Multiple sequence alignment - TraesCS7D01G432100

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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 TraesCS7D01G432100 chr7D 100.000 2779 0 0 1 2779 551810109 551807331 0.000000e+00 5132
1 TraesCS7D01G432100 chr7D 88.025 952 70 20 884 1811 551928655 551927724 0.000000e+00 1086
2 TraesCS7D01G432100 chr7D 82.042 852 106 35 968 1802 551000372 550999551 0.000000e+00 682
3 TraesCS7D01G432100 chr7D 80.348 804 112 27 972 1759 551500682 551499909 4.020000e-158 568
4 TraesCS7D01G432100 chr7D 95.014 361 18 0 1 361 589511150 589510790 4.020000e-158 568
5 TraesCS7D01G432100 chr7D 86.779 416 35 8 1299 1708 551114374 551113973 1.960000e-121 446
6 TraesCS7D01G432100 chr7D 87.339 387 24 11 884 1264 551114731 551114364 1.190000e-113 420
7 TraesCS7D01G432100 chr7B 92.953 965 24 21 904 1861 596680839 596679912 0.000000e+00 1365
8 TraesCS7D01G432100 chr7B 85.333 750 96 8 1056 1802 596782523 596781785 0.000000e+00 763
9 TraesCS7D01G432100 chr7B 94.505 455 22 3 377 829 596681545 596681092 0.000000e+00 699
10 TraesCS7D01G432100 chr7B 83.445 749 92 22 972 1708 595882196 595881468 0.000000e+00 667
11 TraesCS7D01G432100 chr7B 80.572 839 108 33 972 1788 596516148 596515343 1.840000e-166 595
12 TraesCS7D01G432100 chr7B 80.430 838 111 31 972 1788 596538984 596538179 8.570000e-165 590
13 TraesCS7D01G432100 chr7B 87.476 527 34 15 2284 2779 488398392 488398917 1.860000e-161 579
14 TraesCS7D01G432100 chr7B 87.042 409 27 12 1882 2287 488397839 488398224 3.290000e-119 438
15 TraesCS7D01G432100 chr7B 83.772 456 53 14 1220 1674 595993688 595993253 1.990000e-111 412
16 TraesCS7D01G432100 chr7B 79.695 197 21 14 2401 2586 5041331 5041143 1.050000e-24 124
17 TraesCS7D01G432100 chr7A 87.182 944 76 21 894 1811 637337034 637336110 0.000000e+00 1031
18 TraesCS7D01G432100 chr7A 86.667 840 56 17 884 1698 637036801 637035993 0.000000e+00 880
19 TraesCS7D01G432100 chr7A 83.953 592 78 13 1112 1697 636919475 636918895 4.050000e-153 551
20 TraesCS7D01G432100 chr7A 90.441 408 36 3 1882 2287 547714439 547714033 4.070000e-148 534
21 TraesCS7D01G432100 chr7A 91.386 267 21 2 2514 2779 547687909 547687644 5.660000e-97 364
22 TraesCS7D01G432100 chr7A 87.356 261 23 2 2284 2534 547713882 547713622 9.740000e-75 291
23 TraesCS7D01G432100 chr2D 87.968 507 43 12 2286 2779 610708100 610708601 1.430000e-162 582
24 TraesCS7D01G432100 chr2D 91.892 407 21 6 1882 2287 610707534 610707929 2.420000e-155 558
25 TraesCS7D01G432100 chr2D 94.118 357 21 0 1 357 640367670 640367314 6.770000e-151 544
26 TraesCS7D01G432100 chr2D 94.118 357 19 2 1 357 605779973 605779619 2.430000e-150 542
27 TraesCS7D01G432100 chr2D 93.036 359 23 2 1 357 10487938 10488296 8.820000e-145 523
28 TraesCS7D01G432100 chr2D 93.036 359 23 2 1 357 10505059 10505417 8.820000e-145 523
29 TraesCS7D01G432100 chr3D 91.587 416 20 9 1883 2293 500223179 500222774 6.720000e-156 560
30 TraesCS7D01G432100 chr3D 88.095 336 27 6 2453 2779 500221760 500221429 1.210000e-103 387
31 TraesCS7D01G432100 chr3D 85.152 330 41 8 1882 2206 442500782 442501108 5.740000e-87 331
32 TraesCS7D01G432100 chr3D 83.758 314 29 13 2284 2586 500222612 500222310 7.580000e-71 278
33 TraesCS7D01G432100 chr3D 81.538 130 21 1 2305 2434 610746637 610746511 1.360000e-18 104
34 TraesCS7D01G432100 chr6A 90.887 417 28 7 1882 2293 582917329 582916918 4.050000e-153 551
35 TraesCS7D01G432100 chr6A 85.646 418 43 12 1884 2293 426961225 426961633 9.200000e-115 424
36 TraesCS7D01G432100 chr6A 84.314 357 33 11 2442 2779 582916592 582916240 7.420000e-86 327
37 TraesCS7D01G432100 chr6A 79.104 201 23 16 2401 2586 48905897 48906093 1.350000e-23 121
38 TraesCS7D01G432100 chr6A 95.522 67 3 0 1264 1330 105168425 105168491 1.050000e-19 108
39 TraesCS7D01G432100 chr6D 93.872 359 20 1 1 357 47186872 47186514 8.760000e-150 540
40 TraesCS7D01G432100 chr4D 93.732 351 20 2 8 357 13253607 13253956 2.450000e-145 525
41 TraesCS7D01G432100 chr4D 85.075 335 39 11 1881 2209 3874743 3874414 5.740000e-87 331
42 TraesCS7D01G432100 chr6B 93.017 358 18 4 1 357 124627388 124627739 1.480000e-142 516
43 TraesCS7D01G432100 chr6B 88.783 419 30 12 1872 2287 581289133 581289537 5.350000e-137 497
44 TraesCS7D01G432100 chr6B 85.657 502 38 12 2284 2754 581289706 581290204 5.350000e-137 497
45 TraesCS7D01G432100 chr6B 84.538 498 51 21 2284 2779 603768247 603768720 1.170000e-128 470
46 TraesCS7D01G432100 chr6B 87.470 415 32 10 1878 2287 603767679 603768078 7.010000e-126 460
47 TraesCS7D01G432100 chr5B 92.244 361 26 2 1 361 477557675 477558033 6.870000e-141 510
48 TraesCS7D01G432100 chr5B 78.109 201 25 16 2401 2586 595142460 595142264 2.930000e-20 110
49 TraesCS7D01G432100 chr3B 84.420 276 21 9 2507 2779 783139781 783140037 4.590000e-63 252
