Multiple sequence alignment - TraesCS5A01G352600

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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 TraesCS5A01G352600 chr5A 100.000 3757 0 0 1 3757 554988702 554984946 0.000000e+00 6938.0
1 TraesCS5A01G352600 chr5A 94.390 1925 77 3 579 2476 427853894 427851974 0.000000e+00 2928.0
2 TraesCS5A01G352600 chr5A 98.565 209 3 0 1 209 555013174 555012966 1.650000e-98 370.0
3 TraesCS5A01G352600 chr5A 92.544 228 16 1 2472 2699 548390963 548391189 3.620000e-85 326.0
4 TraesCS5A01G352600 chr2A 93.305 2345 122 8 171 2485 89491944 89489605 0.000000e+00 3428.0
5 TraesCS5A01G352600 chr2A 84.507 142 16 5 3352 3491 4687150 4687287 6.550000e-28 135.0
6 TraesCS5A01G352600 chr2A 83.803 142 17 5 3352 3491 4688133 4688270 3.050000e-26 130.0
7 TraesCS5A01G352600 chr2A 83.099 142 18 5 3352 3491 4689115 4689252 1.420000e-24 124.0
8 TraesCS5A01G352600 chr2A 82.394 142 18 6 3352 3491 4690098 4690234 2.370000e-22 117.0
9 TraesCS5A01G352600 chr2A 82.394 142 18 6 3352 3491 4691082 4691218 2.370000e-22 117.0
10 TraesCS5A01G352600 chr2A 82.394 142 18 6 3352 3491 4692066 4692202 2.370000e-22 117.0
11 TraesCS5A01G352600 chr2D 91.304 2346 155 19 171 2485 89877004 89874677 0.000000e+00 3157.0
12 TraesCS5A01G352600 chr2D 95.636 1375 59 1 579 1953 142216325 142217698 0.000000e+00 2206.0
13 TraesCS5A01G352600 chr2D 96.008 526 21 0 1951 2476 142217723 142218248 0.000000e+00 856.0
14 TraesCS5A01G352600 chr2B 92.294 2193 130 10 326 2485 142378045 142375859 0.000000e+00 3077.0
15 TraesCS5A01G352600 chr2B 83.007 306 34 12 3243 3535 56221613 56221313 1.040000e-65 261.0
16 TraesCS5A01G352600 chr2B 93.966 116 7 0 10 125 747725441 747725326 3.860000e-40 176.0
17 TraesCS5A01G352600 chr2B 95.455 44 2 0 287 330 142378109 142378066 1.870000e-08 71.3
18 TraesCS5A01G352600 chrUn 94.597 1925 77 4 579 2476 19136650 19138574 0.000000e+00 2953.0
19 TraesCS5A01G352600 chr7D 94.545 1925 77 5 579 2476 83434788 83436711 0.000000e+00 2948.0
20 TraesCS5A01G352600 chr7D 94.390 1925 78 6 579 2476 292322914 292324835 0.000000e+00 2929.0
21 TraesCS5A01G352600 chr7D 82.951 305 36 7 3243 3535 207220622 207220322 1.040000e-65 261.0
22 TraesCS5A01G352600 chr6A 94.338 1925 80 2 579 2476 517540134 517538212 0.000000e+00 2924.0
23 TraesCS5A01G352600 chr4D 94.237 1926 77 6 579 2476 215025472 215023553 0.000000e+00 2911.0
24 TraesCS5A01G352600 chr4D 90.244 533 49 3 2599 3130 505472964 505473494 0.000000e+00 693.0
25 TraesCS5A01G352600 chr4A 93.666 1926 82 6 579 2476 679659559 679657646 0.000000e+00 2844.0
26 TraesCS5A01G352600 chr4A 93.492 630 39 2 2501 3130 708847486 708846859 0.000000e+00 935.0
27 TraesCS5A01G352600 chr4A 93.333 225 14 1 2475 2699 708848614 708848391 7.780000e-87 331.0
28 TraesCS5A01G352600 chr5D 96.358 659 23 1 2475 3133 327294350 327293693 0.000000e+00 1083.0
29 TraesCS5A01G352600 chr5D 90.449 534 47 4 2598 3130 449312087 449312617 0.000000e+00 701.0
30 TraesCS5A01G352600 chr5D 93.778 225 14 0 2475 2699 327295474 327295250 4.650000e-89 339.0
31 TraesCS5A01G352600 chr5D 84.302 344 49 4 3243 3585 327266168 327265829 7.780000e-87 331.0
32 TraesCS5A01G352600 chr5D 94.595 111 6 0 15 125 231599444 231599334 4.990000e-39 172.0
33 TraesCS5A01G352600 chr5D 85.207 169 15 9 3181 3344 327266353 327266190 8.350000e-37 165.0
34 TraesCS5A01G352600 chr7A 94.697 660 29 4 2475 3133 299564958 299564304 0.000000e+00 1020.0
35 TraesCS5A01G352600 chr7A 80.100 201 34 5 3352 3550 8425935 8425739 1.090000e-30 145.0
36 TraesCS5A01G352600 chr7A 98.000 50 1 0 3413 3462 8426548 8426499 1.860000e-13 87.9
37 TraesCS5A01G352600 chr7A 88.406 69 5 3 3413 3480 299541704 299541638 3.110000e-11 80.5
38 TraesCS5A01G352600 chr1D 90.449 534 47 4 2598 3130 288333794 288334324 0.000000e+00 701.0
39 TraesCS5A01G352600 chr1D 90.130 537 49 4 2598 3133 46660976 46660443 0.000000e+00 695.0
40 TraesCS5A01G352600 chr1D 84.018 219 20 2 2475 2679 40859024 40859241 2.960000e-46 196.0
41 TraesCS5A01G352600 chr6D 90.262 534 48 4 2598 3130 56356396 56356926 0.000000e+00 695.0
42 TraesCS5A01G352600 chr3D 90.130 537 49 4 2598 3133 567181585 567181052 0.000000e+00 695.0
43 TraesCS5A01G352600 chr3D 96.407 167 6 0 5 171 48643096 48643262 3.700000e-70 276.0
44 TraesCS5A01G352600 chr3A 85.256 312 32 5 3243 3543 717804390 717804698 3.640000e-80 309.0
45 TraesCS5A01G352600 chr3A 88.235 153 15 3 3243 3394 717804042 717804192 2.980000e-41 180.0
46 TraesCS5A01G352600 chr3A 91.736 121 10 0 3595 3715 717804821 717804941 6.450000e-38 169.0
47 TraesCS5A01G352600 chr4B 92.241 116 9 0 10 125 488121708 488121593 8.350000e-37 165.0
48 TraesCS5A01G352600 chr4B 91.089 101 7 2 3243 3342 488080815 488080716 6.550000e-28 135.0
49 TraesCS5A01G352600 chr4B 93.750 48 2 1 3421 3467 77053785 77053738 1.870000e-08 71.3
50 TraesCS5A01G352600 chr1A 83.784 148 18 5 3352 3497 568498324 568498181 6.550000e-28 135.0
51 TraesCS5A01G352600 chr6B 81.513 119 15 6 3353 3467 646047235 646047350 1.440000e-14 91.6
52 TraesCS5A01G352600 chr6B 80.952 105 13 6 3367 3467 646048506 646048607 4.020000e-10 76.8


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 TraesCS5A01G352600 chr5A 554984946 554988702 3756 True 6938.000000 6938 100.0000 1 3757 1 chr5A.!!$R2 3756
1 TraesCS5A01G352600 chr5A 427851974 427853894 1920 True 2928.000000 2928 94.3900 579 2476 1 chr5A.!!$R1 1897
2 TraesCS5A01G352600 chr2A 89489605 89491944 2339 True 3428.000000 3428 93.3050 171 2485 1 chr2A.!!$R1 2314
