Multiple sequence alignment - TraesCS3D01G115000

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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 TraesCS3D01G115000 chr3D 100.000 2480 0 0 1 2480 68336786 68334307 0.000000e+00 4580.0
1 TraesCS3D01G115000 chr3D 93.296 895 42 8 663 1553 68430239 68431119 0.000000e+00 1304.0
2 TraesCS3D01G115000 chr3D 86.222 1125 85 39 665 1770 68832964 68834037 0.000000e+00 1155.0
3 TraesCS3D01G115000 chr3D 90.545 899 40 16 663 1553 68388863 68389724 0.000000e+00 1147.0
4 TraesCS3D01G115000 chr3D 85.938 1024 84 26 775 1769 68325791 68324799 0.000000e+00 1038.0
5 TraesCS3D01G115000 chr3D 87.421 787 41 21 777 1553 68842748 68843486 0.000000e+00 852.0
6 TraesCS3D01G115000 chr3D 85.737 624 55 17 1876 2480 68469937 68469329 1.620000e-176 628.0
7 TraesCS3D01G115000 chr3D 93.077 260 10 6 1515 1770 68431154 68431409 8.380000e-100 374.0
8 TraesCS3D01G115000 chr3D 94.211 190 4 3 1769 1951 68329365 68329176 1.450000e-72 283.0
9 TraesCS3D01G115000 chr3D 87.719 228 18 6 1947 2172 68329007 68328788 8.800000e-65 257.0
10 TraesCS3D01G115000 chr3D 87.097 217 16 5 1555 1771 68389804 68390008 4.120000e-58 235.0
11 TraesCS3D01G115000 chr3D 90.351 114 8 1 1769 1879 68431478 68431591 1.990000e-31 147.0
12 TraesCS3D01G115000 chr3D 89.474 114 9 1 1769 1879 68390036 68390149 9.250000e-30 141.0
13 TraesCS3D01G115000 chr3D 91.304 92 4 2 1769 1857 68324729 68324639 3.350000e-24 122.0
14 TraesCS3D01G115000 chr3D 91.525 59 2 3 1999 2054 68835222 68835164 7.350000e-11 78.7
15 TraesCS3D01G115000 chr3D 95.122 41 1 1 2015 2054 68391037 68390997 2.060000e-06 63.9
16 TraesCS3D01G115000 chr3D 97.143 35 1 0 1845 1879 68834202 68834236 2.660000e-05 60.2
17 TraesCS3D01G115000 chr3B 91.281 1124 70 15 663 1770 112497468 112496357 0.000000e+00 1507.0
18 TraesCS3D01G115000 chr3B 93.508 878 46 6 663 1535 112948712 112947841 0.000000e+00 1295.0
19 TraesCS3D01G115000 chr3B 94.299 842 28 9 700 1528 112465931 112465097 0.000000e+00 1271.0
20 TraesCS3D01G115000 chr3B 93.350 812 45 7 663 1471 113483186 113483991 0.000000e+00 1192.0
21 TraesCS3D01G115000 chr3B 90.289 865 67 8 669 1527 113299572 113298719 0.000000e+00 1116.0
22 TraesCS3D01G115000 chr3B 84.741 793 99 14 702 1484 113304445 113303665 0.000000e+00 774.0
23 TraesCS3D01G115000 chr3B 85.499 731 63 20 1769 2480 113487678 113488384 0.000000e+00 723.0
24 TraesCS3D01G115000 chr3B 88.358 335 32 3 1551 1879 112947759 112947426 1.790000e-106 396.0
25 TraesCS3D01G115000 chr3B 96.818 220 5 2 1551 1770 112835387 112835170 1.400000e-97 366.0
26 TraesCS3D01G115000 chr3B 84.595 370 36 7 300 654 798651274 798651637 5.080000e-92 348.0
27 TraesCS3D01G115000 chr3B 95.349 215 8 2 1551 1765 113298613 113298401 8.490000e-90 340.0
28 TraesCS3D01G115000 chr3B 85.837 233 21 6 1548 1770 113504339 113504569 1.150000e-58 237.0
29 TraesCS3D01G115000 chr3B 92.121 165 5 4 1555 1711 113487442 113487606 2.480000e-55 226.0
30 TraesCS3D01G115000 chr3B 92.982 114 5 1 1769 1879 112835101 112834988 1.970000e-36 163.0
31 TraesCS3D01G115000 chr3B 92.920 113 6 1 1769 1879 113298224 113298112 1.970000e-36 163.0
32 TraesCS3D01G115000 chr3A 94.072 894 40 8 666 1553 80412785 80413671 0.000000e+00 1345.0
33 TraesCS3D01G115000 chr3A 85.279 754 49 23 1770 2480 80409899 80409165 0.000000e+00 721.0
34 TraesCS3D01G115000 chr3A 85.000 620 67 16 1877 2480 80411384 80410775 7.590000e-170 606.0
35 TraesCS3D01G115000 chr3A 94.595 259 13 1 1 259 232390015 232390272 1.380000e-107 399.0
36 TraesCS3D01G115000 chr3A 88.690 336 22 2 338 657 731003896 731003561 1.790000e-106 396.0
37 TraesCS3D01G115000 chr3A 95.814 215 9 0 1556 1770 80410188 80409974 5.080000e-92 348.0
38 TraesCS3D01G115000 chr3A 91.304 92 5 2 1769 1857 80288550 80288459 3.350000e-24 122.0
39 TraesCS3D01G115000 chr4D 88.323 1139 78 27 670 1770 134550696 134549575 0.000000e+00 1315.0
40 TraesCS3D01G115000 chr4D 95.736 258 9 2 1 258 277530296 277530041 4.930000e-112 414.0
41 TraesCS3D01G115000 chr4D 95.736 258 10 1 1 258 465027779 465028035 4.930000e-112 414.0
42 TraesCS3D01G115000 chr4D 84.211 323 27 14 318 623 44834035 44833720 2.410000e-75 292.0
43 TraesCS3D01G115000 chr4D 85.047 214 13 11 1548 1750 134563912 134564117 1.500000e-47 200.0
44 TraesCS3D01G115000 chr5D 95.753 259 9 2 1 258 223166806 223167063 1.370000e-112 416.0
45 TraesCS3D01G115000 chr5D 89.790 333 19 1 338 655 35155168 35154836 1.770000e-111 412.0
46 TraesCS3D01G115000 chr5D 91.626 203 14 3 315 517 134476087 134475888 6.760000e-71 278.0
47 TraesCS3D01G115000 chr1D 89.645 338 20 6 323 645 15302808 15303145 1.370000e-112 416.0
48 TraesCS3D01G115000 chr1D 95.385 260 10 2 1 259 129685831 129686089 1.770000e-111 412.0