50 TraesCS7D01G432100 chr3B 90.643 171 15 1 2609 2779 29689118 29689287 2.780000e-55 226
51 TraesCS7D01G432100 chr3B 81.503 173 18 10 2401 2562 783139587 783139756 2.250000e-26 130
52 TraesCS7D01G432100 chr1D 90.323 93 9 0 2337 2429 370340794 370340886 3.760000e-24 122
53 TraesCS7D01G432100 chr2A 79.104 201 23 16 2401 2586 758319377 758319573 1.350000e-23 121


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 TraesCS7D01G432100 chr7D 551807331 551810109 2778 True 5132.000000 5132 100.000000 1 2779 1 chr7D.!!$R3 2778
1 TraesCS7D01G432100 chr7D 551927724 551928655 931 True 1086.000000 1086 88.025000 884 1811 1 chr7D.!!$R4 927
2 TraesCS7D01G432100 chr7D 550999551 551000372 821 True 682.000000 682 82.042000 968 1802 1 chr7D.!!$R1 834
3 TraesCS7D01G432100 chr7D 551499909 551500682 773 True 568.000000 568 80.348000 972 1759 1 chr7D.!!$R2 787
4 TraesCS7D01G432100 chr7D 551113973 551114731 758 True 433.000000 446 87.059000 884 1708 2 chr7D.!!$R6 824
5 TraesCS7D01G432100 chr7B 596679912 596681545 1633 True 1032.000000 1365 93.729000 377 1861 2 chr7B.!!$R7 1484
6 TraesCS7D01G432100 chr7B 596781785 596782523 738 True 763.000000 763 85.333000 1056 1802 1 chr7B.!!$R6 746
7 TraesCS7D01G432100 chr7B 595881468 595882196 728 True 667.000000 667 83.445000 972 1708 1 chr7B.!!$R2 736
8 TraesCS7D01G432100 chr7B 596515343 596516148 805 True 595.000000 595 80.572000 972 1788 1 chr7B.!!$R4 816
9 TraesCS7D01G432100 chr7B 596538179 596538984 805 True 590.000000 590 80.430000 972 1788 1 chr7B.!!$R5 816
10 TraesCS7D01G432100 chr7B 488397839 488398917 1078 False 508.500000 579 87.259000 1882 2779 2 chr7B.!!$F1 897
11 TraesCS7D01G432100 chr7A 637336110 637337034 924 True 1031.000000 1031 87.182000 894 1811 1 chr7A.!!$R4 917
12 TraesCS7D01G432100 chr7A 637035993 637036801 808 True 880.000000 880 86.667000 884 1698 1 chr7A.!!$R3 814
13 TraesCS7D01G432100 chr7A 636918895 636919475 580 True 551.000000 551 83.953000 1112 1697 1 chr7A.!!$R2 585
14 TraesCS7D01G432100 chr7A 547713622 547714439 817 True 412.500000 534 88.898500 1882 2534 2 chr7A.!!$R5 652
15 TraesCS7D01G432100 chr2D 610707534 610708601 1067 False 570.000000 582 89.930000 1882 2779 2 chr2D.!!$F3 897
16 TraesCS7D01G432100 chr3D 500221429 500223179 1750 True 408.333333 560 87.813333 1883 2779 3 chr3D.!!$R2 896
17 TraesCS7D01G432100 chr6A 582916240 582917329 1089 True 439.000000 551 87.600500 1882 2779 2 chr6A.!!$R1 897
18 TraesCS7D01G432100 chr6B 581289133 581290204 1071 False 497.000000 497 87.220000 1872 2754 2 chr6B.!!$F2 882
19 TraesCS7D01G432100 chr6B 603767679 603768720 1041 False 465.000000 470 86.004000 1878 2779 2 chr6B.!!$F3 901

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
343 344 0.103937 CCTTCATGGAGCTCGGTCTC 59.896 60.0 7.83 0.0 38.35 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1866 2185 0.035739 TACTCGTTCCAAACAGCCCC 59.964 55.0 0.0 0.0 0.0 5.8 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
64 65 7.408756 AAAATACACATGTATGCAAGGATGT 57.591 32.000 0.00 0.00 40.78 3.06
65 66 8.518430 AAAATACACATGTATGCAAGGATGTA 57.482 30.769 0.00 4.93 40.78 2.29
66 67 8.518430 AAATACACATGTATGCAAGGATGTAA 57.482 30.769 0.00 1.61 40.78 2.41
67 68 8.518430 AATACACATGTATGCAAGGATGTAAA 57.482 30.769 0.00 1.34 40.78 2.01
68 69 6.832520 ACACATGTATGCAAGGATGTAAAA 57.167 33.333 0.00 0.00 0.00 1.52
69 70 7.408756 ACACATGTATGCAAGGATGTAAAAT 57.591 32.000 0.00 0.00 0.00 1.82
70 71 7.259882 ACACATGTATGCAAGGATGTAAAATG 58.740 34.615 0.00 0.00 0.00 2.32
71 72 6.199531 CACATGTATGCAAGGATGTAAAATGC 59.800 38.462 0.00 0.00 37.52 3.56
75 76 4.804868 TGCAAGGATGTAAAATGCATGT 57.195 36.364 0.00 0.00 41.67 3.21
76 77 4.496360 TGCAAGGATGTAAAATGCATGTG 58.504 39.130 0.00 0.00 41.67 3.21
77 78 4.021280 TGCAAGGATGTAAAATGCATGTGT 60.021 37.500 0.00 0.00 41.67 3.72
78 79 4.327898 GCAAGGATGTAAAATGCATGTGTG 59.672 41.667 0.00 0.00 37.00 3.82
79 80 5.712004 CAAGGATGTAAAATGCATGTGTGA 58.288 37.500 0.00 0.00 0.00 3.58
80 81 5.981088 AGGATGTAAAATGCATGTGTGAA 57.019 34.783 0.00 0.00 0.00 3.18
81 82 6.343716 AGGATGTAAAATGCATGTGTGAAA 57.656 33.333 0.00 0.00 0.00 2.69
82 83 6.757237 AGGATGTAAAATGCATGTGTGAAAA 58.243 32.000 0.00 0.00 0.00 2.29
83 84 7.215789 AGGATGTAAAATGCATGTGTGAAAAA 58.784 30.769 0.00 0.00 0.00 1.94
84 85 7.879160 AGGATGTAAAATGCATGTGTGAAAAAT 59.121 29.630 0.00 0.00 0.00 1.82
85 86 8.505625 GGATGTAAAATGCATGTGTGAAAAATT 58.494 29.630 0.00 0.00 0.00 1.82
86 87 9.881529 GATGTAAAATGCATGTGTGAAAAATTT 57.118 25.926 0.00 0.00 0.00 1.82
87 88 9.881529 ATGTAAAATGCATGTGTGAAAAATTTC 57.118 25.926 0.00 0.00 37.69 2.17
88 89 8.886719 TGTAAAATGCATGTGTGAAAAATTTCA 58.113 25.926 0.00 4.52 44.31 2.69
89 90 9.372541 GTAAAATGCATGTGTGAAAAATTTCAG 57.627 29.630 8.76 0.00 46.80 3.02
90 91 6.548441 AATGCATGTGTGAAAAATTTCAGG 57.452 33.333 8.76 0.00 46.80 3.86