3 TraesCS5A01G352600 chr2D 89874677 89877004 2327 True 3157.000000 3157 91.3040 171 2485 1 chr2D.!!$R1 2314
4 TraesCS5A01G352600 chr2D 142216325 142218248 1923 False 1531.000000 2206 95.8220 579 2476 2 chr2D.!!$F1 1897
5 TraesCS5A01G352600 chr2B 142375859 142378109 2250 True 1574.150000 3077 93.8745 287 2485 2 chr2B.!!$R3 2198
6 TraesCS5A01G352600 chrUn 19136650 19138574 1924 False 2953.000000 2953 94.5970 579 2476 1 chrUn.!!$F1 1897
7 TraesCS5A01G352600 chr7D 83434788 83436711 1923 False 2948.000000 2948 94.5450 579 2476 1 chr7D.!!$F1 1897
8 TraesCS5A01G352600 chr7D 292322914 292324835 1921 False 2929.000000 2929 94.3900 579 2476 1 chr7D.!!$F2 1897
9 TraesCS5A01G352600 chr6A 517538212 517540134 1922 True 2924.000000 2924 94.3380 579 2476 1 chr6A.!!$R1 1897
10 TraesCS5A01G352600 chr4D 215023553 215025472 1919 True 2911.000000 2911 94.2370 579 2476 1 chr4D.!!$R1 1897
11 TraesCS5A01G352600 chr4D 505472964 505473494 530 False 693.000000 693 90.2440 2599 3130 1 chr4D.!!$F1 531
12 TraesCS5A01G352600 chr4A 679657646 679659559 1913 True 2844.000000 2844 93.6660 579 2476 1 chr4A.!!$R1 1897
13 TraesCS5A01G352600 chr4A 708846859 708848614 1755 True 633.000000 935 93.4125 2475 3130 2 chr4A.!!$R2 655
14 TraesCS5A01G352600 chr5D 327293693 327295474 1781 True 711.000000 1083 95.0680 2475 3133 2 chr5D.!!$R3 658
15 TraesCS5A01G352600 chr5D 449312087 449312617 530 False 701.000000 701 90.4490 2598 3130 1 chr5D.!!$F1 532
16 TraesCS5A01G352600 chr5D 327265829 327266353 524 True 248.000000 331 84.7545 3181 3585 2 chr5D.!!$R2 404
17 TraesCS5A01G352600 chr7A 299564304 299564958 654 True 1020.000000 1020 94.6970 2475 3133 1 chr7A.!!$R2 658
18 TraesCS5A01G352600 chr1D 288333794 288334324 530 False 701.000000 701 90.4490 2598 3130 1 chr1D.!!$F2 532
19 TraesCS5A01G352600 chr1D 46660443 46660976 533 True 695.000000 695 90.1300 2598 3133 1 chr1D.!!$R1 535
20 TraesCS5A01G352600 chr6D 56356396 56356926 530 False 695.000000 695 90.2620 2598 3130 1 chr6D.!!$F1 532
21 TraesCS5A01G352600 chr3D 567181052 567181585 533 True 695.000000 695 90.1300 2598 3133 1 chr3D.!!$R1 535
22 TraesCS5A01G352600 chr3A 717804042 717804941 899 False 219.333333 309 88.4090 3243 3715 3 chr3A.!!$F1 472

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
153 154 1.123077 TTGCCGAGATAGGATGCACT 58.877 50.000 0.0 0.0 0.0 4.40 F
1472 1511 1.002544 AGAGGTCAAGTAGCTGGCAAC 59.997 52.381 0.0 0.0 35.6 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2069 2135 0.975887 GCAGGCCCCTGAAAATTTGA 59.024 50.000 18.20 0.0 46.30 2.69 R
3441 4972 1.002033 GAGTTTGCAGCTCACAACAGG 60.002 52.381 13.39 0.0 33.45 4.00 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
72 73 7.782897 TCTATAACTTATGATCCCACAGAGG 57.217 40.000 0.00 0.00 37.03 3.69
75 76 7.931015 ATAACTTATGATCCCACAGAGGTTA 57.069 36.000 0.00 0.00 37.71 2.85
76 77 5.878406 ACTTATGATCCCACAGAGGTTAG 57.122 43.478 0.00 0.00 34.66 2.34
77 78 5.529289 ACTTATGATCCCACAGAGGTTAGA 58.471 41.667 0.00 0.00 34.66 2.10
78 79 5.964477 ACTTATGATCCCACAGAGGTTAGAA 59.036 40.000 0.00 0.00 34.66 2.10
79 80 6.617371 ACTTATGATCCCACAGAGGTTAGAAT 59.383 38.462 0.00 0.00 34.66 2.40
80 81 5.983333 ATGATCCCACAGAGGTTAGAATT 57.017 39.130 0.00 0.00 34.66 2.17
81 82 5.102953 TGATCCCACAGAGGTTAGAATTG 57.897 43.478 0.00 0.00 34.66 2.32
82 83 4.536090 TGATCCCACAGAGGTTAGAATTGT 59.464 41.667 0.00 0.00 34.66 2.71
83 84 4.286297 TCCCACAGAGGTTAGAATTGTG 57.714 45.455 0.00 0.00 38.99 3.33
84 85 3.650942 TCCCACAGAGGTTAGAATTGTGT 59.349 43.478 2.74 0.00 37.91 3.72
85 86 4.841813 TCCCACAGAGGTTAGAATTGTGTA 59.158 41.667 2.74 0.00 37.91 2.90
87 88 5.817816 CCCACAGAGGTTAGAATTGTGTATC 59.182 44.000 2.74 0.00 37.91 2.24
89 90 6.352222 CCACAGAGGTTAGAATTGTGTATCCT 60.352 42.308 2.74 0.00 37.91 3.24
90 91 6.536582 CACAGAGGTTAGAATTGTGTATCCTG 59.463 42.308 0.00 0.00 35.59 3.86
91 92 6.213600 ACAGAGGTTAGAATTGTGTATCCTGT 59.786 38.462 0.00 0.00 0.00 4.00
92 93 7.106239 CAGAGGTTAGAATTGTGTATCCTGTT 58.894 38.462 0.00 0.00 0.00 3.16
93 94 7.278868 CAGAGGTTAGAATTGTGTATCCTGTTC 59.721 40.741 0.00 0.00 0.00 3.18
95 96 7.690256 AGGTTAGAATTGTGTATCCTGTTCTT 58.310 34.615 0.00 0.00 0.00 2.52
97 98 9.444600 GGTTAGAATTGTGTATCCTGTTCTTTA 57.555 33.333 0.00 0.00 0.00 1.85
100 101 8.511604 AGAATTGTGTATCCTGTTCTTTATGG 57.488 34.615 0.00 0.00 0.00 2.74
101 102 6.699575 ATTGTGTATCCTGTTCTTTATGGC 57.300 37.500 0.00 0.00 0.00 4.40
102 103 5.435686 TGTGTATCCTGTTCTTTATGGCT 57.564 39.130 0.00 0.00 0.00 4.75
103 104 5.815581 TGTGTATCCTGTTCTTTATGGCTT 58.184 37.500 0.00 0.00 0.00 4.35
105 106 7.047891 TGTGTATCCTGTTCTTTATGGCTTAG 58.952 38.462 0.00 0.00 0.00 2.18
106 107 6.483640 GTGTATCCTGTTCTTTATGGCTTAGG 59.516 42.308 0.00 0.00 0.00 2.69
108 109 5.514500 TCCTGTTCTTTATGGCTTAGGTT 57.486 39.130 0.00 0.00 0.00 3.50
109 110 5.497474 TCCTGTTCTTTATGGCTTAGGTTC 58.503 41.667 0.00 0.00 0.00 3.62
110 111 4.640647 CCTGTTCTTTATGGCTTAGGTTCC 59.359 45.833 0.00 0.00 0.00 3.62
112 113 5.826643 TGTTCTTTATGGCTTAGGTTCCAT 58.173 37.500 0.00 0.00 44.62 3.41
113 114 5.885912 TGTTCTTTATGGCTTAGGTTCCATC 59.114 40.000 0.00 0.00 41.81 3.51
115 116 5.684704 TCTTTATGGCTTAGGTTCCATCAG 58.315 41.667 0.00 0.00 41.81 2.90
116 117 5.191722 TCTTTATGGCTTAGGTTCCATCAGT 59.808 40.000 0.00 0.00 41.81 3.41
117 118 6.385759 TCTTTATGGCTTAGGTTCCATCAGTA 59.614 38.462 0.00 0.00 41.81 2.74
118 119 4.696479 ATGGCTTAGGTTCCATCAGTAG 57.304 45.455 0.00 0.00 38.65 2.57
120 121 3.844211 TGGCTTAGGTTCCATCAGTAGTT 59.156 43.478 0.00 0.00 0.00 2.24