49 TraesCS3D01G115000 chr1D 94.737 266 12 2 1 266 274996988 274996725 1.770000e-111 412.0
50 TraesCS3D01G115000 chr5A 95.736 258 10 1 1 258 470441240 470441496 4.930000e-112 414.0
51 TraesCS3D01G115000 chr5A 88.968 281 16 1 380 645 445192495 445192775 1.420000e-87 333.0
52 TraesCS3D01G115000 chr5A 81.163 361 46 11 311 655 440675628 440675274 1.130000e-68 270.0
53 TraesCS3D01G115000 chr7D 95.057 263 9 3 1 259 343107113 343106851 6.380000e-111 411.0
54 TraesCS3D01G115000 chr7A 87.432 366 31 4 295 645 521210655 521211020 8.260000e-110 407.0
55 TraesCS3D01G115000 chr7A 88.439 346 24 5 315 645 592922504 592922160 1.070000e-108 403.0
56 TraesCS3D01G115000 chr7A 88.545 323 22 1 338 645 496837308 496837630 6.470000e-101 377.0
57 TraesCS3D01G115000 chrUn 94.961 258 11 2 1 258 99372627 99372882 1.070000e-108 403.0
58 TraesCS3D01G115000 chr6A 89.394 330 20 4 338 652 209390395 209390066 3.840000e-108 401.0
59 TraesCS3D01G115000 chr6A 87.283 346 24 10 316 643 27549470 27549813 6.470000e-101 377.0
60 TraesCS3D01G115000 chr6A 86.686 338 30 6 311 633 53585662 53585999 6.520000e-96 361.0
61 TraesCS3D01G115000 chr1A 87.187 359 25 5 318 657 299633209 299632853 2.990000e-104 388.0
62 TraesCS3D01G115000 chr1A 88.545 323 22 7 338 645 541320888 541321210 6.470000e-101 377.0
63 TraesCS3D01G115000 chr1A 87.059 340 25 8 321 645 574817004 574816669 1.400000e-97 366.0
64 TraesCS3D01G115000 chr1A 86.111 324 30 6 338 646 347639402 347639079 3.950000e-88 335.0
65 TraesCS3D01G115000 chr1A 82.175 331 40 10 309 622 585451098 585450770 1.460000e-67 267.0
66 TraesCS3D01G115000 chr2B 87.941 340 24 3 321 645 234830802 234830465 3.870000e-103 385.0
67 TraesCS3D01G115000 chr2B 85.950 363 34 8 309 654 746718657 746719019 3.010000e-99 372.0
68 TraesCS3D01G115000 chr2B 90.476 168 16 0 315 482 476399803 476399636 3.210000e-54 222.0
69 TraesCS3D01G115000 chr2A 86.571 350 32 7 311 645 507090813 507090464 3.010000e-99 372.0
70 TraesCS3D01G115000 chr2A 87.651 332 24 3 338 652 79759199 79758868 1.080000e-98 370.0
71 TraesCS3D01G115000 chr2D 97.436 39 1 0 2015 2053 69266812 69266774 1.590000e-07 67.6


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 TraesCS3D01G115000 chr3D 68334307 68336786 2479 True 4580.000000 4580 100.000000 1 2480 1 chr3D.!!$R1 2479
1 TraesCS3D01G115000 chr3D 68842748 68843486 738 False 852.000000 852 87.421000 777 1553 1 chr3D.!!$F1 776
2 TraesCS3D01G115000 chr3D 68469329 68469937 608 True 628.000000 628 85.737000 1876 2480 1 chr3D.!!$R3 604
3 TraesCS3D01G115000 chr3D 68430239 68431591 1352 False 608.333333 1304 92.241333 663 1879 3 chr3D.!!$F3 1216
4 TraesCS3D01G115000 chr3D 68832964 68834236 1272 False 607.600000 1155 91.682500 665 1879 2 chr3D.!!$F4 1214
5 TraesCS3D01G115000 chr3D 68388863 68390149 1286 False 507.666667 1147 89.038667 663 1879 3 chr3D.!!$F2 1216
6 TraesCS3D01G115000 chr3D 68324639 68329365 4726 True 425.000000 1038 89.793000 775 2172 4 chr3D.!!$R5 1397
7 TraesCS3D01G115000 chr3B 112496357 112497468 1111 True 1507.000000 1507 91.281000 663 1770 1 chr3B.!!$R2 1107
8 TraesCS3D01G115000 chr3B 112465097 112465931 834 True 1271.000000 1271 94.299000 700 1528 1 chr3B.!!$R1 828
9 TraesCS3D01G115000 chr3B 112947426 112948712 1286 True 845.500000 1295 90.933000 663 1879 2 chr3B.!!$R5 1216
10 TraesCS3D01G115000 chr3B 113303665 113304445 780 True 774.000000 774 84.741000 702 1484 1 chr3B.!!$R3 782
11 TraesCS3D01G115000 chr3B 113483186 113488384 5198 False 713.666667 1192 90.323333 663 2480 3 chr3B.!!$F3 1817
12 TraesCS3D01G115000 chr3B 113298112 113299572 1460 True 539.666667 1116 92.852667 669 1879 3 chr3B.!!$R6 1210
13 TraesCS3D01G115000 chr3A 80412785 80413671 886 False 1345.000000 1345 94.072000 666 1553 1 chr3A.!!$F1 887
14 TraesCS3D01G115000 chr3A 80409165 80411384 2219 True 558.333333 721 88.697667 1556 2480 3 chr3A.!!$R3 924
15 TraesCS3D01G115000 chr4D 134549575 134550696 1121 True 1315.000000 1315 88.323000 670 1770 1 chr4D.!!$R2 1100

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
386 387 0.037697 CCAAACCATCTCGACCGTCA 60.038 55.0 0.0 0.0 0.0 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2059 8571 0.889306 ACTCTGCTCCGACAAGTACC 59.111 55.0 0.0 0.0 0.0 3.34 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
25 26 5.982391 TGGAGAAGTCATATTATCCCCTCT 58.018 41.667 0.00 0.00 39.37 3.69
26 27 6.019748 TGGAGAAGTCATATTATCCCCTCTC 58.980 44.000 0.00 0.00 39.37 3.20
29 30 7.841729 GGAGAAGTCATATTATCCCCTCTCATA 59.158 40.741 0.00 0.00 35.02 2.15
30 31 9.432982 GAGAAGTCATATTATCCCCTCTCATAT 57.567 37.037 0.00 0.00 0.00 1.78
90 91 8.846943 ATTAAAACCAAAATGATCCCTGTTTC 57.153 30.769 0.00 0.00 0.00 2.78
91 92 5.885449 AAACCAAAATGATCCCTGTTTCA 57.115 34.783 0.00 0.00 0.00 2.69