91 92 5.273674 TGCATGTGTGAAAAATTTCAGGA 57.726 34.783 8.76 0.00 46.80 3.86
92 93 5.856156 TGCATGTGTGAAAAATTTCAGGAT 58.144 33.333 8.76 0.00 46.80 3.24
93 94 5.697178 TGCATGTGTGAAAAATTTCAGGATG 59.303 36.000 8.76 11.29 46.80 3.51
94 95 5.927689 GCATGTGTGAAAAATTTCAGGATGA 59.072 36.000 17.52 2.71 46.80 2.92
110 111 7.395190 TCAGGATGAAATACCTTGAATTGTG 57.605 36.000 0.00 0.00 45.97 3.33
111 112 7.174413 TCAGGATGAAATACCTTGAATTGTGA 58.826 34.615 0.00 0.00 45.97 3.58
112 113 7.337689 TCAGGATGAAATACCTTGAATTGTGAG 59.662 37.037 0.00 0.00 45.97 3.51
113 114 6.096001 AGGATGAAATACCTTGAATTGTGAGC 59.904 38.462 0.00 0.00 31.95 4.26
114 115 6.096001 GGATGAAATACCTTGAATTGTGAGCT 59.904 38.462 0.00 0.00 0.00 4.09
115 116 6.258230 TGAAATACCTTGAATTGTGAGCTG 57.742 37.500 0.00 0.00 0.00 4.24
116 117 4.708726 AATACCTTGAATTGTGAGCTGC 57.291 40.909 0.00 0.00 0.00 5.25
117 118 1.985473 ACCTTGAATTGTGAGCTGCA 58.015 45.000 1.02 0.00 0.00 4.41
152 153 9.696917 ACAAAATCATGGACTTTAAAGATGAAC 57.303 29.630 21.92 7.20 0.00 3.18
153 154 9.695526 CAAAATCATGGACTTTAAAGATGAACA 57.304 29.630 21.92 12.00 0.00 3.18
154 155 9.918630 AAAATCATGGACTTTAAAGATGAACAG 57.081 29.630 21.92 5.57 0.00 3.16
155 156 8.641498 AATCATGGACTTTAAAGATGAACAGT 57.359 30.769 21.92 3.41 0.00 3.55
156 157 9.739276 AATCATGGACTTTAAAGATGAACAGTA 57.261 29.630 21.92 5.83 0.00 2.74
157 158 8.547967 TCATGGACTTTAAAGATGAACAGTAC 57.452 34.615 21.92 0.00 0.00 2.73
158 159 8.154203 TCATGGACTTTAAAGATGAACAGTACA 58.846 33.333 21.92 4.66 29.71 2.90
159 160 8.950210 CATGGACTTTAAAGATGAACAGTACAT 58.050 33.333 21.92 6.87 36.43 2.29
172 173 9.413048 GATGAACAGTACATATACTAAAGAGCC 57.587 37.037 0.00 0.00 39.80 4.70
173 174 7.723324 TGAACAGTACATATACTAAAGAGCCC 58.277 38.462 0.00 0.00 39.80 5.19
174 175 6.667558 ACAGTACATATACTAAAGAGCCCC 57.332 41.667 0.00 0.00 39.80 5.80
175 176 6.141083 ACAGTACATATACTAAAGAGCCCCA 58.859 40.000 0.00 0.00 39.80 4.96
176 177 6.267928 ACAGTACATATACTAAAGAGCCCCAG 59.732 42.308 0.00 0.00 39.80 4.45
177 178 6.493802 CAGTACATATACTAAAGAGCCCCAGA 59.506 42.308 0.00 0.00 39.80 3.86
178 179 7.179338 CAGTACATATACTAAAGAGCCCCAGAT 59.821 40.741 0.00 0.00 39.80 2.90
179 180 7.735321 AGTACATATACTAAAGAGCCCCAGATT 59.265 37.037 0.00 0.00 40.02 2.40
180 181 7.394144 ACATATACTAAAGAGCCCCAGATTT 57.606 36.000 0.00 0.00 0.00 2.17
181 182 7.227156 ACATATACTAAAGAGCCCCAGATTTG 58.773 38.462 0.00 0.00 0.00 2.32
182 183 5.717119 ATACTAAAGAGCCCCAGATTTGT 57.283 39.130 0.00 0.00 0.00 2.83
183 184 3.956744 ACTAAAGAGCCCCAGATTTGTC 58.043 45.455 0.00 0.00 0.00 3.18
184 185 3.589288 ACTAAAGAGCCCCAGATTTGTCT 59.411 43.478 0.00 0.00 0.00 3.41
185 186 3.532641 AAAGAGCCCCAGATTTGTCTT 57.467 42.857 0.00 0.00 0.00 3.01
186 187 3.532641 AAGAGCCCCAGATTTGTCTTT 57.467 42.857 0.00 0.00 0.00 2.52
187 188 3.532641 AGAGCCCCAGATTTGTCTTTT 57.467 42.857 0.00 0.00 0.00 2.27
188 189 3.849527 AGAGCCCCAGATTTGTCTTTTT 58.150 40.909 0.00 0.00 0.00 1.94
215 216 8.870242 GTGTAGGTCACGTTTTAATGTATTTC 57.130 34.615 0.00 0.00 37.31 2.17
216 217 7.685304 GTGTAGGTCACGTTTTAATGTATTTCG 59.315 37.037 0.00 0.00 37.31 3.46
217 218 7.598118 TGTAGGTCACGTTTTAATGTATTTCGA 59.402 33.333 0.00 0.00 0.00 3.71
218 219 6.824557 AGGTCACGTTTTAATGTATTTCGAC 58.175 36.000 0.00 0.00 0.00 4.20
219 220 6.017325 GGTCACGTTTTAATGTATTTCGACC 58.983 40.000 0.00 0.00 32.44 4.79
220 221 6.128472 GGTCACGTTTTAATGTATTTCGACCT 60.128 38.462 11.26 0.00 35.11 3.85
221 222 7.063308 GGTCACGTTTTAATGTATTTCGACCTA 59.937 37.037 11.26 0.00 35.11 3.08
222 223 8.434661 GTCACGTTTTAATGTATTTCGACCTAA 58.565 33.333 0.00 0.00 0.00 2.69
223 224 8.986847 TCACGTTTTAATGTATTTCGACCTAAA 58.013 29.630 0.00 0.00 0.00 1.85
224 225 9.596677 CACGTTTTAATGTATTTCGACCTAAAA 57.403 29.630 0.00 0.00 0.00 1.52
230 231 9.997482 TTAATGTATTTCGACCTAAAAATCTGC 57.003 29.630 0.00 0.00 0.00 4.26
231 232 7.624360 ATGTATTTCGACCTAAAAATCTGCA 57.376 32.000 0.00 0.00 0.00 4.41
232 233 6.837992 TGTATTTCGACCTAAAAATCTGCAC 58.162 36.000 0.00 0.00 0.00 4.57
233 234 5.957842 ATTTCGACCTAAAAATCTGCACA 57.042 34.783 0.00 0.00 0.00 4.57
234 235 4.742438 TTCGACCTAAAAATCTGCACAC 57.258 40.909 0.00 0.00 0.00 3.82
235 236 3.734463 TCGACCTAAAAATCTGCACACA 58.266 40.909 0.00 0.00 0.00 3.72
236 237 4.323417 TCGACCTAAAAATCTGCACACAT 58.677 39.130 0.00 0.00 0.00 3.21
237 238 4.154015 TCGACCTAAAAATCTGCACACATG 59.846 41.667 0.00 0.00 0.00 3.21
238 239 4.083324 CGACCTAAAAATCTGCACACATGT 60.083 41.667 0.00 0.00 0.00 3.21
239 240 5.121611 CGACCTAAAAATCTGCACACATGTA 59.878 40.000 0.00 0.00 0.00 2.29
240 241 6.254281 ACCTAAAAATCTGCACACATGTAC 57.746 37.500 0.00 0.00 0.00 2.90
241 242 5.767665 ACCTAAAAATCTGCACACATGTACA 59.232 36.000 0.00 0.00 0.00 2.90
242 243 6.434028 ACCTAAAAATCTGCACACATGTACAT 59.566 34.615 1.41 1.41 0.00 2.29