121 122 4.192317 GGCTTAGGTTCCATCAGTAGTTG 58.808 47.826 0.00 0.00 0.00 3.16
122 123 4.323562 GGCTTAGGTTCCATCAGTAGTTGT 60.324 45.833 0.00 0.00 0.00 3.32
123 124 4.631813 GCTTAGGTTCCATCAGTAGTTGTG 59.368 45.833 0.00 0.00 0.00 3.33
125 126 6.573680 GCTTAGGTTCCATCAGTAGTTGTGTA 60.574 42.308 0.00 0.00 0.00 2.90
126 127 5.148651 AGGTTCCATCAGTAGTTGTGTAC 57.851 43.478 0.00 0.00 0.00 2.90
127 128 4.838986 AGGTTCCATCAGTAGTTGTGTACT 59.161 41.667 0.00 0.00 41.04 2.73
128 129 6.014647 AGGTTCCATCAGTAGTTGTGTACTA 58.985 40.000 0.00 0.00 38.33 1.82
130 131 6.979238 GGTTCCATCAGTAGTTGTGTACTATC 59.021 42.308 0.00 0.00 41.26 2.08
131 132 6.373186 TCCATCAGTAGTTGTGTACTATCG 57.627 41.667 0.00 0.00 41.26 2.92
132 133 5.884232 TCCATCAGTAGTTGTGTACTATCGT 59.116 40.000 0.00 0.00 41.26 3.73
134 135 7.033791 CCATCAGTAGTTGTGTACTATCGTTT 58.966 38.462 0.00 0.00 41.26 3.60
136 137 7.862741 TCAGTAGTTGTGTACTATCGTTTTG 57.137 36.000 0.00 0.00 41.26 2.44
137 138 6.364165 TCAGTAGTTGTGTACTATCGTTTTGC 59.636 38.462 0.00 0.00 41.26 3.68
138 139 5.636543 AGTAGTTGTGTACTATCGTTTTGCC 59.363 40.000 0.00 0.00 41.26 4.52
139 140 3.430895 AGTTGTGTACTATCGTTTTGCCG 59.569 43.478 0.00 0.00 34.56 5.69
140 141 3.300852 TGTGTACTATCGTTTTGCCGA 57.699 42.857 0.00 0.00 41.73 5.54
141 142 3.247442 TGTGTACTATCGTTTTGCCGAG 58.753 45.455 0.00 0.00 40.68 4.63
144 145 5.163632 TGTGTACTATCGTTTTGCCGAGATA 60.164 40.000 0.00 0.00 40.68 1.98
145 146 5.398711 GTGTACTATCGTTTTGCCGAGATAG 59.601 44.000 9.09 9.09 44.73 2.08
146 147 3.978687 ACTATCGTTTTGCCGAGATAGG 58.021 45.455 13.65 0.00 43.96 2.57
147 148 3.635373 ACTATCGTTTTGCCGAGATAGGA 59.365 43.478 13.65 0.00 43.96 2.94
148 149 3.753294 ATCGTTTTGCCGAGATAGGAT 57.247 42.857 0.00 0.00 40.68 3.24
149 150 2.821546 TCGTTTTGCCGAGATAGGATG 58.178 47.619 0.00 0.00 32.18 3.51
150 151 1.261619 CGTTTTGCCGAGATAGGATGC 59.738 52.381 0.00 0.00 0.00 3.91
151 152 2.288666 GTTTTGCCGAGATAGGATGCA 58.711 47.619 0.00 0.00 0.00 3.96
152 153 1.953559 TTTGCCGAGATAGGATGCAC 58.046 50.000 0.00 0.00 0.00 4.57
153 154 1.123077 TTGCCGAGATAGGATGCACT 58.877 50.000 0.00 0.00 0.00 4.40
154 155 1.995376 TGCCGAGATAGGATGCACTA 58.005 50.000 0.00 0.00 0.00 2.74
155 156 2.529632 TGCCGAGATAGGATGCACTAT 58.470 47.619 0.00 0.00 36.41 2.12
158 159 4.526650 TGCCGAGATAGGATGCACTATAAA 59.473 41.667 0.00 0.00 33.95 1.40
159 160 5.011635 TGCCGAGATAGGATGCACTATAAAA 59.988 40.000 0.00 0.00 33.95 1.52
161 162 6.595716 GCCGAGATAGGATGCACTATAAAAAT 59.404 38.462 0.00 0.00 33.95 1.82
162 163 7.413438 GCCGAGATAGGATGCACTATAAAAATG 60.413 40.741 0.00 0.00 33.95 2.32
163 164 7.819415 CCGAGATAGGATGCACTATAAAAATGA 59.181 37.037 0.00 0.00 33.95 2.57
164 165 9.208022 CGAGATAGGATGCACTATAAAAATGAA 57.792 33.333 0.00 0.00 33.95 2.57
169 170 8.579850 AGGATGCACTATAAAAATGAACTCAA 57.420 30.769 0.00 0.00 0.00 3.02
170 171 8.680903 AGGATGCACTATAAAAATGAACTCAAG 58.319 33.333 0.00 0.00 0.00 3.02
171 172 8.677300 GGATGCACTATAAAAATGAACTCAAGA 58.323 33.333 0.00 0.00 0.00 3.02
172 173 9.713740 GATGCACTATAAAAATGAACTCAAGAG 57.286 33.333 0.00 0.00 0.00 2.85
173 174 8.846943 TGCACTATAAAAATGAACTCAAGAGA 57.153 30.769 3.73 0.00 0.00 3.10
174 175 9.283768 TGCACTATAAAAATGAACTCAAGAGAA 57.716 29.630 3.73 0.00 0.00 2.87
195 196 6.424032 AGAAACTGAGTGGATTTTATACCCC 58.576 40.000 0.00 0.00 0.00 4.95
233 234 9.959749 CTGGACTAACTATTGCAAAAACTTAAA 57.040 29.630 1.71 0.00 0.00 1.52
352 378 6.243811 TGTACACGATTCCACAATTAAACC 57.756 37.500 0.00 0.00 0.00 3.27
370 396 5.754543 AAACCGACACCGAAGAATTTTTA 57.245 34.783 0.00 0.00 38.22 1.52
436 462 8.450964 CCTTGTATTCCTGTGTATTAACAACAG 58.549 37.037 6.93 6.93 37.36 3.16
505 536 3.815401 CCTTATGATTCCCGTTGACCATC 59.185 47.826 0.00 0.00 0.00 3.51
596 628 3.634910 GCAAAAGTTAGTTGGTTCTCCCA 59.365 43.478 0.00 0.00 43.27 4.37
613 645 2.852449 TCCCAATCCCAGTTGCTTCTAT 59.148 45.455 0.00 0.00 0.00 1.98
644 676 4.228824 TGTAGTCCTGAGTTTAGTGGGTT 58.771 43.478 0.00 0.00 0.00 4.11
654 686 8.701895 CCTGAGTTTAGTGGGTTATTCTGTATA 58.298 37.037 0.00 0.00 0.00 1.47
738 770 5.240623 TGATGAACTCGTATGGCTTTTGTTT 59.759 36.000 0.00 0.00 0.00 2.83
827 860 9.239002 CAGTTTGACAATTTTTATTTCGGTGTA 57.761 29.630 0.00 0.00 0.00 2.90
881 914 6.582677 TGTTTGTCGATGGGTCATTAAAAT 57.417 33.333 0.00 0.00 0.00 1.82
969 1006 5.342806 TGAGATACTGACGCTTGTTTTTG 57.657 39.130 0.00 0.00 0.00 2.44
1065 1104 1.150536 GAACAACTGGACTGGGCCA 59.849 57.895 5.85 5.85 36.30 5.36
1070 1109 2.036098 CTGGACTGGGCCATTGCA 59.964 61.111 16.87 16.87 40.13 4.08
1181 1220 4.563580 GCCATCACTTAAGGAGTCTGTTGA 60.564 45.833 7.53 0.00 36.10 3.18
1219 1258 1.226575 CTTGATCGGCGTCAGCGTA 60.227 57.895 6.85 0.00 46.35 4.42
1251 1290 3.688272 CGAGCTCGCAATGAAATTTGAT 58.312 40.909 25.07 0.00 31.22 2.57
1261 1300 5.604565 CAATGAAATTTGATAAGGGCCTCC 58.395 41.667 6.46 0.00 31.22 4.30
1265 1304 4.513406 AATTTGATAAGGGCCTCCGTAA 57.487 40.909 6.46 0.00 38.33 3.18
1302 1341 3.393426 AACGAGGTATGGGTCTTCCTA 57.607 47.619 0.00 0.00 36.20 2.94
1321 1360 7.944554 TCTTCCTAATTCCTGAACACTCATTTT 59.055 33.333 0.00 0.00 0.00 1.82
1382 1421 6.623767 GCATTGGCTTTAACTCTCAGGTTAAG 60.624 42.308 0.00 0.00 40.98 1.85
1420 1459 1.266178 TTGGAGCGAGACATCCTTCA 58.734 50.000 0.00 0.00 36.50 3.02
1472 1511 1.002544 AGAGGTCAAGTAGCTGGCAAC 59.997 52.381 0.00 0.00 35.60 4.17
1478 1517 5.131142 AGGTCAAGTAGCTGGCAACTATAAT 59.869 40.000 0.28 0.00 33.68 1.28
1533 1572 9.541143 TTGGTTTTTCTTCTTTTGAACCATATC 57.459 29.630 6.59 0.00 44.06 1.63
1581 1620 6.519679 TCCTCAGTGCGTTTTTAGAGTATA 57.480 37.500 0.00 0.00 0.00 1.47