92 93 5.885449 AACCAAAATGATCCCTGTTTCAA 57.115 34.783 0.00 0.00 0.00 2.69
94 95 7.552050 AACCAAAATGATCCCTGTTTCAATA 57.448 32.000 0.00 0.00 0.00 1.90
98 99 8.885722 CCAAAATGATCCCTGTTTCAATATTTG 58.114 33.333 0.00 0.00 31.21 2.32
99 100 9.656040 CAAAATGATCCCTGTTTCAATATTTGA 57.344 29.630 0.00 0.00 38.04 2.69
131 132 9.671279 ATTCAAATAGGAAAAATGTGAAATCCC 57.329 29.630 0.00 0.00 34.92 3.85
132 133 7.619965 TCAAATAGGAAAAATGTGAAATCCCC 58.380 34.615 0.00 0.00 0.00 4.81
135 136 5.227569 AGGAAAAATGTGAAATCCCCAAC 57.772 39.130 0.00 0.00 0.00 3.77
139 140 5.728637 AAAATGTGAAATCCCCAACTCTC 57.271 39.130 0.00 0.00 0.00 3.20
140 141 4.664688 AATGTGAAATCCCCAACTCTCT 57.335 40.909 0.00 0.00 0.00 3.10
141 142 3.703001 TGTGAAATCCCCAACTCTCTC 57.297 47.619 0.00 0.00 0.00 3.20
142 143 2.305927 TGTGAAATCCCCAACTCTCTCC 59.694 50.000 0.00 0.00 0.00 3.71
143 144 1.555075 TGAAATCCCCAACTCTCTCCG 59.445 52.381 0.00 0.00 0.00 4.63
146 147 0.978146 ATCCCCAACTCTCTCCGTGG 60.978 60.000 0.00 0.00 0.00 4.94
147 148 2.660064 CCCCAACTCTCTCCGTGGG 61.660 68.421 0.30 0.30 36.40 4.61
149 150 1.592223 CCAACTCTCTCCGTGGGTC 59.408 63.158 0.00 0.00 0.00 4.46
150 151 1.592223 CAACTCTCTCCGTGGGTCC 59.408 63.158 0.00 0.00 0.00 4.46
151 152 0.900647 CAACTCTCTCCGTGGGTCCT 60.901 60.000 0.00 0.00 0.00 3.85
154 155 0.612174 CTCTCTCCGTGGGTCCTTGA 60.612 60.000 0.00 0.00 0.00 3.02
155 156 0.612174 TCTCTCCGTGGGTCCTTGAG 60.612 60.000 0.00 0.00 0.00 3.02
156 157 0.900647 CTCTCCGTGGGTCCTTGAGT 60.901 60.000 0.00 0.00 0.00 3.41
160 161 1.071471 CGTGGGTCCTTGAGTTGCT 59.929 57.895 0.00 0.00 0.00 3.91
162 163 1.270625 CGTGGGTCCTTGAGTTGCTTA 60.271 52.381 0.00 0.00 0.00 3.09
165 166 2.708861 TGGGTCCTTGAGTTGCTTAGAA 59.291 45.455 0.00 0.00 0.00 2.10
166 167 3.330701 TGGGTCCTTGAGTTGCTTAGAAT 59.669 43.478 0.00 0.00 0.00 2.40
167 168 4.202567 TGGGTCCTTGAGTTGCTTAGAATT 60.203 41.667 0.00 0.00 0.00 2.17
169 170 5.106118 GGGTCCTTGAGTTGCTTAGAATTTC 60.106 44.000 0.00 0.00 0.00 2.17
173 174 5.163814 CCTTGAGTTGCTTAGAATTTCGAGG 60.164 44.000 0.00 0.00 0.00 4.63
174 175 5.147330 TGAGTTGCTTAGAATTTCGAGGA 57.853 39.130 0.00 0.68 0.00 3.71
233 234 8.454106 GCATGAATGACCTATGTATAACATTCC 58.546 37.037 0.00 0.00 41.22 3.01
236 237 9.913310 TGAATGACCTATGTATAACATTCCAAA 57.087 29.630 0.00 0.00 41.22 3.28
240 241 9.913310 TGACCTATGTATAACATTCCAAATTGA 57.087 29.630 0.00 0.00 39.88 2.57
259 260 9.828852 CAAATTGAAAATTTGGGATGTTACATG 57.171 29.630 14.76 0.00 35.87 3.21
260 261 7.614124 ATTGAAAATTTGGGATGTTACATGC 57.386 32.000 8.36 8.36 0.00 4.06
261 262 6.106648 TGAAAATTTGGGATGTTACATGCA 57.893 33.333 17.98 2.51 0.00 3.96
262 263 6.709281 TGAAAATTTGGGATGTTACATGCAT 58.291 32.000 17.98 0.00 0.00 3.96
263 264 7.845037 TGAAAATTTGGGATGTTACATGCATA 58.155 30.769 17.98 4.29 0.00 3.14
266 267 9.683870 AAAATTTGGGATGTTACATGCATATTT 57.316 25.926 17.98 14.99 0.00 1.40
267 268 8.665643 AATTTGGGATGTTACATGCATATTTG 57.334 30.769 17.98 0.00 0.00 2.32
268 269 5.787953 TGGGATGTTACATGCATATTTGG 57.212 39.130 17.98 0.00 0.00 3.28
269 270 4.039004 TGGGATGTTACATGCATATTTGGC 59.961 41.667 17.98 0.00 0.00 4.52
270 271 4.281688 GGGATGTTACATGCATATTTGGCT 59.718 41.667 17.98 0.00 0.00 4.75
271 272 5.476599 GGGATGTTACATGCATATTTGGCTA 59.523 40.000 17.98 0.00 0.00 3.93
272 273 6.015519 GGGATGTTACATGCATATTTGGCTAA 60.016 38.462 17.98 0.00 0.00 3.09
273 274 7.086376 GGATGTTACATGCATATTTGGCTAAG 58.914 38.462 11.90 0.00 0.00 2.18
274 275 6.389830 TGTTACATGCATATTTGGCTAAGG 57.610 37.500 0.00 0.00 0.00 2.69
275 276 6.125719 TGTTACATGCATATTTGGCTAAGGA 58.874 36.000 0.00 0.00 0.00 3.36
277 278 4.796606 ACATGCATATTTGGCTAAGGACT 58.203 39.130 0.00 0.00 0.00 3.85
279 280 3.820557 TGCATATTTGGCTAAGGACTCC 58.179 45.455 0.00 0.00 0.00 3.85
280 281 3.149981 GCATATTTGGCTAAGGACTCCC 58.850 50.000 0.00 0.00 0.00 4.30
283 284 2.193087 TTTGGCTAAGGACTCCCGCC 62.193 60.000 11.86 11.86 41.06 6.13
284 285 4.222847 GGCTAAGGACTCCCGCCG 62.223 72.222 5.22 0.00 37.58 6.46
285 286 3.459063 GCTAAGGACTCCCGCCGT 61.459 66.667 0.00 0.00 37.58 5.68
287 288 1.461911 GCTAAGGACTCCCGCCGTAT 61.462 60.000 0.00 0.00 37.58 3.06
289 290 0.748450 TAAGGACTCCCGCCGTATTG 59.252 55.000 0.00 0.00 37.58 1.90
292 293 1.227556 GACTCCCGCCGTATTGCAT 60.228 57.895 0.00 0.00 0.00 3.96
295 296 0.249699 CTCCCGCCGTATTGCATGTA 60.250 55.000 0.00 0.00 0.00 2.29
296 297 0.394938 TCCCGCCGTATTGCATGTAT 59.605 50.000 0.00 0.00 0.00 2.29
298 299 1.608025 CCCGCCGTATTGCATGTATCT 60.608 52.381 0.00 0.00 0.00 1.98
302 303 3.612717 CGCCGTATTGCATGTATCTCTCT 60.613 47.826 0.00 0.00 0.00 3.10
305 306 5.398169 CCGTATTGCATGTATCTCTCTCTC 58.602 45.833 0.00 0.00 0.00 3.20
306 307 5.182950 CCGTATTGCATGTATCTCTCTCTCT 59.817 44.000 0.00 0.00 0.00 3.10
307 308 6.314018 CGTATTGCATGTATCTCTCTCTCTC 58.686 44.000 0.00 0.00 0.00 3.20