243 244 7.039784 ACCTAAAAATCTGCACACATGTACATT 60.040 33.333 5.37 0.00 0.00 2.71
244 245 8.458052 CCTAAAAATCTGCACACATGTACATTA 58.542 33.333 5.37 0.00 0.00 1.90
246 247 8.692110 AAAAATCTGCACACATGTACATTATG 57.308 30.769 5.37 10.25 0.00 1.90
247 248 7.395190 AAATCTGCACACATGTACATTATGT 57.605 32.000 14.24 14.24 39.23 2.29
248 249 8.504812 AAATCTGCACACATGTACATTATGTA 57.495 30.769 17.98 0.29 36.67 2.29
249 250 8.681486 AATCTGCACACATGTACATTATGTAT 57.319 30.769 17.98 8.77 36.67 2.29
250 251 9.777297 AATCTGCACACATGTACATTATGTATA 57.223 29.630 17.98 6.31 36.67 1.47
251 252 9.948964 ATCTGCACACATGTACATTATGTATAT 57.051 29.630 17.98 8.44 35.47 0.86
329 330 7.118496 TGAAGTTTTCAAATAAAGGCCTTCA 57.882 32.000 20.79 3.87 36.59 3.02
330 331 7.734942 TGAAGTTTTCAAATAAAGGCCTTCAT 58.265 30.769 20.79 6.96 36.59 2.57
331 332 7.656948 TGAAGTTTTCAAATAAAGGCCTTCATG 59.343 33.333 20.79 14.99 36.59 3.07
332 333 6.466812 AGTTTTCAAATAAAGGCCTTCATGG 58.533 36.000 20.79 6.33 39.35 3.66
333 334 6.269769 AGTTTTCAAATAAAGGCCTTCATGGA 59.730 34.615 20.79 8.83 38.35 3.41
334 335 5.920193 TTCAAATAAAGGCCTTCATGGAG 57.080 39.130 20.79 7.92 38.35 3.86
335 336 3.701040 TCAAATAAAGGCCTTCATGGAGC 59.299 43.478 20.79 0.00 38.35 4.70
336 337 3.677156 AATAAAGGCCTTCATGGAGCT 57.323 42.857 20.79 2.41 38.35 4.09
337 338 2.717639 TAAAGGCCTTCATGGAGCTC 57.282 50.000 20.79 4.71 38.35 4.09
338 339 0.393537 AAAGGCCTTCATGGAGCTCG 60.394 55.000 20.79 0.00 38.35 5.03
339 340 2.203126 GGCCTTCATGGAGCTCGG 60.203 66.667 7.83 2.99 38.35 4.63
340 341 2.586792 GCCTTCATGGAGCTCGGT 59.413 61.111 7.83 0.00 38.35 4.69
341 342 1.522580 GCCTTCATGGAGCTCGGTC 60.523 63.158 7.83 0.00 38.35 4.79
342 343 1.965754 GCCTTCATGGAGCTCGGTCT 61.966 60.000 7.83 0.00 38.35 3.85
343 344 0.103937 CCTTCATGGAGCTCGGTCTC 59.896 60.000 7.83 0.00 38.35 3.36
354 355 3.981308 CGGTCTCCGTTTGGCATT 58.019 55.556 0.00 0.00 42.73 3.56
355 356 2.253513 CGGTCTCCGTTTGGCATTT 58.746 52.632 0.00 0.00 42.73 2.32
356 357 0.596082 CGGTCTCCGTTTGGCATTTT 59.404 50.000 0.00 0.00 42.73 1.82
357 358 1.000717 CGGTCTCCGTTTGGCATTTTT 60.001 47.619 0.00 0.00 42.73 1.94
358 359 2.403259 GGTCTCCGTTTGGCATTTTTG 58.597 47.619 0.00 0.00 34.14 2.44
359 360 2.403259 GTCTCCGTTTGGCATTTTTGG 58.597 47.619 0.00 0.00 34.14 3.28
360 361 2.035632 TCTCCGTTTGGCATTTTTGGT 58.964 42.857 0.00 0.00 34.14 3.67
361 362 2.432510 TCTCCGTTTGGCATTTTTGGTT 59.567 40.909 0.00 0.00 34.14 3.67
362 363 2.799978 CTCCGTTTGGCATTTTTGGTTC 59.200 45.455 0.00 0.00 34.14 3.62
363 364 2.432510 TCCGTTTGGCATTTTTGGTTCT 59.567 40.909 0.00 0.00 34.14 3.01
364 365 3.637229 TCCGTTTGGCATTTTTGGTTCTA 59.363 39.130 0.00 0.00 34.14 2.10
365 366 4.282195 TCCGTTTGGCATTTTTGGTTCTAT 59.718 37.500 0.00 0.00 34.14 1.98
366 367 4.994217 CCGTTTGGCATTTTTGGTTCTATT 59.006 37.500 0.00 0.00 0.00 1.73
367 368 5.120053 CCGTTTGGCATTTTTGGTTCTATTC 59.880 40.000 0.00 0.00 0.00 1.75
368 369 5.925969 CGTTTGGCATTTTTGGTTCTATTCT 59.074 36.000 0.00 0.00 0.00 2.40
369 370 6.089417 CGTTTGGCATTTTTGGTTCTATTCTC 59.911 38.462 0.00 0.00 0.00 2.87
370 371 6.916360 TTGGCATTTTTGGTTCTATTCTCT 57.084 33.333 0.00 0.00 0.00 3.10
371 372 6.271488 TGGCATTTTTGGTTCTATTCTCTG 57.729 37.500 0.00 0.00 0.00 3.35
372 373 5.774690 TGGCATTTTTGGTTCTATTCTCTGT 59.225 36.000 0.00 0.00 0.00 3.41
373 374 6.267471 TGGCATTTTTGGTTCTATTCTCTGTT 59.733 34.615 0.00 0.00 0.00 3.16
374 375 6.587608 GGCATTTTTGGTTCTATTCTCTGTTG 59.412 38.462 0.00 0.00 0.00 3.33
375 376 6.587608 GCATTTTTGGTTCTATTCTCTGTTGG 59.412 38.462 0.00 0.00 0.00 3.77
386 387 7.608153 TCTATTCTCTGTTGGATTGTTCGTTA 58.392 34.615 0.00 0.00 0.00 3.18
432 433 7.593875 TTGAAGCAATGTGGTAAAAATATGC 57.406 32.000 0.00 0.00 0.00 3.14
458 459 8.773645 CATTCGTCACTTGGAAGCAATATAATA 58.226 33.333 0.00 0.00 0.00 0.98
509 510 5.230306 CGGAGCATCTTTACTAGTTTCGAAG 59.770 44.000 0.00 1.41 33.73 3.79
539 540 4.631813 ACTAGATGGAAGCAATGTTCGTTC 59.368 41.667 0.00 0.00 0.00 3.95
560 561 3.316588 TCGTCTATGAAGCAGTCTCCATC 59.683 47.826 0.00 0.00 0.00 3.51
576 577 5.406477 GTCTCCATCACAAGCAAAATTTTCC 59.594 40.000 0.00 0.00 0.00 3.13
633 634 5.922544 AGATTTTTGCAGCAATCAGTAACAC 59.077 36.000 9.12 0.00 32.61 3.32
635 636 4.645762 TTTGCAGCAATCAGTAACACAA 57.354 36.364 9.12 0.00 0.00 3.33
741 743 7.019418 ACGTTCCTTAAATGCGAAATTAGTTC 58.981 34.615 0.00 0.00 0.00 3.01
781 784 7.636150 ACAGAATCAGCAAGCAGTTAATATT 57.364 32.000 0.00 0.00 0.00 1.28
815 818 4.164822 ACAAGGAAGCAATCAATCAACG 57.835 40.909 0.00 0.00 0.00 4.10
825 828 6.732154 AGCAATCAATCAACGAATGGAATAG 58.268 36.000 0.00 0.00 0.00 1.73
844 911 1.415659 AGCCACTAGTCTGATGGATGC 59.584 52.381 8.11 0.00 35.33 3.91
845 912 1.415659 GCCACTAGTCTGATGGATGCT 59.584 52.381 8.11 0.00 35.33 3.79
1384 1651 2.821366 TCCTCGAGGCCGTACGTC 60.821 66.667 27.39 0.00 37.05 4.34
1425 1699 0.383002 GTGCGTTCGTCACACACATG 60.383 55.000 12.13 0.00 38.20 3.21