1878 1917 7.998383 AGCACATTTTAGTACCATGATCCATTA 59.002 33.333 0.00 0.00 0.00 1.90
2135 2201 6.976934 TTTTAGGAGTTCTGCCTGATTTTT 57.023 33.333 0.00 0.00 36.96 1.94
2280 2347 9.515226 GTATGCTTAATCTTGGTATATTCCCAA 57.485 33.333 6.43 6.43 39.62 4.12
2281 2348 7.817418 TGCTTAATCTTGGTATATTCCCAAC 57.183 36.000 3.14 0.00 37.05 3.77
2323 2394 5.980116 CACTCTTTCTATATCGTTCACAGGG 59.020 44.000 0.00 0.00 0.00 4.45
2325 2396 5.902681 TCTTTCTATATCGTTCACAGGGTG 58.097 41.667 0.00 0.00 34.45 4.61
2338 2409 1.630369 ACAGGGTGCTGAAGATGCTAA 59.370 47.619 0.00 0.00 0.00 3.09
2341 2412 2.573462 AGGGTGCTGAAGATGCTAAGAA 59.427 45.455 0.00 0.00 0.00 2.52
2456 2527 4.936891 AGAACAGTTCACAAAGAATTGGC 58.063 39.130 15.85 0.00 45.31 4.52
2463 2534 2.957680 TCACAAAGAATTGGCAAGCAGA 59.042 40.909 5.96 0.00 41.01 4.26
2732 3904 9.227777 AGTATACCTCAACCAAACATACTTTTC 57.772 33.333 0.00 0.00 0.00 2.29
2768 3940 9.891828 CTCAAGCAAACATAACAACTATTACAA 57.108 29.630 0.00 0.00 0.00 2.41
2806 3978 7.872113 AAAGATCCAGAATTGTTCATACCTC 57.128 36.000 0.00 0.00 0.00 3.85
2953 4125 5.484290 AGGTTCACATATATAGGTAGGCCAC 59.516 44.000 5.01 0.31 37.19 5.01
2955 4127 4.925836 TCACATATATAGGTAGGCCACGA 58.074 43.478 5.01 0.00 37.19 4.35
2976 4148 2.477245 TGGAGGATAACTGGCTAGCAA 58.523 47.619 18.24 3.74 0.00 3.91
3039 4211 5.576774 GGTGCAGATTTATTTCCTTTTTCCG 59.423 40.000 0.00 0.00 0.00 4.30
3130 4302 2.612493 GCAGGGGAAGGCTGGGTAA 61.612 63.158 0.00 0.00 0.00 2.85
3133 4305 0.774491 AGGGGAAGGCTGGGTAACAA 60.774 55.000 0.00 0.00 39.74 2.83
3134 4306 0.113580 GGGGAAGGCTGGGTAACAAA 59.886 55.000 0.00 0.00 39.74 2.83
3135 4307 1.545841 GGGAAGGCTGGGTAACAAAG 58.454 55.000 0.00 0.00 39.74 2.77
3136 4308 1.203013 GGGAAGGCTGGGTAACAAAGT 60.203 52.381 0.00 0.00 39.74 2.66
3137 4309 2.040679 GGGAAGGCTGGGTAACAAAGTA 59.959 50.000 0.00 0.00 39.74 2.24
3138 4310 3.499021 GGGAAGGCTGGGTAACAAAGTAA 60.499 47.826 0.00 0.00 39.74 2.24
3139 4311 4.146564 GGAAGGCTGGGTAACAAAGTAAA 58.853 43.478 0.00 0.00 39.74 2.01
3140 4312 4.022589 GGAAGGCTGGGTAACAAAGTAAAC 60.023 45.833 0.00 0.00 39.74 2.01
3141 4313 3.493334 AGGCTGGGTAACAAAGTAAACC 58.507 45.455 0.00 0.00 39.74 3.27
3148 4320 6.957920 GGGTAACAAAGTAAACCCTTTACA 57.042 37.500 11.43 0.00 46.80 2.41
3149 4321 7.528996 GGGTAACAAAGTAAACCCTTTACAT 57.471 36.000 11.43 0.00 46.80 2.29
3150 4322 7.372714 GGGTAACAAAGTAAACCCTTTACATG 58.627 38.462 11.43 0.00 46.80 3.21
3151 4323 7.372714 GGTAACAAAGTAAACCCTTTACATGG 58.627 38.462 0.00 0.00 46.11 3.66
3152 4324 7.014518 GGTAACAAAGTAAACCCTTTACATGGT 59.985 37.037 0.00 6.93 46.11 3.55
3153 4325 6.399639 ACAAAGTAAACCCTTTACATGGTG 57.600 37.500 0.00 3.12 46.11 4.17
3154 4326 5.303333 ACAAAGTAAACCCTTTACATGGTGG 59.697 40.000 0.00 0.00 46.11 4.61
3155 4327 4.734843 AGTAAACCCTTTACATGGTGGT 57.265 40.909 0.00 0.00 46.11 4.16
3156 4328 4.659115 AGTAAACCCTTTACATGGTGGTC 58.341 43.478 0.00 0.00 46.11 4.02
3157 4329 3.603965 AAACCCTTTACATGGTGGTCA 57.396 42.857 0.00 0.00 34.34 4.02
3158 4330 2.579410 ACCCTTTACATGGTGGTCAC 57.421 50.000 0.00 0.00 32.36 3.67
3159 4331 6.779882 GTAAACCCTTTACATGGTGGTCACC 61.780 48.000 12.89 12.89 45.96 4.02
3160 4332 8.885151 GTAAACCCTTTACATGGTGGTCACCT 62.885 46.154 19.44 3.98 45.95 4.00
3186 4358 9.887629 TTAATGACCACATTAATGAAAATGCAT 57.112 25.926 22.16 12.99 46.97 3.96
3202 4374 6.513806 AAATGCATGCAGTTTCATACTACA 57.486 33.333 26.47 0.00 34.68 2.74
3206 4378 9.506018 AATGCATGCAGTTTCATACTACATATA 57.494 29.630 26.69 0.00 38.53 0.86
3288 4635 9.219603 CAGTTTGTCTTTCTATCATGAAGGTTA 57.780 33.333 0.00 0.00 0.00 2.85
3402 4933 4.644685 GGAAGCTATTTTCCATAAGTGCCA 59.355 41.667 0.00 0.00 44.90 4.92
3407 4938 6.833416 AGCTATTTTCCATAAGTGCCATAACA 59.167 34.615 0.00 0.00 0.00 2.41
3408 4939 6.918022 GCTATTTTCCATAAGTGCCATAACAC 59.082 38.462 0.00 0.00 41.02 3.32
3411 4942 2.578480 TCCATAAGTGCCATAACACCCA 59.422 45.455 0.00 0.00 41.67 4.51
3412 4943 2.951642 CCATAAGTGCCATAACACCCAG 59.048 50.000 0.00 0.00 41.67 4.45
3413 4944 3.620488 CATAAGTGCCATAACACCCAGT 58.380 45.455 0.00 0.00 41.67 4.00
3434 4965 6.264832 CAGTTTATTTGTGTCACTTCTTGCA 58.735 36.000 4.27 0.00 0.00 4.08
3441 4972 3.499537 TGTGTCACTTCTTGCATGTGATC 59.500 43.478 4.27 10.62 40.36 2.92
3442 4973 3.076621 TGTCACTTCTTGCATGTGATCC 58.923 45.455 12.93 5.18 40.36 3.36
3466 4997 0.723981 GTGAGCTGCAAACTCGGATC 59.276 55.000 1.02 0.00 36.94 3.36
3467 4998 0.321346 TGAGCTGCAAACTCGGATCA 59.679 50.000 1.02 0.00 35.62 2.92
3469 5000 0.674895 AGCTGCAAACTCGGATCACC 60.675 55.000 1.02 0.00 0.00 4.02
3485 5016 0.393402 CACCTTGCCAGATGCTGCTA 60.393 55.000 0.00 0.00 42.00 3.49
3491 5022 1.211212 TGCCAGATGCTGCTACTGATT 59.789 47.619 21.16 0.00 42.00 2.57
3497 5028 0.837272 TGCTGCTACTGATTACCCCC 59.163 55.000 0.00 0.00 0.00 5.40
3531 5062 1.347707 TCACCACCTGCAAACTCCTAG 59.652 52.381 0.00 0.00 0.00 3.02
3535 5066 2.832129 CCACCTGCAAACTCCTAGAGTA 59.168 50.000 0.00 0.00 42.59 2.59
3537 5068 4.262894 CCACCTGCAAACTCCTAGAGTAAA 60.263 45.833 0.00 0.00 42.59 2.01
3544 5095 5.989777 GCAAACTCCTAGAGTAAAAGTCACA 59.010 40.000 0.00 0.00 42.59 3.58
3561 5112 8.659925 AAAGTCACATGCAAATTCAATTAACA 57.340 26.923 0.00 0.00 0.00 2.41
3564 5115 8.089597 AGTCACATGCAAATTCAATTAACATCA 58.910 29.630 0.00 0.00 0.00 3.07
3567 5118 7.638295 CACATGCAAATTCAATTAACATCATGC 59.362 33.333 0.00 3.16 33.08 4.06
3575 5126 8.836268 ATTCAATTAACATCATGCTGTTTGTT 57.164 26.923 19.15 11.79 39.88 2.83
3578 5129 5.903764 TTAACATCATGCTGTTTGTTTGC 57.096 34.783 19.15 0.00 39.88 3.68