309 310 6.579666 ATTGCATGTATCTCTCTCTCTCTC 57.420 41.667 0.00 0.00 0.00 3.20
311 312 5.308014 TGCATGTATCTCTCTCTCTCTCTC 58.692 45.833 0.00 0.00 0.00 3.20
312 313 5.072193 TGCATGTATCTCTCTCTCTCTCTCT 59.928 44.000 0.00 0.00 0.00 3.10
313 314 5.641209 GCATGTATCTCTCTCTCTCTCTCTC 59.359 48.000 0.00 0.00 0.00 3.20
315 316 6.656632 TGTATCTCTCTCTCTCTCTCTCTC 57.343 45.833 0.00 0.00 0.00 3.20
316 317 6.377080 TGTATCTCTCTCTCTCTCTCTCTCT 58.623 44.000 0.00 0.00 0.00 3.10
319 320 9.688091 GTATCTCTCTCTCTCTCTCTCTCTATA 57.312 40.741 0.00 0.00 0.00 1.31
353 354 7.875327 ATACACACACCAATATAAAAGGACC 57.125 36.000 0.00 0.00 0.00 4.46
354 355 5.014202 ACACACACCAATATAAAAGGACCC 58.986 41.667 0.00 0.00 0.00 4.46
355 356 5.013547 CACACACCAATATAAAAGGACCCA 58.986 41.667 0.00 0.00 0.00 4.51
356 357 5.478679 CACACACCAATATAAAAGGACCCAA 59.521 40.000 0.00 0.00 0.00 4.12
358 359 6.728632 ACACACCAATATAAAAGGACCCAAAT 59.271 34.615 0.00 0.00 0.00 2.32
360 361 6.156083 ACACCAATATAAAAGGACCCAAATGG 59.844 38.462 0.00 0.00 41.37 3.16
375 376 4.289245 CCAAATGGGTAGATCCAAACCAT 58.711 43.478 9.04 9.04 43.39 3.55
376 377 4.342092 CCAAATGGGTAGATCCAAACCATC 59.658 45.833 14.09 0.00 40.84 3.51
379 380 2.434336 TGGGTAGATCCAAACCATCTCG 59.566 50.000 10.66 0.00 37.51 4.04
380 381 2.698797 GGGTAGATCCAAACCATCTCGA 59.301 50.000 10.66 0.00 37.51 4.04
381 382 3.492829 GGGTAGATCCAAACCATCTCGAC 60.493 52.174 10.66 0.00 37.51 4.20
382 383 2.990066 AGATCCAAACCATCTCGACC 57.010 50.000 0.00 0.00 0.00 4.79
383 384 1.137086 AGATCCAAACCATCTCGACCG 59.863 52.381 0.00 0.00 0.00 4.79
385 386 0.245539 TCCAAACCATCTCGACCGTC 59.754 55.000 0.00 0.00 0.00 4.79
386 387 0.037697 CCAAACCATCTCGACCGTCA 60.038 55.000 0.00 0.00 0.00 4.35
389 390 2.742053 CAAACCATCTCGACCGTCAAAT 59.258 45.455 0.00 0.00 0.00 2.32
390 391 2.295253 ACCATCTCGACCGTCAAATC 57.705 50.000 0.00 0.00 0.00 2.17
393 394 2.541346 CCATCTCGACCGTCAAATCATG 59.459 50.000 0.00 0.00 0.00 3.07
396 397 4.443913 TCTCGACCGTCAAATCATGTTA 57.556 40.909 0.00 0.00 0.00 2.41
398 399 5.041287 TCTCGACCGTCAAATCATGTTATC 58.959 41.667 0.00 0.00 0.00 1.75
399 400 5.006153 TCGACCGTCAAATCATGTTATCT 57.994 39.130 0.00 0.00 0.00 1.98
400 401 4.803613 TCGACCGTCAAATCATGTTATCTG 59.196 41.667 0.00 0.00 0.00 2.90
401 402 4.025730 CGACCGTCAAATCATGTTATCTGG 60.026 45.833 0.00 0.00 0.00 3.86
402 403 3.627577 ACCGTCAAATCATGTTATCTGGC 59.372 43.478 0.00 0.00 0.00 4.85
403 404 3.303329 CCGTCAAATCATGTTATCTGGCG 60.303 47.826 0.00 0.00 0.00 5.69
404 405 3.303329 CGTCAAATCATGTTATCTGGCGG 60.303 47.826 0.00 0.00 0.00 6.13
407 408 4.335315 TCAAATCATGTTATCTGGCGGTTC 59.665 41.667 0.00 0.00 0.00 3.62
412 413 4.335315 TCATGTTATCTGGCGGTTCAAATC 59.665 41.667 0.00 0.00 0.00 2.17
422 423 3.201726 CGGTTCAAATCGCTTCAATGT 57.798 42.857 0.00 0.00 0.00 2.71
424 425 3.361644 CGGTTCAAATCGCTTCAATGTTG 59.638 43.478 0.00 0.00 0.00 3.33
426 427 4.618489 GGTTCAAATCGCTTCAATGTTGAG 59.382 41.667 0.00 0.00 38.61 3.02
427 428 3.825308 TCAAATCGCTTCAATGTTGAGC 58.175 40.909 0.00 2.30 38.61 4.26
428 429 3.252944 TCAAATCGCTTCAATGTTGAGCA 59.747 39.130 13.55 5.58 38.61 4.26
429 430 2.907910 ATCGCTTCAATGTTGAGCAC 57.092 45.000 13.55 0.00 38.61 4.40
430 431 0.874390 TCGCTTCAATGTTGAGCACC 59.126 50.000 13.55 0.00 38.61 5.01
432 433 1.001487 CGCTTCAATGTTGAGCACCAA 60.001 47.619 13.55 0.00 38.61 3.67
434 435 2.796593 GCTTCAATGTTGAGCACCAAAC 59.203 45.455 10.31 0.00 38.61 2.93
436 437 3.435105 TCAATGTTGAGCACCAAACAC 57.565 42.857 0.00 0.00 36.36 3.32
438 439 1.388547 ATGTTGAGCACCAAACACGT 58.611 45.000 0.00 0.00 36.36 4.49
439 440 1.169577 TGTTGAGCACCAAACACGTT 58.830 45.000 0.00 0.00 36.36 3.99
440 441 1.542030 TGTTGAGCACCAAACACGTTT 59.458 42.857 0.00 0.00 36.36 3.60
441 442 2.747989 TGTTGAGCACCAAACACGTTTA 59.252 40.909 0.00 0.00 36.36 2.01
442 443 3.190744 TGTTGAGCACCAAACACGTTTAA 59.809 39.130 0.00 0.00 36.36 1.52
443 444 3.408288 TGAGCACCAAACACGTTTAAC 57.592 42.857 0.00 0.00 0.00 2.01
444 445 5.756694 GTTGAGCACCAAACACGTTTAACG 61.757 45.833 16.31 16.31 41.26 3.18
461 462 6.509039 CGTTTAACGCTCTAATTATCCACCAC 60.509 42.308 4.11 0.00 33.65 4.16
462 463 4.755266 AACGCTCTAATTATCCACCACT 57.245 40.909 0.00 0.00 0.00 4.00
463 464 4.060038 ACGCTCTAATTATCCACCACTG 57.940 45.455 0.00 0.00 0.00 3.66
466 467 4.441495 CGCTCTAATTATCCACCACTGTCA 60.441 45.833 0.00 0.00 0.00 3.58
467 468 5.615289 GCTCTAATTATCCACCACTGTCAT 58.385 41.667 0.00 0.00 0.00 3.06
468 469 6.058183 GCTCTAATTATCCACCACTGTCATT 58.942 40.000 0.00 0.00 0.00 2.57
469 470 7.217200 GCTCTAATTATCCACCACTGTCATTA 58.783 38.462 0.00 0.00 0.00 1.90
470 471 7.386299 GCTCTAATTATCCACCACTGTCATTAG 59.614 40.741 0.00 0.00 0.00 1.73
481 482 7.412563 CCACCACTGTCATTAGTTATAAACACG 60.413 40.741 0.00 0.00 0.00 4.49
482 483 7.117236 CACCACTGTCATTAGTTATAAACACGT 59.883 37.037 0.00 0.00 0.00 4.49