1428 1709 1.136721 GCGTTCGTCACACACATGTAC 60.137 52.381 0.00 0.00 36.72 2.90
1488 1770 0.537653 GGTAGAGAAGGCACCTCACC 59.462 60.000 8.50 9.27 33.25 4.02
1650 1940 0.458543 CGAGTTCCTGGACGATGTGG 60.459 60.000 0.00 0.00 0.00 4.17
1655 1945 0.109532 TCCTGGACGATGTGGCAAAA 59.890 50.000 0.00 0.00 0.00 2.44
1861 2180 8.956426 AGGTCTAGCATTTTCGATTCAAATAAA 58.044 29.630 0.00 0.00 0.00 1.40
1862 2181 9.226345 GGTCTAGCATTTTCGATTCAAATAAAG 57.774 33.333 0.00 0.00 0.00 1.85
1863 2182 9.774742 GTCTAGCATTTTCGATTCAAATAAAGT 57.225 29.630 0.00 0.00 0.00 2.66
1867 2186 8.711457 AGCATTTTCGATTCAAATAAAGTTTGG 58.289 29.630 0.00 0.00 0.00 3.28
1868 2187 7.956943 GCATTTTCGATTCAAATAAAGTTTGGG 59.043 33.333 0.00 0.00 0.00 4.12
1869 2188 7.954788 TTTTCGATTCAAATAAAGTTTGGGG 57.045 32.000 0.00 0.00 0.00 4.96
1870 2189 5.066968 TCGATTCAAATAAAGTTTGGGGC 57.933 39.130 0.00 0.00 0.00 5.80
1879 2198 1.872773 AAGTTTGGGGCTGTTTGGAA 58.127 45.000 0.00 0.00 0.00 3.53
1981 2306 7.285401 ACACCATGTCTTCAGTAATCTTTTTGT 59.715 33.333 0.00 0.00 0.00 2.83
2047 2372 3.396276 TGACAGATGGGTCCCTGTTTTTA 59.604 43.478 10.00 0.00 43.02 1.52
2051 2376 4.218417 CAGATGGGTCCCTGTTTTTACTTG 59.782 45.833 10.00 0.00 0.00 3.16
2149 2475 5.301551 ACCCCTTAATAAAAACCGAAAACGT 59.698 36.000 0.00 0.00 0.00 3.99
2185 2513 1.005294 CACAAAATCGGCAGCACAGC 61.005 55.000 0.00 0.00 0.00 4.40
2186 2514 1.798725 CAAAATCGGCAGCACAGCG 60.799 57.895 0.00 0.00 34.64 5.18
2187 2515 3.615536 AAAATCGGCAGCACAGCGC 62.616 57.895 0.00 0.00 42.91 5.92
2215 2556 2.171489 GACGCGAGCAAAACAGGACC 62.171 60.000 15.93 0.00 0.00 4.46
2222 2563 0.534203 GCAAAACAGGACCCTCGTCA 60.534 55.000 0.00 0.00 41.13 4.35
2252 2593 0.834687 GGTGGCTATCGGGGTATGGA 60.835 60.000 0.00 0.00 0.00 3.41
2294 2808 2.526888 TGAGGGTTAGAGATGGTCGT 57.473 50.000 0.00 0.00 0.00 4.34
2339 2854 2.125106 GGGGATGTGGACGCTGTC 60.125 66.667 0.79 0.79 0.00 3.51
2660 3888 1.895131 GGCTGCATGGAGGAAGAAAAA 59.105 47.619 16.65 0.00 0.00 1.94
2663 3891 4.440663 GGCTGCATGGAGGAAGAAAAATAC 60.441 45.833 16.65 0.00 0.00 1.89
2669 3897 3.585732 TGGAGGAAGAAAAATACGGGACT 59.414 43.478 0.00 0.00 0.00 3.85
2698 3926 3.243035 GCTTTAAACCCAAACCGTTACGT 60.243 43.478 3.52 0.00 0.00 3.57
2700 3928 0.936600 AAACCCAAACCGTTACGTCG 59.063 50.000 3.52 0.00 0.00 5.12
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
39 40 7.839907 ACATCCTTGCATACATGTGTATTTTT 58.160 30.769 9.11 0.00 39.06 1.94
40 41 7.408756 ACATCCTTGCATACATGTGTATTTT 57.591 32.000 9.11 0.00 39.06 1.82
41 42 8.518430 TTACATCCTTGCATACATGTGTATTT 57.482 30.769 9.11 0.00 39.06 1.40
42 43 8.518430 TTTACATCCTTGCATACATGTGTATT 57.482 30.769 9.11 0.00 39.06 1.89
43 44 8.518430 TTTTACATCCTTGCATACATGTGTAT 57.482 30.769 9.11 0.00 41.58 2.29
44 45 7.929941 TTTTACATCCTTGCATACATGTGTA 57.070 32.000 9.11 0.00 31.83 2.90
45 46 6.832520 TTTTACATCCTTGCATACATGTGT 57.167 33.333 9.11 0.00 31.83 3.72
46 47 6.199531 GCATTTTACATCCTTGCATACATGTG 59.800 38.462 9.11 0.00 33.58 3.21
47 48 6.127394 TGCATTTTACATCCTTGCATACATGT 60.127 34.615 2.69 2.69 38.32 3.21
48 49 6.274579 TGCATTTTACATCCTTGCATACATG 58.725 36.000 0.00 0.00 38.32 3.21
49 50 6.468333 TGCATTTTACATCCTTGCATACAT 57.532 33.333 0.00 0.00 38.32 2.29
50 51 5.911378 TGCATTTTACATCCTTGCATACA 57.089 34.783 0.00 0.00 38.32 2.29
54 55 4.021280 ACACATGCATTTTACATCCTTGCA 60.021 37.500 0.00 0.00 46.22 4.08
55 56 4.327898 CACACATGCATTTTACATCCTTGC 59.672 41.667 0.00 0.00 0.00 4.01
56 57 5.712004 TCACACATGCATTTTACATCCTTG 58.288 37.500 0.00 0.00 0.00 3.61
57 58 5.981088 TCACACATGCATTTTACATCCTT 57.019 34.783 0.00 0.00 0.00 3.36
58 59 5.981088 TTCACACATGCATTTTACATCCT 57.019 34.783 0.00 0.00 0.00 3.24
59 60 7.418840 TTTTTCACACATGCATTTTACATCC 57.581 32.000 0.00 0.00 0.00 3.51
60 61 9.881529 AAATTTTTCACACATGCATTTTACATC 57.118 25.926 0.00 0.00 0.00 3.06
61 62 9.881529 GAAATTTTTCACACATGCATTTTACAT 57.118 25.926 0.00 0.00 37.15 2.29
62 63 8.886719 TGAAATTTTTCACACATGCATTTTACA 58.113 25.926 0.00 0.00 41.88 2.41
63 64 9.372541 CTGAAATTTTTCACACATGCATTTTAC 57.627 29.630 0.00 0.00 41.88 2.01
64 65 8.557864 CCTGAAATTTTTCACACATGCATTTTA 58.442 29.630 0.00 0.00 41.88 1.52
65 66 7.282675 TCCTGAAATTTTTCACACATGCATTTT 59.717 29.630 0.00 0.00 41.88 1.82
66 67 6.766944 TCCTGAAATTTTTCACACATGCATTT 59.233 30.769 0.00 0.00 41.88 2.32
67 68 6.289834 TCCTGAAATTTTTCACACATGCATT 58.710 32.000 0.00 0.00 41.88 3.56
68 69 5.856156 TCCTGAAATTTTTCACACATGCAT 58.144 33.333 0.00 0.00 41.88 3.96
69 70 5.273674 TCCTGAAATTTTTCACACATGCA 57.726 34.783 1.66 0.00 41.88 3.96
70 71 5.927689 TCATCCTGAAATTTTTCACACATGC 59.072 36.000 1.66 0.00 41.88 4.06
71 72 7.949903 TTCATCCTGAAATTTTTCACACATG 57.050 32.000 1.66 0.00 41.88 3.21
85 86 7.669304 TCACAATTCAAGGTATTTCATCCTGAA 59.331 33.333 0.00 0.00 34.03 3.02
86 87 7.174413 TCACAATTCAAGGTATTTCATCCTGA 58.826 34.615 0.00 0.00 33.97 3.86