3581 5132 4.382291 ACATCATGCTGTTTGTTTGCAAT 58.618 34.783 0.00 0.00 40.24 3.56
3582 5133 5.539979 ACATCATGCTGTTTGTTTGCAATA 58.460 33.333 0.00 0.00 40.24 1.90
3583 5134 5.406175 ACATCATGCTGTTTGTTTGCAATAC 59.594 36.000 0.00 2.31 40.24 1.89
3584 5135 5.199024 TCATGCTGTTTGTTTGCAATACT 57.801 34.783 0.00 0.00 40.24 2.12
3585 5136 5.221880 TCATGCTGTTTGTTTGCAATACTC 58.778 37.500 0.00 0.00 40.24 2.59
3586 5137 4.916983 TGCTGTTTGTTTGCAATACTCT 57.083 36.364 0.00 0.00 34.18 3.24
3587 5138 4.858935 TGCTGTTTGTTTGCAATACTCTC 58.141 39.130 0.00 0.00 34.18 3.20
3588 5139 4.337836 TGCTGTTTGTTTGCAATACTCTCA 59.662 37.500 0.00 0.00 34.18 3.27
3590 5141 5.922544 GCTGTTTGTTTGCAATACTCTCATT 59.077 36.000 0.00 0.00 34.18 2.57
3591 5142 6.088616 GCTGTTTGTTTGCAATACTCTCATTC 59.911 38.462 0.00 0.00 34.18 2.67
3594 5145 8.791675 TGTTTGTTTGCAATACTCTCATTCATA 58.208 29.630 0.00 0.00 34.18 2.15
3595 5146 9.065871 GTTTGTTTGCAATACTCTCATTCATAC 57.934 33.333 0.00 0.00 34.18 2.39
3596 5147 7.320443 TGTTTGCAATACTCTCATTCATACC 57.680 36.000 0.00 0.00 0.00 2.73
3609 5211 7.623630 TCTCATTCATACCTCTTGATTGTGAA 58.376 34.615 0.00 0.00 30.42 3.18
3621 5223 5.647658 TCTTGATTGTGAAGTTGTTGTGAGT 59.352 36.000 0.00 0.00 0.00 3.41
3625 5227 3.081061 TGTGAAGTTGTTGTGAGTTGCT 58.919 40.909 0.00 0.00 0.00 3.91
3637 5239 4.385825 TGTGAGTTGCTAAATCGGAAACT 58.614 39.130 0.00 0.00 35.46 2.66
3689 5291 0.891373 ACGAGATGACTGACCACCTG 59.109 55.000 0.00 0.00 0.00 4.00
3693 5295 1.002888 AGATGACTGACCACCTGCAAG 59.997 52.381 0.00 0.00 0.00 4.01
3697 5299 2.031012 TGACCACCTGCAAGCTCG 59.969 61.111 0.00 0.00 0.00 5.03
3715 5317 3.303791 GCTCGAAAAGTGGGTGTTAGTTG 60.304 47.826 0.00 0.00 0.00 3.16
3716 5318 2.614983 TCGAAAAGTGGGTGTTAGTTGC 59.385 45.455 0.00 0.00 0.00 4.17
3717 5319 2.616842 CGAAAAGTGGGTGTTAGTTGCT 59.383 45.455 0.00 0.00 0.00 3.91
3718 5320 3.548014 CGAAAAGTGGGTGTTAGTTGCTG 60.548 47.826 0.00 0.00 0.00 4.41
3719 5321 1.981256 AAGTGGGTGTTAGTTGCTGG 58.019 50.000 0.00 0.00 0.00 4.85
3720 5322 1.136828 AGTGGGTGTTAGTTGCTGGA 58.863 50.000 0.00 0.00 0.00 3.86
3721 5323 1.072331 AGTGGGTGTTAGTTGCTGGAG 59.928 52.381 0.00 0.00 0.00 3.86
3722 5324 0.250727 TGGGTGTTAGTTGCTGGAGC 60.251 55.000 0.00 0.00 42.50 4.70
3723 5325 0.036875 GGGTGTTAGTTGCTGGAGCT 59.963 55.000 0.00 0.00 42.66 4.09
3724 5326 1.278127 GGGTGTTAGTTGCTGGAGCTA 59.722 52.381 0.00 0.00 42.66 3.32
3725 5327 2.622436 GGTGTTAGTTGCTGGAGCTAG 58.378 52.381 0.00 0.00 42.66 3.42
3726 5328 2.003301 GTGTTAGTTGCTGGAGCTAGC 58.997 52.381 6.62 6.62 43.95 3.42
3734 5336 2.547299 GCTGGAGCTAGCATTCAGAT 57.453 50.000 25.70 3.47 43.17 2.90
3735 5337 2.415776 GCTGGAGCTAGCATTCAGATC 58.584 52.381 25.70 11.43 43.17 2.75
3736 5338 2.871236 GCTGGAGCTAGCATTCAGATCC 60.871 54.545 25.70 18.59 46.62 3.36
3738 5340 3.482156 GGAGCTAGCATTCAGATCCAA 57.518 47.619 18.83 0.00 45.89 3.53
3739 5341 3.401182 GGAGCTAGCATTCAGATCCAAG 58.599 50.000 18.83 0.00 45.89 3.61
3740 5342 3.401182 GAGCTAGCATTCAGATCCAAGG 58.599 50.000 18.83 0.00 0.00 3.61
3741 5343 3.044156 AGCTAGCATTCAGATCCAAGGA 58.956 45.455 18.83 0.00 0.00 3.36
3742 5344 3.071312 AGCTAGCATTCAGATCCAAGGAG 59.929 47.826 18.83 0.00 0.00 3.69
3743 5345 3.806507 GCTAGCATTCAGATCCAAGGAGG 60.807 52.174 10.63 0.00 39.47 4.30
3744 5346 2.203584 AGCATTCAGATCCAAGGAGGT 58.796 47.619 0.00 0.00 39.02 3.85
3745 5347 3.387962 AGCATTCAGATCCAAGGAGGTA 58.612 45.455 0.00 0.00 39.02 3.08
3746 5348 3.135530 AGCATTCAGATCCAAGGAGGTAC 59.864 47.826 0.00 0.00 39.02 3.34
3747 5349 3.118261 GCATTCAGATCCAAGGAGGTACA 60.118 47.826 0.00 0.00 39.02 2.90
3748 5350 4.701765 CATTCAGATCCAAGGAGGTACAG 58.298 47.826 0.00 0.00 39.02 2.74
3749 5351 2.111384 TCAGATCCAAGGAGGTACAGC 58.889 52.381 0.00 0.00 39.02 4.40
3750 5352 1.139853 CAGATCCAAGGAGGTACAGCC 59.860 57.143 0.00 0.00 39.02 4.85
3751 5353 1.204146 GATCCAAGGAGGTACAGCCA 58.796 55.000 6.09 0.00 40.61 4.75
3752 5354 0.912486 ATCCAAGGAGGTACAGCCAC 59.088 55.000 6.09 0.00 40.61 5.01
3753 5355 0.472925 TCCAAGGAGGTACAGCCACA 60.473 55.000 6.09 0.00 40.61 4.17
3754 5356 0.620556 CCAAGGAGGTACAGCCACAT 59.379 55.000 6.09 0.00 40.61 3.21
3755 5357 1.407437 CCAAGGAGGTACAGCCACATC 60.407 57.143 6.09 0.00 40.61 3.06
3756 5358 1.278985 CAAGGAGGTACAGCCACATCA 59.721 52.381 6.09 0.00 40.61 3.07
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
46 47 8.651389 CCTCTGTGGGATCATAAGTTATAGAAA 58.349 37.037 0.00 0.00 0.00 2.52
49 50 7.546250 ACCTCTGTGGGATCATAAGTTATAG 57.454 40.000 0.00 0.00 41.11 1.31
50 51 7.931015 AACCTCTGTGGGATCATAAGTTATA 57.069 36.000 0.00 0.00 41.11 0.98
55 56 6.485830 TTCTAACCTCTGTGGGATCATAAG 57.514 41.667 0.00 0.00 41.11 1.73
56 57 7.092444 ACAATTCTAACCTCTGTGGGATCATAA 60.092 37.037 0.00 0.00 41.11 1.90
57 58 6.386927 ACAATTCTAACCTCTGTGGGATCATA 59.613 38.462 0.00 0.00 41.11 2.15
58 59 5.192522 ACAATTCTAACCTCTGTGGGATCAT 59.807 40.000 0.00 0.00 41.11 2.45
60 61 4.878397 CACAATTCTAACCTCTGTGGGATC 59.122 45.833 0.33 0.00 41.11 3.36
61 62 4.289672 ACACAATTCTAACCTCTGTGGGAT 59.710 41.667 5.59 0.00 41.32 3.85
63 64 4.021102 ACACAATTCTAACCTCTGTGGG 57.979 45.455 5.59 0.00 41.32 4.61
64 65 5.817816 GGATACACAATTCTAACCTCTGTGG 59.182 44.000 5.59 0.00 41.32 4.17
65 66 6.536582 CAGGATACACAATTCTAACCTCTGTG 59.463 42.308 0.00 0.00 42.43 3.66
66 67 6.213600 ACAGGATACACAATTCTAACCTCTGT 59.786 38.462 0.00 0.00 41.41 3.41
67 68 6.644347 ACAGGATACACAATTCTAACCTCTG 58.356 40.000 0.00 0.00 41.41 3.35
68 69 6.875972 ACAGGATACACAATTCTAACCTCT 57.124 37.500 0.00 0.00 41.41 3.69