483 484 7.658575 ACCACTGTCATTAGTTATAAACACGTT 59.341 33.333 0.00 0.00 0.00 3.99
484 485 8.500773 CCACTGTCATTAGTTATAAACACGTTT 58.499 33.333 0.22 0.22 36.63 3.60
485 486 9.872757 CACTGTCATTAGTTATAAACACGTTTT 57.127 29.630 0.00 0.00 34.23 2.43
486 487 9.872757 ACTGTCATTAGTTATAAACACGTTTTG 57.127 29.630 0.00 0.00 34.23 2.44
493 494 9.919348 TTAGTTATAAACACGTTTTGACTCAAC 57.081 29.630 0.00 0.00 34.23 3.18
496 497 4.759516 AAACACGTTTTGACTCAACACT 57.240 36.364 6.52 0.00 0.00 3.55
499 500 5.652744 ACACGTTTTGACTCAACACTATC 57.347 39.130 6.52 0.00 0.00 2.08
501 502 4.062991 ACGTTTTGACTCAACACTATCCC 58.937 43.478 6.52 0.00 0.00 3.85
505 506 5.560722 TTTGACTCAACACTATCCCTTGA 57.439 39.130 0.00 0.00 0.00 3.02
508 509 6.126863 TGACTCAACACTATCCCTTGAAAT 57.873 37.500 0.00 0.00 0.00 2.17
509 510 6.173339 TGACTCAACACTATCCCTTGAAATC 58.827 40.000 0.00 0.00 0.00 2.17
512 513 4.943705 TCAACACTATCCCTTGAAATCTGC 59.056 41.667 0.00 0.00 0.00 4.26
515 516 4.079558 ACACTATCCCTTGAAATCTGCCAT 60.080 41.667 0.00 0.00 0.00 4.40
516 517 4.277672 CACTATCCCTTGAAATCTGCCATG 59.722 45.833 0.00 0.00 0.00 3.66
517 518 1.477553 TCCCTTGAAATCTGCCATGC 58.522 50.000 0.00 0.00 0.00 4.06
518 519 1.187974 CCCTTGAAATCTGCCATGCA 58.812 50.000 0.00 0.00 36.92 3.96
519 520 1.760613 CCCTTGAAATCTGCCATGCAT 59.239 47.619 0.00 0.00 38.13 3.96
520 521 2.169769 CCCTTGAAATCTGCCATGCATT 59.830 45.455 0.00 0.00 38.13 3.56
521 522 3.454375 CCTTGAAATCTGCCATGCATTC 58.546 45.455 0.00 0.00 38.13 2.67
523 524 4.360563 CTTGAAATCTGCCATGCATTCTC 58.639 43.478 0.00 0.00 38.13 2.87
525 526 2.048444 AATCTGCCATGCATTCTCGT 57.952 45.000 0.00 0.00 38.13 4.18
526 527 1.306148 ATCTGCCATGCATTCTCGTG 58.694 50.000 0.00 0.00 38.13 4.35
528 529 1.089112 CTGCCATGCATTCTCGTGAA 58.911 50.000 0.00 1.90 38.13 3.18
529 530 1.469703 CTGCCATGCATTCTCGTGAAA 59.530 47.619 3.74 0.00 38.13 2.69
533 534 3.612479 GCCATGCATTCTCGTGAAAAAGT 60.612 43.478 3.74 0.00 35.63 2.66
538 539 7.201376 CCATGCATTCTCGTGAAAAAGTAATTG 60.201 37.037 3.74 0.00 35.63 2.32
539 540 6.964908 TGCATTCTCGTGAAAAAGTAATTGA 58.035 32.000 3.74 0.00 35.63 2.57
540 541 7.592938 TGCATTCTCGTGAAAAAGTAATTGAT 58.407 30.769 3.74 0.00 35.63 2.57
542 543 9.722056 GCATTCTCGTGAAAAAGTAATTGATAT 57.278 29.630 3.74 0.00 35.63 1.63
566 567 5.584251 TCTTATCAAATATCAGCGTGCAACA 59.416 36.000 0.00 0.00 35.74 3.33
567 568 3.745332 TCAAATATCAGCGTGCAACAG 57.255 42.857 0.00 0.00 35.74 3.16
569 570 3.940852 TCAAATATCAGCGTGCAACAGAT 59.059 39.130 0.00 0.00 35.74 2.90
571 572 5.759763 TCAAATATCAGCGTGCAACAGATAT 59.240 36.000 9.02 9.02 37.17 1.63
573 574 7.603784 TCAAATATCAGCGTGCAACAGATATAT 59.396 33.333 13.13 0.00 35.65 0.86
577 578 6.084326 TCAGCGTGCAACAGATATATCTTA 57.916 37.500 12.75 0.00 35.74 2.10
578 579 5.920840 TCAGCGTGCAACAGATATATCTTAC 59.079 40.000 12.75 6.63 35.74 2.34
579 580 5.119279 CAGCGTGCAACAGATATATCTTACC 59.881 44.000 12.75 3.07 35.74 2.85
643 644 7.172654 TGCATTGCACGTACATTATTACTAG 57.827 36.000 7.38 0.00 31.71 2.57
644 645 6.759356 TGCATTGCACGTACATTATTACTAGT 59.241 34.615 7.38 0.00 31.71 2.57
645 646 7.042992 TGCATTGCACGTACATTATTACTAGTC 60.043 37.037 7.38 0.00 31.71 2.59
646 647 7.169308 GCATTGCACGTACATTATTACTAGTCT 59.831 37.037 0.00 0.00 0.00 3.24
1452 4295 3.127533 CCCGAGCCAAAGAAGCCG 61.128 66.667 0.00 0.00 0.00 5.52
1487 7632 2.433318 GGTCGCCTGAGCTGTGAC 60.433 66.667 7.51 7.51 41.39 3.67
1553 7725 4.033358 CGAGTTTCCTGTGATGAGTAATGC 59.967 45.833 0.00 0.00 0.00 3.56
1741 8033 4.148128 AGAGCAGAACATGTGGAATAGG 57.852 45.455 0.00 0.00 0.00 2.57
1770 8168 9.588096 AATTAGGTGGAAAATGAACTAGTTCTT 57.412 29.630 30.47 23.53 40.14 2.52
1771 8169 8.990163 TTAGGTGGAAAATGAACTAGTTCTTT 57.010 30.769 30.47 27.05 40.14 2.52
1872 8383 8.830580 GTGAGAATCTCCAAATTCGATTAATCA 58.169 33.333 15.57 0.00 40.00 2.57
1980 8492 6.860790 AGGTTAAGTTTGTTTCCCAAGAAA 57.139 33.333 0.00 0.00 39.70 2.52
1983 8495 7.768582 AGGTTAAGTTTGTTTCCCAAGAAATTG 59.231 33.333 0.00 0.00 43.67 2.32
1984 8496 7.766738 GGTTAAGTTTGTTTCCCAAGAAATTGA 59.233 33.333 0.00 0.00 43.67 2.57
2054 8566 0.741221 CTACACCCGAGAGCCAAAGC 60.741 60.000 0.00 0.00 40.32 3.51
2055 8567 2.180159 TACACCCGAGAGCCAAAGCC 62.180 60.000 0.00 0.00 41.25 4.35
2056 8568 3.249189 ACCCGAGAGCCAAAGCCA 61.249 61.111 0.00 0.00 41.25 4.75
2057 8569 2.034066 CCCGAGAGCCAAAGCCAA 59.966 61.111 0.00 0.00 41.25 4.52
2058 8570 1.603455 CCCGAGAGCCAAAGCCAAA 60.603 57.895 0.00 0.00 41.25 3.28
2059 8571 1.589716 CCCGAGAGCCAAAGCCAAAG 61.590 60.000 0.00 0.00 41.25 2.77
2078 8590 0.889306 GGTACTTGTCGGAGCAGAGT 59.111 55.000 0.00 0.00 0.00 3.24
2174 8709 1.053424 ACCACCATAAGGACACGTGT 58.947 50.000 23.64 23.64 38.69 4.49
2176 8711 1.275291 CCACCATAAGGACACGTGTCT 59.725 52.381 39.01 26.95 44.20 3.41