87 88 7.395190 TCACAATTCAAGGTATTTCATCCTG 57.605 36.000 0.00 0.00 33.97 3.86
88 89 6.096001 GCTCACAATTCAAGGTATTTCATCCT 59.904 38.462 0.00 0.00 35.34 3.24
89 90 6.096001 AGCTCACAATTCAAGGTATTTCATCC 59.904 38.462 0.00 0.00 0.00 3.51
90 91 6.971184 CAGCTCACAATTCAAGGTATTTCATC 59.029 38.462 0.00 0.00 0.00 2.92
91 92 6.626623 GCAGCTCACAATTCAAGGTATTTCAT 60.627 38.462 0.00 0.00 0.00 2.57
92 93 5.335897 GCAGCTCACAATTCAAGGTATTTCA 60.336 40.000 0.00 0.00 0.00 2.69
93 94 5.098211 GCAGCTCACAATTCAAGGTATTTC 58.902 41.667 0.00 0.00 0.00 2.17
94 95 4.523943 TGCAGCTCACAATTCAAGGTATTT 59.476 37.500 0.00 0.00 0.00 1.40
95 96 4.081406 TGCAGCTCACAATTCAAGGTATT 58.919 39.130 0.00 0.00 0.00 1.89
96 97 3.441572 GTGCAGCTCACAATTCAAGGTAT 59.558 43.478 10.30 0.00 44.98 2.73
97 98 2.813754 GTGCAGCTCACAATTCAAGGTA 59.186 45.455 10.30 0.00 44.98 3.08
98 99 1.610522 GTGCAGCTCACAATTCAAGGT 59.389 47.619 10.30 0.00 44.98 3.50
99 100 2.342910 GTGCAGCTCACAATTCAAGG 57.657 50.000 10.30 0.00 44.98 3.61
126 127 9.696917 GTTCATCTTTAAAGTCCATGATTTTGT 57.303 29.630 14.74 0.00 0.00 2.83
127 128 9.695526 TGTTCATCTTTAAAGTCCATGATTTTG 57.304 29.630 14.74 0.53 0.00 2.44
128 129 9.918630 CTGTTCATCTTTAAAGTCCATGATTTT 57.081 29.630 14.74 0.00 0.00 1.82
129 130 9.082313 ACTGTTCATCTTTAAAGTCCATGATTT 57.918 29.630 14.74 0.00 0.00 2.17
130 131 8.641498 ACTGTTCATCTTTAAAGTCCATGATT 57.359 30.769 14.74 1.07 0.00 2.57
131 132 9.167311 GTACTGTTCATCTTTAAAGTCCATGAT 57.833 33.333 14.74 5.19 0.00 2.45
132 133 8.154203 TGTACTGTTCATCTTTAAAGTCCATGA 58.846 33.333 14.74 13.14 0.00 3.07
133 134 8.322906 TGTACTGTTCATCTTTAAAGTCCATG 57.677 34.615 14.74 11.19 0.00 3.66
146 147 9.413048 GGCTCTTTAGTATATGTACTGTTCATC 57.587 37.037 12.05 0.00 41.22 2.92
147 148 8.368668 GGGCTCTTTAGTATATGTACTGTTCAT 58.631 37.037 12.05 5.26 41.22 2.57
148 149 7.201974 GGGGCTCTTTAGTATATGTACTGTTCA 60.202 40.741 12.05 0.00 41.22 3.18
149 150 7.153315 GGGGCTCTTTAGTATATGTACTGTTC 58.847 42.308 12.05 0.00 41.22 3.18
150 151 6.614087 TGGGGCTCTTTAGTATATGTACTGTT 59.386 38.462 12.05 0.00 41.22 3.16
151 152 6.141083 TGGGGCTCTTTAGTATATGTACTGT 58.859 40.000 12.05 0.00 41.22 3.55
152 153 6.493802 TCTGGGGCTCTTTAGTATATGTACTG 59.506 42.308 12.05 0.00 41.22 2.74
153 154 6.621394 TCTGGGGCTCTTTAGTATATGTACT 58.379 40.000 7.35 7.35 43.45 2.73
154 155 6.912951 TCTGGGGCTCTTTAGTATATGTAC 57.087 41.667 0.00 0.00 0.00 2.90
155 156 8.375506 CAAATCTGGGGCTCTTTAGTATATGTA 58.624 37.037 0.00 0.00 0.00 2.29
156 157 7.147302 ACAAATCTGGGGCTCTTTAGTATATGT 60.147 37.037 0.00 0.00 0.00 2.29
157 158 7.227156 ACAAATCTGGGGCTCTTTAGTATATG 58.773 38.462 0.00 0.00 0.00 1.78
158 159 7.293535 AGACAAATCTGGGGCTCTTTAGTATAT 59.706 37.037 0.00 0.00 32.29 0.86
159 160 6.615726 AGACAAATCTGGGGCTCTTTAGTATA 59.384 38.462 0.00 0.00 32.29 1.47
160 161 5.430089 AGACAAATCTGGGGCTCTTTAGTAT 59.570 40.000 0.00 0.00 32.29 2.12
161 162 4.783227 AGACAAATCTGGGGCTCTTTAGTA 59.217 41.667 0.00 0.00 32.29 1.82
162 163 3.589288 AGACAAATCTGGGGCTCTTTAGT 59.411 43.478 0.00 0.00 32.29 2.24
163 164 4.227864 AGACAAATCTGGGGCTCTTTAG 57.772 45.455 0.00 0.00 32.29 1.85
164 165 4.657814 AAGACAAATCTGGGGCTCTTTA 57.342 40.909 0.00 0.00 34.48 1.85
165 166 3.532641 AAGACAAATCTGGGGCTCTTT 57.467 42.857 0.00 0.00 34.48 2.52
166 167 3.532641 AAAGACAAATCTGGGGCTCTT 57.467 42.857 0.00 0.00 34.48 2.85
167 168 3.532641 AAAAGACAAATCTGGGGCTCT 57.467 42.857 0.00 0.00 34.48 4.09
190 191 7.685304 CGAAATACATTAAAACGTGACCTACAC 59.315 37.037 0.00 0.00 45.11 2.90
191 192 7.598118 TCGAAATACATTAAAACGTGACCTACA 59.402 33.333 0.00 0.00 0.00 2.74
192 193 7.894753 GTCGAAATACATTAAAACGTGACCTAC 59.105 37.037 0.00 0.00 0.00 3.18
193 194 7.063308 GGTCGAAATACATTAAAACGTGACCTA 59.937 37.037 0.00 0.00 38.32 3.08
194 195 6.128472 GGTCGAAATACATTAAAACGTGACCT 60.128 38.462 0.00 0.00 38.32 3.85
195 196 6.017325 GGTCGAAATACATTAAAACGTGACC 58.983 40.000 0.00 0.00 34.84 4.02
196 197 6.824557 AGGTCGAAATACATTAAAACGTGAC 58.175 36.000 0.00 0.00 0.00 3.67
197 198 8.531622 TTAGGTCGAAATACATTAAAACGTGA 57.468 30.769 0.00 0.00 0.00 4.35
198 199 9.596677 TTTTAGGTCGAAATACATTAAAACGTG 57.403 29.630 0.00 0.00 0.00 4.49
204 205 9.997482 GCAGATTTTTAGGTCGAAATACATTAA 57.003 29.630 0.00 0.00 0.00 1.40
205 206 9.168451 TGCAGATTTTTAGGTCGAAATACATTA 57.832 29.630 0.00 0.00 0.00 1.90
206 207 7.968405 GTGCAGATTTTTAGGTCGAAATACATT 59.032 33.333 0.00 0.00 0.00 2.71
207 208 7.120579 TGTGCAGATTTTTAGGTCGAAATACAT 59.879 33.333 0.00 0.00 0.00 2.29
208 209 6.428465 TGTGCAGATTTTTAGGTCGAAATACA 59.572 34.615 0.00 0.00 0.00 2.29
209 210 6.741358 GTGTGCAGATTTTTAGGTCGAAATAC 59.259 38.462 0.00 0.00 0.00 1.89
210 211 6.428465 TGTGTGCAGATTTTTAGGTCGAAATA 59.572 34.615 0.00 0.00 0.00 1.40
211 212 5.240623 TGTGTGCAGATTTTTAGGTCGAAAT 59.759 36.000 0.00 0.00 0.00 2.17