69 70 7.331791 AGAACAGGATACACAATTCTAACCTC 58.668 38.462 0.00 0.00 41.41 3.85
70 71 7.259088 AGAACAGGATACACAATTCTAACCT 57.741 36.000 0.00 0.00 41.41 3.50
71 72 7.923414 AAGAACAGGATACACAATTCTAACC 57.077 36.000 0.00 0.00 41.41 2.85
75 76 7.067494 GCCATAAAGAACAGGATACACAATTCT 59.933 37.037 0.00 0.00 41.41 2.40
76 77 7.067494 AGCCATAAAGAACAGGATACACAATTC 59.933 37.037 0.00 0.00 41.41 2.17
77 78 6.891908 AGCCATAAAGAACAGGATACACAATT 59.108 34.615 0.00 0.00 41.41 2.32
78 79 6.426587 AGCCATAAAGAACAGGATACACAAT 58.573 36.000 0.00 0.00 41.41 2.71
79 80 5.815581 AGCCATAAAGAACAGGATACACAA 58.184 37.500 0.00 0.00 41.41 3.33
80 81 5.435686 AGCCATAAAGAACAGGATACACA 57.564 39.130 0.00 0.00 41.41 3.72
81 82 6.483640 CCTAAGCCATAAAGAACAGGATACAC 59.516 42.308 0.00 0.00 41.41 2.90
82 83 6.157994 ACCTAAGCCATAAAGAACAGGATACA 59.842 38.462 0.00 0.00 41.41 2.29
83 84 6.592870 ACCTAAGCCATAAAGAACAGGATAC 58.407 40.000 0.00 0.00 0.00 2.24
84 85 6.824958 ACCTAAGCCATAAAGAACAGGATA 57.175 37.500 0.00 0.00 0.00 2.59
85 86 5.717119 ACCTAAGCCATAAAGAACAGGAT 57.283 39.130 0.00 0.00 0.00 3.24
87 88 4.640647 GGAACCTAAGCCATAAAGAACAGG 59.359 45.833 0.00 0.00 0.00 4.00
89 90 5.249780 TGGAACCTAAGCCATAAAGAACA 57.750 39.130 0.00 0.00 0.00 3.18
90 91 5.885912 TGATGGAACCTAAGCCATAAAGAAC 59.114 40.000 0.00 0.00 44.60 3.01
91 92 6.073447 TGATGGAACCTAAGCCATAAAGAA 57.927 37.500 0.00 0.00 44.60 2.52
92 93 5.191722 ACTGATGGAACCTAAGCCATAAAGA 59.808 40.000 0.00 0.00 44.60 2.52
93 94 5.440610 ACTGATGGAACCTAAGCCATAAAG 58.559 41.667 0.00 0.00 44.60 1.85
95 96 5.665812 ACTACTGATGGAACCTAAGCCATAA 59.334 40.000 0.00 0.00 44.60 1.90
98 99 3.450904 ACTACTGATGGAACCTAAGCCA 58.549 45.455 0.00 0.00 38.78 4.75
99 100 4.192317 CAACTACTGATGGAACCTAAGCC 58.808 47.826 0.00 0.00 0.00 4.35
100 101 4.631813 CACAACTACTGATGGAACCTAAGC 59.368 45.833 0.00 0.00 0.00 3.09
101 102 5.794894 ACACAACTACTGATGGAACCTAAG 58.205 41.667 0.00 0.00 0.00 2.18
102 103 5.818678 ACACAACTACTGATGGAACCTAA 57.181 39.130 0.00 0.00 0.00 2.69
103 104 6.014647 AGTACACAACTACTGATGGAACCTA 58.985 40.000 0.00 0.00 36.36 3.08
105 106 5.148651 AGTACACAACTACTGATGGAACC 57.851 43.478 0.00 0.00 36.36 3.62
106 107 6.691818 CGATAGTACACAACTACTGATGGAAC 59.308 42.308 0.00 0.00 43.47 3.62
108 109 6.373186 CGATAGTACACAACTACTGATGGA 57.627 41.667 0.00 0.00 43.47 3.41
126 127 4.238761 TCCTATCTCGGCAAAACGATAG 57.761 45.455 0.00 0.00 42.62 2.08
127 128 4.556233 CATCCTATCTCGGCAAAACGATA 58.444 43.478 0.00 0.00 42.62 2.92
128 129 3.393800 CATCCTATCTCGGCAAAACGAT 58.606 45.455 0.00 0.00 42.62 3.73
130 131 1.261619 GCATCCTATCTCGGCAAAACG 59.738 52.381 0.00 0.00 0.00 3.60
131 132 2.032178 GTGCATCCTATCTCGGCAAAAC 59.968 50.000 0.00 0.00 36.08 2.43
132 133 2.092968 AGTGCATCCTATCTCGGCAAAA 60.093 45.455 0.00 0.00 36.08 2.44
134 135 1.123077 AGTGCATCCTATCTCGGCAA 58.877 50.000 0.00 0.00 36.08 4.52
136 137 4.720649 TTATAGTGCATCCTATCTCGGC 57.279 45.455 0.37 0.00 0.00 5.54
137 138 7.819415 TCATTTTTATAGTGCATCCTATCTCGG 59.181 37.037 0.37 0.00 0.00 4.63
138 139 8.763049 TCATTTTTATAGTGCATCCTATCTCG 57.237 34.615 0.37 0.00 0.00 4.04
144 145 8.579850 TTGAGTTCATTTTTATAGTGCATCCT 57.420 30.769 0.00 0.00 0.00 3.24
145 146 8.677300 TCTTGAGTTCATTTTTATAGTGCATCC 58.323 33.333 0.00 0.00 0.00 3.51
146 147 9.713740 CTCTTGAGTTCATTTTTATAGTGCATC 57.286 33.333 0.00 0.00 0.00 3.91
147 148 9.453572 TCTCTTGAGTTCATTTTTATAGTGCAT 57.546 29.630 0.00 0.00 0.00 3.96
148 149 8.846943 TCTCTTGAGTTCATTTTTATAGTGCA 57.153 30.769 0.00 0.00 0.00 4.57
155 156 9.396022 ACTCAGTTTCTCTTGAGTTCATTTTTA 57.604 29.630 1.53 0.00 38.32 1.52
158 159 6.261826 CCACTCAGTTTCTCTTGAGTTCATTT 59.738 38.462 4.51 0.00 39.33 2.32
159 160 5.762218 CCACTCAGTTTCTCTTGAGTTCATT 59.238 40.000 4.51 0.00 39.33 2.57
161 162 4.405680 TCCACTCAGTTTCTCTTGAGTTCA 59.594 41.667 4.51 0.00 39.33 3.18
162 163 4.950050 TCCACTCAGTTTCTCTTGAGTTC 58.050 43.478 4.51 0.00 39.33 3.01
163 164 5.559148 ATCCACTCAGTTTCTCTTGAGTT 57.441 39.130 4.51 0.00 39.33 3.01
164 165 5.559148 AATCCACTCAGTTTCTCTTGAGT 57.441 39.130 1.53 1.53 41.70 3.41
165 166 6.874288 AAAATCCACTCAGTTTCTCTTGAG 57.126 37.500 0.27 0.27 34.81 3.02
166 167 9.436957 GTATAAAATCCACTCAGTTTCTCTTGA 57.563 33.333 0.00 0.00 0.00 3.02
167 168 8.669243 GGTATAAAATCCACTCAGTTTCTCTTG 58.331 37.037 0.00 0.00 0.00 3.02
169 170 7.339482 GGGTATAAAATCCACTCAGTTTCTCT 58.661 38.462 0.00 0.00 0.00 3.10
170 171 6.542735 GGGGTATAAAATCCACTCAGTTTCTC 59.457 42.308 0.00 0.00 0.00 2.87
171 172 6.424032 GGGGTATAAAATCCACTCAGTTTCT 58.576 40.000 0.00 0.00 0.00 2.52
172 173 5.296035 CGGGGTATAAAATCCACTCAGTTTC 59.704 44.000 0.00 0.00 0.00 2.78
173 174 5.190677 CGGGGTATAAAATCCACTCAGTTT 58.809 41.667 0.00 0.00 0.00 2.66
174 175 4.384868 CCGGGGTATAAAATCCACTCAGTT 60.385 45.833 0.00 0.00 0.00 3.16
175 176 3.135895 CCGGGGTATAAAATCCACTCAGT 59.864 47.826 0.00 0.00 0.00 3.41
176 177 3.389983 TCCGGGGTATAAAATCCACTCAG 59.610 47.826 0.00 0.00 0.00 3.35
179 180 3.660959 TCTCCGGGGTATAAAATCCACT 58.339 45.455 0.00 0.00 0.00 4.00
195 196 5.012328 AGTTAGTCCAGCTAATTTCTCCG 57.988 43.478 0.00 0.00 41.25 4.63
233 234 6.207691 AGTTGTTGAAAAACACATAGTGCT 57.792 33.333 0.52 0.00 36.98 4.40
293 294 4.211125 TGACCTTCCAACAGCAATAACAA 58.789 39.130 0.00 0.00 0.00 2.83
339 365 2.144730 CGGTGTCGGTTTAATTGTGGA 58.855 47.619 0.00 0.00 0.00 4.02
352 378 5.981174 TCAAGTAAAAATTCTTCGGTGTCG 58.019 37.500 0.00 0.00 37.82 4.35
390 416 6.891908 ACAAGGCTGATTCTGGTTACAATATT 59.108 34.615 0.00 0.00 0.00 1.28
392 418 5.815581 ACAAGGCTGATTCTGGTTACAATA 58.184 37.500 0.00 0.00 0.00 1.90