2179 8714 2.832129 ACCATAAGGACACGTGTCTGAT 59.168 45.455 39.01 27.96 44.20 2.90
2193 8728 2.632512 TGTCTGATGCTTGTGGTAGTCA 59.367 45.455 0.00 0.00 0.00 3.41
2217 8752 3.403881 GCGCGCCTATTAGTCGGC 61.404 66.667 23.24 0.00 42.86 5.54
2220 8759 2.733593 CGCCTATTAGTCGGCCGC 60.734 66.667 23.51 16.31 43.38 6.53
2238 8777 5.346281 CGGCCGCTAACAATTATTTTGAAAA 59.654 36.000 14.67 0.00 0.00 2.29
2289 8828 5.523438 AAACACGATTAAAAGCAAAGGGA 57.477 34.783 0.00 0.00 0.00 4.20
2290 8829 5.722021 AACACGATTAAAAGCAAAGGGAT 57.278 34.783 0.00 0.00 0.00 3.85
2292 8831 6.436843 ACACGATTAAAAGCAAAGGGATAG 57.563 37.500 0.00 0.00 0.00 2.08
2330 8870 9.729281 ATTTGAAAGACATGGATTTTTATGCTT 57.271 25.926 0.00 0.00 0.00 3.91
2367 8908 2.897326 GGGTTGTTTGGTTCCAAGCTAT 59.103 45.455 16.73 0.00 38.69 2.97
2368 8909 3.306019 GGGTTGTTTGGTTCCAAGCTATG 60.306 47.826 16.73 0.00 38.69 2.23
2382 8933 8.408601 GTTCCAAGCTATGATTTGTCACATATT 58.591 33.333 0.00 0.00 0.00 1.28
2431 8982 2.106566 TGTGTGTTTGGTTCTTGCCAT 58.893 42.857 0.00 0.00 38.48 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 7.732222 ATGAGAGGGGATAATATGACTTCTC 57.268 40.000 0.00 0.00 0.00 2.87
64 65 9.936759 GAAACAGGGATCATTTTGGTTTTAATA 57.063 29.630 0.00 0.00 0.00 0.98
65 66 8.435982 TGAAACAGGGATCATTTTGGTTTTAAT 58.564 29.630 0.00 0.00 0.00 1.40
69 70 5.885449 TGAAACAGGGATCATTTTGGTTT 57.115 34.783 0.00 0.00 0.00 3.27
72 73 8.885722 CAAATATTGAAACAGGGATCATTTTGG 58.114 33.333 0.00 0.00 0.00 3.28
73 74 9.656040 TCAAATATTGAAACAGGGATCATTTTG 57.344 29.630 0.00 0.00 36.59 2.44
108 109 7.393216 TGGGGATTTCACATTTTTCCTATTTG 58.607 34.615 0.00 0.00 0.00 2.32
109 110 7.566658 TGGGGATTTCACATTTTTCCTATTT 57.433 32.000 0.00 0.00 0.00 1.40
110 111 7.237471 AGTTGGGGATTTCACATTTTTCCTATT 59.763 33.333 0.00 0.00 0.00 1.73
114 115 5.012046 AGAGTTGGGGATTTCACATTTTTCC 59.988 40.000 0.00 0.00 0.00 3.13
115 116 6.015095 AGAGAGTTGGGGATTTCACATTTTTC 60.015 38.462 0.00 0.00 0.00 2.29
116 117 5.840693 AGAGAGTTGGGGATTTCACATTTTT 59.159 36.000 0.00 0.00 0.00 1.94
118 119 5.003096 AGAGAGTTGGGGATTTCACATTT 57.997 39.130 0.00 0.00 0.00 2.32
120 121 3.054065 GGAGAGAGTTGGGGATTTCACAT 60.054 47.826 0.00 0.00 0.00 3.21
124 125 1.555533 ACGGAGAGAGTTGGGGATTTC 59.444 52.381 0.00 0.00 0.00 2.17
125 126 1.279271 CACGGAGAGAGTTGGGGATTT 59.721 52.381 0.00 0.00 0.00 2.17
127 128 0.978146 CCACGGAGAGAGTTGGGGAT 60.978 60.000 0.00 0.00 0.00 3.85
130 131 1.889530 GACCCACGGAGAGAGTTGGG 61.890 65.000 3.87 3.87 42.05 4.12
131 132 1.592223 GACCCACGGAGAGAGTTGG 59.408 63.158 0.00 0.00 0.00 3.77
132 133 0.900647 AGGACCCACGGAGAGAGTTG 60.901 60.000 0.00 0.00 0.00 3.16
135 136 0.612174 TCAAGGACCCACGGAGAGAG 60.612 60.000 0.00 0.00 0.00 3.20
139 140 0.320771 CAACTCAAGGACCCACGGAG 60.321 60.000 0.00 0.00 0.00 4.63
140 141 1.752198 CAACTCAAGGACCCACGGA 59.248 57.895 0.00 0.00 0.00 4.69
141 142 1.966451 GCAACTCAAGGACCCACGG 60.966 63.158 0.00 0.00 0.00 4.94
142 143 0.535102 AAGCAACTCAAGGACCCACG 60.535 55.000 0.00 0.00 0.00 4.94
143 144 2.038557 TCTAAGCAACTCAAGGACCCAC 59.961 50.000 0.00 0.00 0.00 4.61
146 147 5.390991 CGAAATTCTAAGCAACTCAAGGACC 60.391 44.000 0.00 0.00 0.00 4.46
147 148 5.408604 TCGAAATTCTAAGCAACTCAAGGAC 59.591 40.000 0.00 0.00 0.00 3.85
149 150 5.163814 CCTCGAAATTCTAAGCAACTCAAGG 60.164 44.000 0.00 0.00 0.00 3.61
150 151 5.639506 TCCTCGAAATTCTAAGCAACTCAAG 59.360 40.000 0.00 0.00 0.00 3.02
151 152 5.547465 TCCTCGAAATTCTAAGCAACTCAA 58.453 37.500 0.00 0.00 0.00 3.02
154 155 4.806247 CGATCCTCGAAATTCTAAGCAACT 59.194 41.667 0.00 0.00 43.74 3.16
155 156 4.551024 GCGATCCTCGAAATTCTAAGCAAC 60.551 45.833 0.00 0.00 43.74 4.17
156 157 3.555956 GCGATCCTCGAAATTCTAAGCAA 59.444 43.478 0.00 0.00 43.74 3.91
160 161 5.445407 CGTTTTGCGATCCTCGAAATTCTAA 60.445 40.000 0.00 0.00 43.74 2.10
162 163 3.181520 CGTTTTGCGATCCTCGAAATTCT 60.182 43.478 0.00 0.00 43.74 2.40
165 166 2.343101 TCGTTTTGCGATCCTCGAAAT 58.657 42.857 0.00 0.00 45.68 2.17
166 167 1.785768 TCGTTTTGCGATCCTCGAAA 58.214 45.000 0.00 0.00 45.68 3.46
167 168 3.500455 TCGTTTTGCGATCCTCGAA 57.500 47.368 0.00 0.00 45.68 3.71
206 207 8.922931 AATGTTATACATAGGTCATTCATGCA 57.077 30.769 0.00 0.00 37.97 3.96
207 208 8.454106 GGAATGTTATACATAGGTCATTCATGC 58.546 37.037 16.60 4.46 37.97 4.06
233 234 9.828852 CATGTAACATCCCAAATTTTCAATTTG 57.171 29.630 12.97 12.97 38.39 2.32
235 236 7.664731 TGCATGTAACATCCCAAATTTTCAATT 59.335 29.630 0.00 0.00 0.00 2.32
236 237 7.166851 TGCATGTAACATCCCAAATTTTCAAT 58.833 30.769 0.00 0.00 0.00 2.57
238 239 6.106648 TGCATGTAACATCCCAAATTTTCA 57.893 33.333 0.00 0.00 0.00 2.69
239 240 8.891671 ATATGCATGTAACATCCCAAATTTTC 57.108 30.769 10.16 0.00 0.00 2.29
240 241 9.683870 AAATATGCATGTAACATCCCAAATTTT 57.316 25.926 10.16 0.00 0.00 1.82
244 245 6.580788 CCAAATATGCATGTAACATCCCAAA 58.419 36.000 10.16 0.00 0.00 3.28