212 213 4.576873 TGTGTGCAGATTTTTAGGTCGAAA 59.423 37.500 0.00 0.00 0.00 3.46
213 214 4.130857 TGTGTGCAGATTTTTAGGTCGAA 58.869 39.130 0.00 0.00 0.00 3.71
214 215 3.734463 TGTGTGCAGATTTTTAGGTCGA 58.266 40.909 0.00 0.00 0.00 4.20
215 216 4.083324 ACATGTGTGCAGATTTTTAGGTCG 60.083 41.667 0.00 0.00 0.00 4.79
216 217 5.376854 ACATGTGTGCAGATTTTTAGGTC 57.623 39.130 0.00 0.00 0.00 3.85
217 218 5.767665 TGTACATGTGTGCAGATTTTTAGGT 59.232 36.000 9.11 0.00 35.76 3.08
218 219 6.252967 TGTACATGTGTGCAGATTTTTAGG 57.747 37.500 9.11 0.00 35.76 2.69
220 221 9.786105 CATAATGTACATGTGTGCAGATTTTTA 57.214 29.630 9.63 4.06 43.50 1.52
221 222 8.306038 ACATAATGTACATGTGTGCAGATTTTT 58.694 29.630 20.33 2.16 43.50 1.94
222 223 7.829725 ACATAATGTACATGTGTGCAGATTTT 58.170 30.769 20.33 2.48 43.50 1.82
223 224 7.395190 ACATAATGTACATGTGTGCAGATTT 57.605 32.000 20.33 2.78 43.50 2.17
224 225 8.681486 ATACATAATGTACATGTGTGCAGATT 57.319 30.769 25.77 1.22 43.50 2.40
225 226 9.948964 ATATACATAATGTACATGTGTGCAGAT 57.051 29.630 25.77 17.70 43.50 2.90
305 306 7.118496 TGAAGGCCTTTATTTGAAAACTTCA 57.882 32.000 21.54 4.52 39.33 3.02
306 307 7.118245 CCATGAAGGCCTTTATTTGAAAACTTC 59.882 37.037 21.54 1.46 34.11 3.01
307 308 6.936335 CCATGAAGGCCTTTATTTGAAAACTT 59.064 34.615 21.54 0.00 0.00 2.66
308 309 6.269769 TCCATGAAGGCCTTTATTTGAAAACT 59.730 34.615 21.54 0.00 37.29 2.66
309 310 6.463360 TCCATGAAGGCCTTTATTTGAAAAC 58.537 36.000 21.54 2.76 37.29 2.43
310 311 6.678568 TCCATGAAGGCCTTTATTTGAAAA 57.321 33.333 21.54 0.00 37.29 2.29
311 312 5.337491 GCTCCATGAAGGCCTTTATTTGAAA 60.337 40.000 21.54 3.38 37.29 2.69
312 313 4.160252 GCTCCATGAAGGCCTTTATTTGAA 59.840 41.667 21.54 5.11 37.29 2.69
313 314 3.701040 GCTCCATGAAGGCCTTTATTTGA 59.299 43.478 21.54 17.32 37.29 2.69
314 315 3.703052 AGCTCCATGAAGGCCTTTATTTG 59.297 43.478 21.54 14.05 37.29 2.32
315 316 3.956848 GAGCTCCATGAAGGCCTTTATTT 59.043 43.478 21.54 0.00 37.29 1.40
316 317 3.560105 GAGCTCCATGAAGGCCTTTATT 58.440 45.455 21.54 5.18 37.29 1.40
317 318 2.486191 CGAGCTCCATGAAGGCCTTTAT 60.486 50.000 21.54 18.94 37.29 1.40
318 319 1.134401 CGAGCTCCATGAAGGCCTTTA 60.134 52.381 21.54 17.17 37.29 1.85
319 320 0.393537 CGAGCTCCATGAAGGCCTTT 60.394 55.000 21.54 0.44 37.29 3.11
320 321 1.222936 CGAGCTCCATGAAGGCCTT 59.777 57.895 20.65 20.65 37.29 4.35
321 322 2.739996 CCGAGCTCCATGAAGGCCT 61.740 63.158 8.47 0.00 37.29 5.19
322 323 2.203126 CCGAGCTCCATGAAGGCC 60.203 66.667 8.47 0.00 37.29 5.19
323 324 1.522580 GACCGAGCTCCATGAAGGC 60.523 63.158 8.47 0.00 37.29 4.35
324 325 0.103937 GAGACCGAGCTCCATGAAGG 59.896 60.000 8.47 4.75 39.47 3.46
325 326 3.657956 GAGACCGAGCTCCATGAAG 57.342 57.895 8.47 0.00 0.00 3.02
338 339 2.403259 CAAAAATGCCAAACGGAGACC 58.597 47.619 0.00 0.00 0.00 3.85
339 340 2.223947 ACCAAAAATGCCAAACGGAGAC 60.224 45.455 0.00 0.00 0.00 3.36
340 341 2.035632 ACCAAAAATGCCAAACGGAGA 58.964 42.857 0.00 0.00 0.00 3.71
341 342 2.524569 ACCAAAAATGCCAAACGGAG 57.475 45.000 0.00 0.00 0.00 4.63
342 343 2.432510 AGAACCAAAAATGCCAAACGGA 59.567 40.909 0.00 0.00 0.00 4.69
343 344 2.832563 AGAACCAAAAATGCCAAACGG 58.167 42.857 0.00 0.00 0.00 4.44
344 345 5.925969 AGAATAGAACCAAAAATGCCAAACG 59.074 36.000 0.00 0.00 0.00 3.60
345 346 7.116805 CAGAGAATAGAACCAAAAATGCCAAAC 59.883 37.037 0.00 0.00 0.00 2.93
346 347 7.153985 CAGAGAATAGAACCAAAAATGCCAAA 58.846 34.615 0.00 0.00 0.00 3.28
347 348 6.267471 ACAGAGAATAGAACCAAAAATGCCAA 59.733 34.615 0.00 0.00 0.00 4.52
348 349 5.774690 ACAGAGAATAGAACCAAAAATGCCA 59.225 36.000 0.00 0.00 0.00 4.92
349 350 6.272822 ACAGAGAATAGAACCAAAAATGCC 57.727 37.500 0.00 0.00 0.00 4.40
350 351 6.587608 CCAACAGAGAATAGAACCAAAAATGC 59.412 38.462 0.00 0.00 0.00 3.56
351 352 7.885297 TCCAACAGAGAATAGAACCAAAAATG 58.115 34.615 0.00 0.00 0.00 2.32
352 353 8.655935 ATCCAACAGAGAATAGAACCAAAAAT 57.344 30.769 0.00 0.00 0.00 1.82
353 354 8.359642 CAATCCAACAGAGAATAGAACCAAAAA 58.640 33.333 0.00 0.00 0.00 1.94
354 355 7.505585 ACAATCCAACAGAGAATAGAACCAAAA 59.494 33.333 0.00 0.00 0.00 2.44
355 356 7.004086 ACAATCCAACAGAGAATAGAACCAAA 58.996 34.615 0.00 0.00 0.00 3.28
356 357 6.542821 ACAATCCAACAGAGAATAGAACCAA 58.457 36.000 0.00 0.00 0.00 3.67
357 358 6.126863 ACAATCCAACAGAGAATAGAACCA 57.873 37.500 0.00 0.00 0.00 3.67
358 359 6.183360 CGAACAATCCAACAGAGAATAGAACC 60.183 42.308 0.00 0.00 0.00 3.62
359 360 6.369065 ACGAACAATCCAACAGAGAATAGAAC 59.631 38.462 0.00 0.00 0.00 3.01
360 361 6.464222 ACGAACAATCCAACAGAGAATAGAA 58.536 36.000 0.00 0.00 0.00 2.10
361 362 6.037786 ACGAACAATCCAACAGAGAATAGA 57.962 37.500 0.00 0.00 0.00 1.98
362 363 6.727824 AACGAACAATCCAACAGAGAATAG 57.272 37.500 0.00 0.00 0.00 1.73
363 364 7.608153 TCTAACGAACAATCCAACAGAGAATA 58.392 34.615 0.00 0.00 0.00 1.75
364 365 6.464222 TCTAACGAACAATCCAACAGAGAAT 58.536 36.000 0.00 0.00 0.00 2.40