436 462 0.399233 ATCCCTGGAGTGGAGGCTAC 60.399 60.000 0.00 0.00 34.80 3.58
505 536 0.034896 AACTCCCCTGTACACTTGCG 59.965 55.000 0.00 0.00 0.00 4.85
596 628 5.044846 ACCTACAATAGAAGCAACTGGGATT 60.045 40.000 0.00 0.00 0.00 3.01
613 645 4.383931 ACTCAGGACTACAGACCTACAA 57.616 45.455 0.00 0.00 38.11 2.41
738 770 4.168088 AGTTCTCCCCTCCAAAAGAAAGAA 59.832 41.667 0.00 0.00 30.10 2.52
881 914 5.795972 TGGTTCATACATCACCGTTTTCTA 58.204 37.500 0.00 0.00 32.71 2.10
969 1006 6.890268 AGTAATTCTCACCCCTAATTCCAAAC 59.110 38.462 0.00 0.00 0.00 2.93
1027 1066 1.191489 TGATCCTGTGTCTTCCGCCA 61.191 55.000 0.00 0.00 0.00 5.69
1065 1104 4.343231 TGATGACATTTACTGGGTGCAAT 58.657 39.130 0.00 0.00 0.00 3.56
1070 1109 8.877864 TTTATTTCTGATGACATTTACTGGGT 57.122 30.769 0.00 0.00 0.00 4.51
1219 1258 1.517257 CGAGCTCGCGGACTGAAAT 60.517 57.895 25.07 0.00 0.00 2.17
1251 1290 1.834301 GGCATTACGGAGGCCCTTA 59.166 57.895 0.00 0.00 41.90 2.69
1261 1300 6.019398 TCGTTAGACAATAATGTGGCATTACG 60.019 38.462 4.00 4.16 40.74 3.18
1265 1304 4.816385 CCTCGTTAGACAATAATGTGGCAT 59.184 41.667 0.00 0.00 40.74 4.40
1302 1341 5.534207 TGCAAAATGAGTGTTCAGGAATT 57.466 34.783 0.00 0.00 36.61 2.17
1321 1360 5.468746 GTCTGTACTAACTGAACCAATTGCA 59.531 40.000 0.00 0.00 35.61 4.08
1382 1421 6.079424 TCCAATAAAGCCACTTGTTTACAC 57.921 37.500 0.00 0.00 0.00 2.90
1420 1459 9.041354 ACTCCAATACACTCTTTAGATTCTTCT 57.959 33.333 0.00 0.00 35.90 2.85
1533 1572 2.386661 AATCCTTCACGTGGCTGTAG 57.613 50.000 17.00 5.74 0.00 2.74
1581 1620 4.503741 AACACTTGCAGCGTCATTAAAT 57.496 36.364 0.00 0.00 0.00 1.40
1634 1673 9.958180 TTTAGGCATATATATTTAGCTGCAGAA 57.042 29.630 20.43 2.80 0.00 3.02
1767 1806 1.081094 TCGCTATTCTCGTGACGTCA 58.919 50.000 15.76 15.76 0.00 4.35
1770 1809 2.102633 GAAGTCGCTATTCTCGTGACG 58.897 52.381 0.00 0.00 44.35 4.35
1878 1917 9.944376 ATAGTACATTGTAAACAGAGAACACAT 57.056 29.630 0.00 0.00 0.00 3.21
1917 1956 4.016444 CCAGTAGCAAGCAGGGAAAATAA 58.984 43.478 0.00 0.00 0.00 1.40
2069 2135 0.975887 GCAGGCCCCTGAAAATTTGA 59.024 50.000 18.20 0.00 46.30 2.69
2135 2201 9.646427 GCATGTTATTTTCTTAACCATGGTAAA 57.354 29.630 20.12 14.87 32.24 2.01
2196 2262 1.741770 GACGCGCCAATCCAAGAGT 60.742 57.895 5.73 0.00 0.00 3.24
2323 2394 6.385033 ACAATTTTCTTAGCATCTTCAGCAC 58.615 36.000 0.00 0.00 0.00 4.40
2325 2396 7.061557 GTCAACAATTTTCTTAGCATCTTCAGC 59.938 37.037 0.00 0.00 0.00 4.26
2338 2409 5.728351 TCGTTCTTCGTCAACAATTTTCT 57.272 34.783 0.00 0.00 40.80 2.52
2341 2412 5.479716 AGTTCGTTCTTCGTCAACAATTT 57.520 34.783 0.00 0.00 40.80 1.82
2550 3722 5.991861 ACCATAATTATGTACGGGTGTCAA 58.008 37.500 21.20 0.00 31.82 3.18
2661 3833 6.844388 TCATAGCCTCATAGGAAAGGAAACTA 59.156 38.462 0.00 0.00 37.31 2.24
2699 3871 8.786826 TGTTTGGTTGAGGTATACTATCAAAG 57.213 34.615 19.11 0.00 34.91 2.77
2732 3904 9.325198 TGTTATGTTTGCTTGAGGTATACTATG 57.675 33.333 2.25 0.00 0.00 2.23
2872 4044 1.604593 GGCCATCACAACAGCCAGT 60.605 57.895 0.00 0.00 45.07 4.00
2953 4125 2.353208 GCTAGCCAGTTATCCTCCATCG 60.353 54.545 2.29 0.00 0.00 3.84
2955 4127 2.694397 TGCTAGCCAGTTATCCTCCAT 58.306 47.619 13.29 0.00 0.00 3.41
2976 4148 4.989875 AGTGCTAGATTAGGCCATGATT 57.010 40.909 5.01 0.00 0.00 2.57
3024 4196 6.422400 GTGCATTTGACGGAAAAAGGAAATAA 59.578 34.615 0.00 0.00 0.00 1.40
3039 4211 8.532977 AATTTATTAACAGGTGTGCATTTGAC 57.467 30.769 0.00 0.00 0.00 3.18
3130 4302 5.303333 CCACCATGTAAAGGGTTTACTTTGT 59.697 40.000 10.15 4.48 44.46 2.83
3133 4305 5.069518 ACCACCATGTAAAGGGTTTACTT 57.930 39.130 10.15 2.57 44.46 2.24
3134 4306 4.105057 TGACCACCATGTAAAGGGTTTACT 59.895 41.667 10.15 0.00 44.46 2.24
3135 4307 4.216902 GTGACCACCATGTAAAGGGTTTAC 59.783 45.833 0.00 3.11 44.43 2.01
3136 4308 4.400120 GTGACCACCATGTAAAGGGTTTA 58.600 43.478 0.00 0.00 34.45 2.01
3137 4309 3.227614 GTGACCACCATGTAAAGGGTTT 58.772 45.455 0.00 0.00 34.45 3.27
3138 4310 2.871453 GTGACCACCATGTAAAGGGTT 58.129 47.619 0.00 0.00 34.45 4.11
3139 4311 2.579410 GTGACCACCATGTAAAGGGT 57.421 50.000 0.00 0.00 38.10 4.34
3161 4333 9.315525 CATGCATTTTCATTAATGTGGTCATTA 57.684 29.630 14.97 0.00 43.12 1.90
3162 4334 7.201661 GCATGCATTTTCATTAATGTGGTCATT 60.202 33.333 14.21 0.00 45.00 2.57
3163 4335 6.259167 GCATGCATTTTCATTAATGTGGTCAT 59.741 34.615 14.21 9.24 37.72 3.06
3164 4336 5.581479 GCATGCATTTTCATTAATGTGGTCA 59.419 36.000 14.21 7.58 37.72 4.02
3165 4337 5.581479 TGCATGCATTTTCATTAATGTGGTC 59.419 36.000 18.46 2.68 37.72 4.02
3166 4338 5.489249 TGCATGCATTTTCATTAATGTGGT 58.511 33.333 18.46 0.00 37.72 4.16
3167 4339 5.583061 ACTGCATGCATTTTCATTAATGTGG 59.417 36.000 22.97 5.85 37.72 4.17
3168 4340 6.656314 ACTGCATGCATTTTCATTAATGTG 57.344 33.333 22.97 6.55 37.72 3.21
3169 4341 7.388224 TGAAACTGCATGCATTTTCATTAATGT 59.612 29.630 40.20 22.66 44.68 2.71
3170 4342 7.744059 TGAAACTGCATGCATTTTCATTAATG 58.256 30.769 40.20 22.12 44.68 1.90
3171 4343 7.908827 TGAAACTGCATGCATTTTCATTAAT 57.091 28.000 40.20 20.38 44.68 1.40
3177 4349 7.028962 TGTAGTATGAAACTGCATGCATTTTC 58.971 34.615 37.26 37.26 44.73 2.29
3178 4350 6.923012 TGTAGTATGAAACTGCATGCATTTT 58.077 32.000 29.46 29.46 44.73 1.82
3179 4351 6.513806 TGTAGTATGAAACTGCATGCATTT 57.486 33.333 22.97 19.56 44.73 2.32
3320 4668 9.846248 GTAATAAGAAACTGAGTGCATTTTCAT 57.154 29.630 10.10 2.91 42.70 2.57
3350 4872 7.417612 CAATAGTCAACATATGTAGGCCAAAC 58.582 38.462 9.21 2.84 0.00 2.93
3400 4931 6.015856 TGACACAAATAAACTGGGTGTTATGG 60.016 38.462 0.00 0.00 42.27 2.74
3402 4933 6.775629 AGTGACACAAATAAACTGGGTGTTAT 59.224 34.615 8.59 0.00 42.27 1.89