247 248 4.281688 AGCCAAATATGCATGTAACATCCC 59.718 41.667 10.16 0.00 0.00 3.85
249 250 7.040478 TCCTTAGCCAAATATGCATGTAACATC 60.040 37.037 10.16 0.00 0.00 3.06
252 253 6.263168 AGTCCTTAGCCAAATATGCATGTAAC 59.737 38.462 10.16 0.00 0.00 2.50
254 255 5.940617 AGTCCTTAGCCAAATATGCATGTA 58.059 37.500 10.16 0.00 0.00 2.29
259 260 3.149981 GGGAGTCCTTAGCCAAATATGC 58.850 50.000 9.58 0.00 0.00 3.14
260 261 3.403038 CGGGAGTCCTTAGCCAAATATG 58.597 50.000 9.58 0.00 0.00 1.78
261 262 2.224548 GCGGGAGTCCTTAGCCAAATAT 60.225 50.000 9.58 0.00 0.00 1.28
262 263 1.140252 GCGGGAGTCCTTAGCCAAATA 59.860 52.381 9.58 0.00 0.00 1.40
263 264 0.107165 GCGGGAGTCCTTAGCCAAAT 60.107 55.000 9.58 0.00 0.00 2.32
266 267 3.081409 GGCGGGAGTCCTTAGCCA 61.081 66.667 27.29 0.00 46.48 4.75
267 268 4.222847 CGGCGGGAGTCCTTAGCC 62.223 72.222 24.42 24.42 44.00 3.93
268 269 1.461911 ATACGGCGGGAGTCCTTAGC 61.462 60.000 13.24 12.17 0.00 3.09
269 270 1.038280 AATACGGCGGGAGTCCTTAG 58.962 55.000 13.24 2.32 0.00 2.18
270 271 0.748450 CAATACGGCGGGAGTCCTTA 59.252 55.000 13.24 0.00 0.00 2.69
271 272 1.520666 CAATACGGCGGGAGTCCTT 59.479 57.895 13.24 0.00 0.00 3.36
272 273 3.090219 GCAATACGGCGGGAGTCCT 62.090 63.158 13.24 0.00 0.00 3.85
273 274 2.588034 GCAATACGGCGGGAGTCC 60.588 66.667 13.24 0.00 0.00 3.85
274 275 1.227556 ATGCAATACGGCGGGAGTC 60.228 57.895 13.24 0.00 36.28 3.36
275 276 1.523711 CATGCAATACGGCGGGAGT 60.524 57.895 13.24 0.00 36.28 3.85
277 278 0.394938 ATACATGCAATACGGCGGGA 59.605 50.000 13.24 0.00 36.28 5.14
279 280 1.726791 GAGATACATGCAATACGGCGG 59.273 52.381 13.24 0.00 36.28 6.13
280 281 2.663602 GAGAGATACATGCAATACGGCG 59.336 50.000 4.80 4.80 36.28 6.46
283 284 6.149308 AGAGAGAGAGAGATACATGCAATACG 59.851 42.308 0.00 0.00 0.00 3.06
284 285 7.391554 AGAGAGAGAGAGAGATACATGCAATAC 59.608 40.741 0.00 0.00 0.00 1.89
285 286 7.460910 AGAGAGAGAGAGAGATACATGCAATA 58.539 38.462 0.00 0.00 0.00 1.90
287 288 5.693961 AGAGAGAGAGAGAGATACATGCAA 58.306 41.667 0.00 0.00 0.00 4.08
289 290 5.555017 AGAGAGAGAGAGAGAGATACATGC 58.445 45.833 0.00 0.00 0.00 4.06
292 293 6.377080 AGAGAGAGAGAGAGAGAGAGATACA 58.623 44.000 0.00 0.00 0.00 2.29
328 329 7.994334 GGGTCCTTTTATATTGGTGTGTGTATA 59.006 37.037 0.00 0.00 0.00 1.47
334 335 6.597832 TTTGGGTCCTTTTATATTGGTGTG 57.402 37.500 0.00 0.00 0.00 3.82
335 336 6.156083 CCATTTGGGTCCTTTTATATTGGTGT 59.844 38.462 0.00 0.00 0.00 4.16
353 354 3.707316 TGGTTTGGATCTACCCATTTGG 58.293 45.455 8.91 0.00 35.87 3.28
354 355 5.203528 AGATGGTTTGGATCTACCCATTTG 58.796 41.667 9.90 0.00 36.08 2.32
355 356 5.449553 GAGATGGTTTGGATCTACCCATTT 58.550 41.667 9.90 5.60 36.08 2.32
356 357 4.444876 CGAGATGGTTTGGATCTACCCATT 60.445 45.833 9.90 2.75 36.08 3.16
358 359 2.434336 CGAGATGGTTTGGATCTACCCA 59.566 50.000 8.91 4.85 38.00 4.51
360 361 3.492829 GGTCGAGATGGTTTGGATCTACC 60.493 52.174 0.00 0.00 39.54 3.18
361 362 3.718815 GGTCGAGATGGTTTGGATCTAC 58.281 50.000 0.00 0.00 29.97 2.59
362 363 2.361119 CGGTCGAGATGGTTTGGATCTA 59.639 50.000 0.00 0.00 29.97 1.98
364 365 1.134788 ACGGTCGAGATGGTTTGGATC 60.135 52.381 0.00 0.00 0.00 3.36
365 366 0.902531 ACGGTCGAGATGGTTTGGAT 59.097 50.000 0.00 0.00 0.00 3.41
367 368 0.037697 TGACGGTCGAGATGGTTTGG 60.038 55.000 3.34 0.00 0.00 3.28
368 369 1.790755 TTGACGGTCGAGATGGTTTG 58.209 50.000 3.34 0.00 0.00 2.93
370 371 2.028476 TGATTTGACGGTCGAGATGGTT 60.028 45.455 3.34 0.00 0.00 3.67
372 373 2.293677 TGATTTGACGGTCGAGATGG 57.706 50.000 3.34 0.00 0.00 3.51
373 374 3.190079 ACATGATTTGACGGTCGAGATG 58.810 45.455 0.00 7.81 0.00 2.90
375 376 3.313012 AACATGATTTGACGGTCGAGA 57.687 42.857 0.00 0.00 0.00 4.04
376 377 5.043903 AGATAACATGATTTGACGGTCGAG 58.956 41.667 0.00 0.00 0.00 4.04
379 380 4.260784 GCCAGATAACATGATTTGACGGTC 60.261 45.833 0.00 0.00 0.00 4.79
380 381 3.627577 GCCAGATAACATGATTTGACGGT 59.372 43.478 0.00 0.00 0.00 4.83
381 382 3.303329 CGCCAGATAACATGATTTGACGG 60.303 47.826 0.00 0.00 0.00 4.79
382 383 3.303329 CCGCCAGATAACATGATTTGACG 60.303 47.826 0.00 0.00 0.00 4.35
383 384 3.627577 ACCGCCAGATAACATGATTTGAC 59.372 43.478 0.00 0.00 0.00 3.18
385 386 4.096231 TGAACCGCCAGATAACATGATTTG 59.904 41.667 0.00 0.00 0.00 2.32
386 387 4.269183 TGAACCGCCAGATAACATGATTT 58.731 39.130 0.00 0.00 0.00 2.17
389 390 3.342377 TTGAACCGCCAGATAACATGA 57.658 42.857 0.00 0.00 0.00 3.07
390 391 4.601019 GATTTGAACCGCCAGATAACATG 58.399 43.478 0.00 0.00 0.00 3.21
393 394 2.538939 GCGATTTGAACCGCCAGATAAC 60.539 50.000 0.00 0.00 45.06 1.89
396 397 2.098293 GCGATTTGAACCGCCAGAT 58.902 52.632 0.00 0.00 45.06 2.90
402 403 3.201726 ACATTGAAGCGATTTGAACCG 57.798 42.857 0.00 0.00 0.00 4.44
403 404 4.545610 TCAACATTGAAGCGATTTGAACC 58.454 39.130 0.00 0.00 33.55 3.62
404 405 4.089065 GCTCAACATTGAAGCGATTTGAAC 59.911 41.667 0.00 0.00 36.64 3.18
