAAGAGTTTGTGTGTGTGTGA 57.248 33.333 0.00 0.00 0.00 3.58
961 1307 8.787852 AGAGACTAAGGCAAATAAAAGAGTTTG 58.212 33.333 0.00 0.00 38.13 2.93
963 1309 8.379331 AGAGAGACTAAGGCAAATAAAAGAGTT 58.621 33.333 0.00 0.00 0.00 3.01
999 1347 9.730420 GATCATGCGTGTGTGTGTATATATATA 57.270 33.333 5.68 0.00 0.00 0.86
1004 1352 4.948847 AGATCATGCGTGTGTGTGTATAT 58.051 39.130 5.68 0.00 0.00 0.86
1007 1355 2.741759 AGATCATGCGTGTGTGTGTA 57.258 45.000 5.68 0.00 0.00 2.90
1008 1356 1.882912 AAGATCATGCGTGTGTGTGT 58.117 45.000 5.68 0.00 0.00 3.72
1182 1740 0.322816 GGGTGATGATGGCAGTGTGT 60.323 55.000 0.00 0.00 0.00 3.72
1241 1799 3.372206 CCTTAGCACGATGACCTTTTGAG 59.628 47.826 0.00 0.00 0.00 3.02
1344 2605 1.078426 GCACGTGGCTGGGTTATCT 60.078 57.895 18.88 0.00 40.25 1.98
1370 2631 6.346919 CGCATACAAAAATATTCGAGAGGGAG 60.347 42.308 0.00 0.00 0.00 4.30
1425 2686 4.251268 GTGGTAGACCTTGTCAATGTACC 58.749 47.826 5.83 5.83 34.60 3.34
1432 2693 1.707106 TTCCGTGGTAGACCTTGTCA 58.293 50.000 0.00 0.00 34.60 3.58
1447 2708 0.460311 AGACGAAGGGTGCTATTCCG 59.540 55.000 0.00 0.00 0.00 4.30
1455 2716 1.003718 GTGGGGAAGACGAAGGGTG 60.004 63.158 0.00 0.00 0.00 4.61
1461 2722 2.522367 GGGTTGGTGGGGAAGACGA 61.522 63.158 0.00 0.00 0.00 4.20
1468 2729 3.396822 TTGGTTGGGGTTGGTGGGG 62.397 63.158 0.00 0.00 0.00 4.96
1556 2817 9.848710 AGTAGTGAGATTGCTACAGTTATACTA 57.151 33.333 0.00 0.00 39.82 1.82
1768 3029 4.035558 TCCTCGAATGTTATTTGCAGATGC 59.964 41.667 0.00 0.00 42.50 3.91
1773 3034 2.682856 GGCTCCTCGAATGTTATTTGCA 59.317 45.455 0.00 0.00 0.00 4.08
1866 3136 2.805671 TCTGCAAGGTCACAAACATACG 59.194 45.455 0.00 0.00 0.00 3.06
1867 3137 5.643777 ACTATCTGCAAGGTCACAAACATAC 59.356 40.000 0.00 0.00 0.00 2.39
1868 3138 5.804639 ACTATCTGCAAGGTCACAAACATA 58.195 37.500 0.00 0.00 0.00 2.29
1869 3139 4.655963 ACTATCTGCAAGGTCACAAACAT 58.344 39.130 0.00 0.00 0.00 2.71
1870 3140 4.085357 ACTATCTGCAAGGTCACAAACA 57.915 40.909 0.00 0.00 0.00 2.83
1871 3141 4.787598 CAACTATCTGCAAGGTCACAAAC 58.212 43.478 0.00 0.00 0.00 2.93
1872 3142 3.253188 GCAACTATCTGCAAGGTCACAAA 59.747 43.478 0.00 0.00 42.17 2.83
1873 3143 2.813754 GCAACTATCTGCAAGGTCACAA 59.186 45.455 0.00 0.00 42.17 3.33
1887 3157 0.398696 TTCCACCGTGGTGCAACTAT 59.601 50.000 17.32 0.00 44.16 2.12
1899 3169 2.092646 TCCTCCCAAACATATTCCACCG 60.093 50.000 0.00 0.00 0.00 4.94
1907 3177 3.907474 TGTCTGTCTTCCTCCCAAACATA 59.093 43.478 0.00 0.00 0.00 2.29
1953 3223 4.940046 TGTCTCCTCTGATGCAAAAATCTC 59.060 41.667 0.00 0.00 0.00 2.75
1957 3227 3.819368 TGTGTCTCCTCTGATGCAAAAA 58.181 40.909 0.00 0.00 0.00 1.94
1961 3231 1.693606 TGTTGTGTCTCCTCTGATGCA 59.306 47.619 0.00 0.00 0.00 3.96
2072 3344 1.376166 CCCGGTTGGTTGCATCGTA 60.376 57.895 0.00 0.00 0.00 3.43
2074 3346 3.439540 CCCCGGTTGGTTGCATCG 61.440 66.667 0.00 0.00 0.00 3.84
2141 3414 5.349817 GCTAAAGTGATCCATCATCCATACG 59.650 44.000 0.00 0.00 39.30 3.06
2156 3429 1.749634 GGGTCTAGCTCGCTAAAGTGA 59.250 52.381 0.00 0.00 0.00 3.41
2240 3517 8.682936 TCATTCCATCTTAATTTAGAGCCTTC 57.317 34.615 0.22 0.00 0.00 3.46
2422 3699 6.264518 GGGAGGAAGTGAAGAATGTAAAAACA 59.735 38.462 0.00 0.00 0.00 2.83
2469 3746 2.022195 CCAGAATCCTAACTCGTCGGA 58.978 52.381 0.00 0.00 0.00 4.55
2568 3845 7.031226 AGCTTAATGCAATAGTTGTACCATG 57.969 36.000 0.00 0.00 45.94 3.66
2723 4000 2.102588 CCATAGTACCCGGAGAAACAGG 59.897 54.545 0.73 0.00 0.00 4.00
2727 4004 3.962718 CCTTACCATAGTACCCGGAGAAA 59.037 47.826 0.73 0.00 0.00 2.52
3080 4368 8.495949 CAAACTACAACATAGTCGATTGAAGTT 58.504 33.333 2.84 0.00 0.00 2.66
3085 4373 6.590292 ACCTCAAACTACAACATAGTCGATTG 59.410 38.462 0.00 0.00 0.00 2.67
3160 4448 5.163893 CGACTTAATTGAAGGTGTTATGCGT 60.164 40.000 0.00 0.00 39.74 5.24


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

AutoCloner maintained by Alex Coulton.