3407 4938 5.445964 AGAAGTGACACAAATAAACTGGGT 58.554 37.500 8.59 0.00 31.50 4.51
3408 4939 6.208644 CAAGAAGTGACACAAATAAACTGGG 58.791 40.000 8.59 0.00 0.00 4.45
3411 4942 6.449635 TGCAAGAAGTGACACAAATAAACT 57.550 33.333 8.59 0.00 0.00 2.66
3412 4943 6.697019 ACATGCAAGAAGTGACACAAATAAAC 59.303 34.615 8.59 0.00 0.00 2.01
3413 4944 6.696583 CACATGCAAGAAGTGACACAAATAAA 59.303 34.615 8.59 0.00 35.33 1.40
3434 4965 2.708051 CAGCTCACAACAGGATCACAT 58.292 47.619 0.00 0.00 0.00 3.21
3441 4972 1.002033 GAGTTTGCAGCTCACAACAGG 60.002 52.381 13.39 0.00 33.45 4.00
3442 4973 1.333524 CGAGTTTGCAGCTCACAACAG 60.334 52.381 16.93 1.11 33.45 3.16
3502 5033 1.977854 TGCAGGTGGTGACTCAGTTAT 59.022 47.619 0.00 0.00 0.00 1.89
3503 5034 1.419381 TGCAGGTGGTGACTCAGTTA 58.581 50.000 0.00 0.00 0.00 2.24
3505 5036 0.546122 TTTGCAGGTGGTGACTCAGT 59.454 50.000 0.00 0.00 0.00 3.41
3506 5037 0.947244 GTTTGCAGGTGGTGACTCAG 59.053 55.000 0.00 0.00 0.00 3.35
3510 5041 0.179018 AGGAGTTTGCAGGTGGTGAC 60.179 55.000 0.00 0.00 0.00 3.67
3531 5062 7.928908 TTGAATTTGCATGTGACTTTTACTC 57.071 32.000 0.00 0.00 0.00 2.59
3535 5066 9.107177 TGTTAATTGAATTTGCATGTGACTTTT 57.893 25.926 0.00 0.00 0.00 2.27
3537 5068 8.836268 ATGTTAATTGAATTTGCATGTGACTT 57.164 26.923 0.00 0.00 0.00 3.01
3544 5095 7.551262 ACAGCATGATGTTAATTGAATTTGCAT 59.449 29.630 11.62 8.32 39.69 3.96
3559 5110 3.455990 TGCAAACAAACAGCATGATGT 57.544 38.095 11.62 11.62 39.69 3.06
3560 5111 5.636121 AGTATTGCAAACAAACAGCATGATG 59.364 36.000 9.94 9.94 37.62 3.07
3561 5112 5.786311 AGTATTGCAAACAAACAGCATGAT 58.214 33.333 1.71 0.00 37.62 2.45
3564 5115 5.009911 TGAGAGTATTGCAAACAAACAGCAT 59.990 36.000 1.71 0.00 39.77 3.79
3567 5118 7.140705 TGAATGAGAGTATTGCAAACAAACAG 58.859 34.615 1.71 0.00 39.77 3.16
3575 5126 7.129457 AGAGGTATGAATGAGAGTATTGCAA 57.871 36.000 0.00 0.00 0.00 4.08
3578 5129 9.775854 AATCAAGAGGTATGAATGAGAGTATTG 57.224 33.333 0.00 0.00 0.00 1.90
3581 5132 8.200120 CACAATCAAGAGGTATGAATGAGAGTA 58.800 37.037 0.00 0.00 33.08 2.59
3582 5133 7.046652 CACAATCAAGAGGTATGAATGAGAGT 58.953 38.462 0.00 0.00 33.08 3.24
3583 5134 7.270779 TCACAATCAAGAGGTATGAATGAGAG 58.729 38.462 0.00 0.00 33.08 3.20
3584 5135 7.186570 TCACAATCAAGAGGTATGAATGAGA 57.813 36.000 0.00 0.00 33.08 3.27
3585 5136 7.551974 ACTTCACAATCAAGAGGTATGAATGAG 59.448 37.037 0.00 0.00 33.08 2.90
3586 5137 7.397221 ACTTCACAATCAAGAGGTATGAATGA 58.603 34.615 0.00 0.00 33.08 2.57
3587 5138 7.621428 ACTTCACAATCAAGAGGTATGAATG 57.379 36.000 0.00 0.00 34.58 2.67
3588 5139 7.667219 ACAACTTCACAATCAAGAGGTATGAAT 59.333 33.333 0.00 0.00 0.00 2.57
3590 5141 6.533730 ACAACTTCACAATCAAGAGGTATGA 58.466 36.000 0.00 0.00 0.00 2.15
3591 5142 6.808008 ACAACTTCACAATCAAGAGGTATG 57.192 37.500 0.00 0.00 0.00 2.39
3594 5145 4.949856 ACAACAACTTCACAATCAAGAGGT 59.050 37.500 0.00 0.00 0.00 3.85
3595 5146 5.066375 TCACAACAACTTCACAATCAAGAGG 59.934 40.000 0.00 0.00 0.00 3.69
3596 5147 6.122850 TCACAACAACTTCACAATCAAGAG 57.877 37.500 0.00 0.00 0.00 2.85
3609 5211 4.024048 CCGATTTAGCAACTCACAACAACT 60.024 41.667 0.00 0.00 0.00 3.16
3621 5223 3.305064 GGCAACAGTTTCCGATTTAGCAA 60.305 43.478 0.00 0.00 0.00 3.91
3651 5253 0.396435 TTGCCGGTGTCATCAGAAGT 59.604 50.000 1.90 0.00 0.00 3.01
3681 5283 0.884704 TTTCGAGCTTGCAGGTGGTC 60.885 55.000 0.00 1.89 0.00 4.02
3689 5291 0.040067 CACCCACTTTTCGAGCTTGC 60.040 55.000 0.00 0.00 0.00 4.01
3693 5295 2.490991 ACTAACACCCACTTTTCGAGC 58.509 47.619 0.00 0.00 0.00 5.03
3697 5299 3.243401 CCAGCAACTAACACCCACTTTTC 60.243 47.826 0.00 0.00 0.00 2.29
3715 5317 2.415776 GATCTGAATGCTAGCTCCAGC 58.584 52.381 17.23 1.26 42.15 4.85
3716 5318 2.367894 TGGATCTGAATGCTAGCTCCAG 59.632 50.000 17.23 18.24 36.00 3.86
3717 5319 2.401568 TGGATCTGAATGCTAGCTCCA 58.598 47.619 17.23 15.32 37.93 3.86
3718 5320 3.401182 CTTGGATCTGAATGCTAGCTCC 58.599 50.000 17.23 12.79 32.43 4.70
3719 5321 3.070734 TCCTTGGATCTGAATGCTAGCTC 59.929 47.826 17.23 6.65 0.00 4.09
3720 5322 3.044156 TCCTTGGATCTGAATGCTAGCT 58.956 45.455 17.23 0.00 0.00 3.32
3721 5323 3.401182 CTCCTTGGATCTGAATGCTAGC 58.599 50.000 8.10 8.10 0.00 3.42
3722 5324 3.390639 ACCTCCTTGGATCTGAATGCTAG 59.609 47.826 0.00 0.00 39.71 3.42
3723 5325 3.387962 ACCTCCTTGGATCTGAATGCTA 58.612 45.455 0.00 0.00 39.71 3.49
3724 5326 2.203584 ACCTCCTTGGATCTGAATGCT 58.796 47.619 0.00 0.00 39.71 3.79
3725 5327 2.725221 ACCTCCTTGGATCTGAATGC 57.275 50.000 0.00 0.00 39.71 3.56
3726 5328 4.701765 CTGTACCTCCTTGGATCTGAATG 58.298 47.826 0.00 0.00 39.71 2.67
3727 5329 3.135530 GCTGTACCTCCTTGGATCTGAAT 59.864 47.826 0.00 0.00 39.71 2.57
3728 5330 2.501723 GCTGTACCTCCTTGGATCTGAA 59.498 50.000 0.00 0.00 39.71 3.02
3729 5331 2.111384 GCTGTACCTCCTTGGATCTGA 58.889 52.381 0.00 0.00 39.71 3.27
3730 5332 1.139853 GGCTGTACCTCCTTGGATCTG 59.860 57.143 0.00 0.00 39.71 2.90
3731 5333 1.273838 TGGCTGTACCTCCTTGGATCT 60.274 52.381 0.00 0.00 40.22 2.75
3732 5334 1.134371 GTGGCTGTACCTCCTTGGATC 60.134 57.143 0.00 0.00 40.22 3.36
3733 5335 0.912486 GTGGCTGTACCTCCTTGGAT 59.088 55.000 0.00 0.00 40.22 3.41
3734 5336 0.472925 TGTGGCTGTACCTCCTTGGA 60.473 55.000 0.00 0.00 40.22 3.53
3735 5337 0.620556 ATGTGGCTGTACCTCCTTGG 59.379 55.000 0.00 0.00 40.22 3.61
3736 5338 1.278985 TGATGTGGCTGTACCTCCTTG 59.721 52.381 0.00 0.00 40.22 3.61
3737 5339 1.656587 TGATGTGGCTGTACCTCCTT 58.343 50.000 0.00 0.00 40.22 3.36
3738 5340 3.399234 TGATGTGGCTGTACCTCCT 57.601 52.632 0.00 0.00 40.22 3.69


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

AutoCloner maintained by Alex Coulton.