365 366 5.849510 TCTAACGAACAATCCAACAGAGAA 58.150 37.500 0.00 0.00 0.00 2.87
366 367 5.462530 TCTAACGAACAATCCAACAGAGA 57.537 39.130 0.00 0.00 0.00 3.10
367 368 5.389935 GCTTCTAACGAACAATCCAACAGAG 60.390 44.000 0.00 0.00 0.00 3.35
368 369 4.451096 GCTTCTAACGAACAATCCAACAGA 59.549 41.667 0.00 0.00 0.00 3.41
369 370 4.452455 AGCTTCTAACGAACAATCCAACAG 59.548 41.667 0.00 0.00 0.00 3.16
370 371 4.385825 AGCTTCTAACGAACAATCCAACA 58.614 39.130 0.00 0.00 0.00 3.33
371 372 6.304882 GTTAGCTTCTAACGAACAATCCAAC 58.695 40.000 0.00 0.00 0.00 3.77
372 373 5.410439 GGTTAGCTTCTAACGAACAATCCAA 59.590 40.000 0.00 0.00 0.00 3.53
373 374 4.933400 GGTTAGCTTCTAACGAACAATCCA 59.067 41.667 0.00 0.00 0.00 3.41
374 375 4.331992 GGGTTAGCTTCTAACGAACAATCC 59.668 45.833 0.00 2.00 0.00 3.01
375 376 5.176592 AGGGTTAGCTTCTAACGAACAATC 58.823 41.667 0.00 0.00 0.00 2.67
408 409 7.157347 TGCATATTTTTACCACATTGCTTCAA 58.843 30.769 0.00 0.00 0.00 2.69
409 410 6.695429 TGCATATTTTTACCACATTGCTTCA 58.305 32.000 0.00 0.00 0.00 3.02
432 433 3.837213 ATTGCTTCCAAGTGACGAATG 57.163 42.857 0.00 0.00 33.80 2.67
458 459 4.724279 ACAGGGAATTGTTTGTAGGAGT 57.276 40.909 0.00 0.00 0.00 3.85
509 510 6.799512 ACATTGCTTCCATCTAGTATTTTGC 58.200 36.000 0.00 0.00 0.00 3.68
539 540 3.067320 TGATGGAGACTGCTTCATAGACG 59.933 47.826 8.26 0.00 40.53 4.18
593 594 6.424812 GCAAAAATCTAATCCTGTGCAACTTT 59.575 34.615 0.00 0.00 38.04 2.66
596 597 5.229423 TGCAAAAATCTAATCCTGTGCAAC 58.771 37.500 0.00 0.00 37.78 4.17
612 613 5.003692 TGTGTTACTGATTGCTGCAAAAA 57.996 34.783 20.06 9.50 0.00 1.94
666 667 7.957002 TCCTTAAGCATTACATTGTTTCCAAA 58.043 30.769 0.00 0.00 33.44 3.28
688 689 4.027782 ACTCTAGGGAAATGGGATTCCT 57.972 45.455 0.00 0.00 46.66 3.36
754 757 6.875948 TTAACTGCTTGCTGATTCTGTTTA 57.124 33.333 6.50 0.00 0.00 2.01
781 784 7.987750 TTGCTTCCTTGTACACATTAATACA 57.012 32.000 0.00 0.00 0.00 2.29
790 793 5.627499 TGATTGATTGCTTCCTTGTACAC 57.373 39.130 0.00 0.00 0.00 2.90
825 828 1.415659 AGCATCCATCAGACTAGTGGC 59.584 52.381 0.00 0.00 33.01 5.01
852 919 6.260870 GTCACTAGACATCAGACTTCTGAA 57.739 41.667 12.86 0.00 45.38 3.02
853 920 5.888691 GTCACTAGACATCAGACTTCTGA 57.111 43.478 11.31 11.31 45.74 3.27
867 934 7.180408 AGGCTTTTAACATTAGGAGTCACTAGA 59.820 37.037 0.00 0.00 0.00 2.43
1126 1334 4.947147 GCCGTCCTGCACCACCAA 62.947 66.667 0.00 0.00 0.00 3.67
1398 1671 1.069432 GTGACGAACGCACTGAGTAGA 60.069 52.381 11.89 0.00 33.57 2.59
1428 1709 7.061027 CGCCAATTATTACAACATACGTACAG 58.939 38.462 0.00 0.00 0.00 2.74
1650 1940 2.426261 GTCGCCGAACCGTTTTGC 60.426 61.111 0.00 0.00 0.00 3.68
1861 2180 1.119684 GTTCCAAACAGCCCCAAACT 58.880 50.000 0.00 0.00 0.00 2.66
1862 2181 0.249280 CGTTCCAAACAGCCCCAAAC 60.249 55.000 0.00 0.00 0.00 2.93
1863 2182 0.395862 TCGTTCCAAACAGCCCCAAA 60.396 50.000 0.00 0.00 0.00 3.28
1864 2183 0.821711 CTCGTTCCAAACAGCCCCAA 60.822 55.000 0.00 0.00 0.00 4.12
1865 2184 1.228124 CTCGTTCCAAACAGCCCCA 60.228 57.895 0.00 0.00 0.00 4.96
1866 2185 0.035739 TACTCGTTCCAAACAGCCCC 59.964 55.000 0.00 0.00 0.00 5.80
1867 2186 1.886886 TTACTCGTTCCAAACAGCCC 58.113 50.000 0.00 0.00 0.00 5.19
1868 2187 4.226761 CAATTTACTCGTTCCAAACAGCC 58.773 43.478 0.00 0.00 0.00 4.85
1869 2188 3.668656 GCAATTTACTCGTTCCAAACAGC 59.331 43.478 0.00 0.00 0.00 4.40
1870 2189 4.854399 TGCAATTTACTCGTTCCAAACAG 58.146 39.130 0.00 0.00 0.00 3.16
1879 2198 4.578928 AGTGGTTTTCTGCAATTTACTCGT 59.421 37.500 0.00 0.00 0.00 4.18
1981 2306 1.002201 TCCGCCGATCAGTGGTTTTTA 59.998 47.619 8.37 0.00 38.61 1.52
2011 2336 1.992667 TCTGTCATAAACGCGCTCAAG 59.007 47.619 5.73 0.00 0.00 3.02
2051 2376 1.919918 GCATGAAAAGTTATGCCACGC 59.080 47.619 0.00 0.00 42.88 5.34
2149 2475 0.393267 GTGCACACGGGGCCTAATTA 60.393 55.000 13.17 0.00 0.00 1.40
2189 2517 2.186350 TTTTGCTCGCGTCAGCCATG 62.186 55.000 16.18 0.00 38.80 3.66
2190 2518 1.965930 TTTTGCTCGCGTCAGCCAT 60.966 52.632 16.18 0.00 38.80 4.40
2191 2519 2.590291 TTTTGCTCGCGTCAGCCA 60.590 55.556 16.18 3.48 38.80 4.75
2192 2520 2.127232 GTTTTGCTCGCGTCAGCC 60.127 61.111 16.18 0.00 38.80 4.85
2193 2521 1.439365 CTGTTTTGCTCGCGTCAGC 60.439 57.895 12.50 12.50 40.13 4.26
2194 2522 1.205064 CCTGTTTTGCTCGCGTCAG 59.795 57.895 5.77 0.00 0.00 3.51
2195 2523 1.227409 TCCTGTTTTGCTCGCGTCA 60.227 52.632 5.77 2.39 0.00 4.35
2196 2524 1.204312 GTCCTGTTTTGCTCGCGTC 59.796 57.895 5.77 0.00 0.00 5.19
2197 2525 2.251642 GGTCCTGTTTTGCTCGCGT 61.252 57.895 5.77 0.00 0.00 6.01
2252 2593 0.462789 ACGTCCGTCCTGTTCTGTTT 59.537 50.000 0.00 0.00 0.00 2.83
2500 3102 2.920384 TACACAGGACGCAGGCCA 60.920 61.111 5.01 0.00 0.00 5.36
2698 3926 0.589223 CCCTGTTTTTGCTTACGCGA 59.411 50.000 15.93 0.00 39.65 5.87
2700 3928 1.335597 GGTCCCTGTTTTTGCTTACGC 60.336 52.381 0.00 0.00 0.00 4.42


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

AutoCloner maintained by Alex Coulton.