407 408 3.362831 GTGCTCAACATTGAAGCGATTTG 59.637 43.478 0.00 0.00 36.64 2.32
412 413 0.592637 TGGTGCTCAACATTGAAGCG 59.407 50.000 0.00 0.00 36.64 4.68
415 416 3.733380 CGTGTTTGGTGCTCAACATTGAA 60.733 43.478 0.00 0.00 36.64 2.69
416 417 2.223456 CGTGTTTGGTGCTCAACATTGA 60.223 45.455 0.00 0.00 34.67 2.57
417 418 2.118683 CGTGTTTGGTGCTCAACATTG 58.881 47.619 0.00 0.00 34.67 2.82
421 422 2.271821 AAACGTGTTTGGTGCTCAAC 57.728 45.000 0.00 0.00 34.67 3.18
422 423 3.728268 CGTTAAACGTGTTTGGTGCTCAA 60.728 43.478 8.19 0.00 36.74 3.02
424 425 2.368685 CGTTAAACGTGTTTGGTGCTC 58.631 47.619 8.19 0.00 36.74 4.26
426 427 0.841356 GCGTTAAACGTGTTTGGTGC 59.159 50.000 8.19 5.33 44.73 5.01
427 428 2.031191 AGAGCGTTAAACGTGTTTGGTG 59.969 45.455 8.19 0.00 44.73 4.17
428 429 2.282407 AGAGCGTTAAACGTGTTTGGT 58.718 42.857 8.19 0.00 44.73 3.67
429 430 4.455917 TTAGAGCGTTAAACGTGTTTGG 57.544 40.909 8.19 0.00 44.73 3.28
430 431 7.424452 GGATAATTAGAGCGTTAAACGTGTTTG 59.576 37.037 8.19 0.00 44.73 2.93
432 433 6.591062 TGGATAATTAGAGCGTTAAACGTGTT 59.409 34.615 0.00 0.00 44.73 3.32
434 435 6.408428 GTGGATAATTAGAGCGTTAAACGTG 58.592 40.000 0.00 0.00 44.73 4.49
436 437 5.521010 TGGTGGATAATTAGAGCGTTAAACG 59.479 40.000 0.00 0.00 45.88 3.60
438 439 6.537301 CAGTGGTGGATAATTAGAGCGTTAAA 59.463 38.462 0.00 0.00 0.00 1.52
439 440 6.046593 CAGTGGTGGATAATTAGAGCGTTAA 58.953 40.000 0.00 0.00 0.00 2.01
440 441 5.128171 ACAGTGGTGGATAATTAGAGCGTTA 59.872 40.000 0.00 0.00 0.00 3.18
441 442 4.081087 ACAGTGGTGGATAATTAGAGCGTT 60.081 41.667 0.00 0.00 0.00 4.84
442 443 3.451178 ACAGTGGTGGATAATTAGAGCGT 59.549 43.478 0.00 0.00 0.00 5.07
443 444 4.051922 GACAGTGGTGGATAATTAGAGCG 58.948 47.826 0.00 0.00 0.00 5.03
444 445 5.023533 TGACAGTGGTGGATAATTAGAGC 57.976 43.478 0.00 0.00 0.00 4.09
445 446 8.424918 ACTAATGACAGTGGTGGATAATTAGAG 58.575 37.037 0.00 0.00 0.00 2.43
447 448 8.964476 AACTAATGACAGTGGTGGATAATTAG 57.036 34.615 0.00 0.00 0.00 1.73
452 453 9.826574 GTTTATAACTAATGACAGTGGTGGATA 57.173 33.333 0.00 0.00 0.00 2.59
453 454 8.325787 TGTTTATAACTAATGACAGTGGTGGAT 58.674 33.333 0.00 0.00 0.00 3.41
454 455 7.604927 GTGTTTATAACTAATGACAGTGGTGGA 59.395 37.037 0.00 0.00 0.00 4.02
455 456 7.412563 CGTGTTTATAACTAATGACAGTGGTGG 60.413 40.741 0.00 0.00 0.00 4.61
462 463 9.866936 GTCAAAACGTGTTTATAACTAATGACA 57.133 29.630 13.55 0.00 31.63 3.58
467 468 9.919348 GTTGAGTCAAAACGTGTTTATAACTAA 57.081 29.630 7.25 0.00 31.63 2.24
468 469 9.096160 TGTTGAGTCAAAACGTGTTTATAACTA 57.904 29.630 7.25 0.00 31.63 2.24
469 470 7.906527 GTGTTGAGTCAAAACGTGTTTATAACT 59.093 33.333 10.41 3.29 31.63 2.24
470 471 7.906527 AGTGTTGAGTCAAAACGTGTTTATAAC 59.093 33.333 18.44 0.00 36.75 1.89
473 474 6.431198 AGTGTTGAGTCAAAACGTGTTTAT 57.569 33.333 18.44 0.00 36.75 1.40
475 476 4.759516 AGTGTTGAGTCAAAACGTGTTT 57.240 36.364 18.44 0.30 36.75 2.83
477 478 4.510340 GGATAGTGTTGAGTCAAAACGTGT 59.490 41.667 18.44 9.86 36.75 4.49
481 482 5.763204 TCAAGGGATAGTGTTGAGTCAAAAC 59.237 40.000 17.14 17.14 32.20 2.43
482 483 5.935945 TCAAGGGATAGTGTTGAGTCAAAA 58.064 37.500 7.25 0.00 0.00 2.44
483 484 5.560722 TCAAGGGATAGTGTTGAGTCAAA 57.439 39.130 7.25 0.00 0.00 2.69
484 485 5.560722 TTCAAGGGATAGTGTTGAGTCAA 57.439 39.130 0.08 0.08 32.00 3.18
485 486 5.560722 TTTCAAGGGATAGTGTTGAGTCA 57.439 39.130 0.00 0.00 32.00 3.41
486 487 6.314896 CAGATTTCAAGGGATAGTGTTGAGTC 59.685 42.308 0.00 0.00 32.00 3.36
489 490 4.943705 GCAGATTTCAAGGGATAGTGTTGA 59.056 41.667 0.00 0.00 0.00 3.18
490 491 4.096984 GGCAGATTTCAAGGGATAGTGTTG 59.903 45.833 0.00 0.00 0.00 3.33
492 493 3.266772 TGGCAGATTTCAAGGGATAGTGT 59.733 43.478 0.00 0.00 0.00 3.55
493 494 3.889815 TGGCAGATTTCAAGGGATAGTG 58.110 45.455 0.00 0.00 0.00 2.74
496 497 3.225104 GCATGGCAGATTTCAAGGGATA 58.775 45.455 0.00 0.00 0.00 2.59
499 500 1.187974 TGCATGGCAGATTTCAAGGG 58.812 50.000 0.00 0.00 33.32 3.95
501 502 4.360563 GAGAATGCATGGCAGATTTCAAG 58.639 43.478 0.00 0.00 43.65 3.02
505 506 2.098607 CACGAGAATGCATGGCAGATTT 59.901 45.455 0.00 0.00 43.65 2.17
508 509 0.249955 TCACGAGAATGCATGGCAGA 59.750 50.000 0.00 0.00 43.65 4.26
509 510 1.089112 TTCACGAGAATGCATGGCAG 58.911 50.000 0.00 0.00 43.65 4.85
512 513 4.164822 ACTTTTTCACGAGAATGCATGG 57.835 40.909 0.00 0.00 32.89 3.66
515 516 6.964908 TCAATTACTTTTTCACGAGAATGCA 58.035 32.000 0.00 0.00 32.89 3.96
516 517 9.722056 ATATCAATTACTTTTTCACGAGAATGC 57.278 29.630 0.00 0.00 32.89 3.56
538 539 8.189709 TGCACGCTGATATTTGATAAGATATC 57.810 34.615 0.00 0.00 36.33 1.63
539 540 8.446273 GTTGCACGCTGATATTTGATAAGATAT 58.554 33.333 0.00 0.00 0.00 1.63
540 541 7.440856 TGTTGCACGCTGATATTTGATAAGATA 59.559 33.333 0.00 0.00 0.00 1.98
542 543 5.584251 TGTTGCACGCTGATATTTGATAAGA 59.416 36.000 0.00 0.00 0.00 2.10
543 544 5.809464 TGTTGCACGCTGATATTTGATAAG 58.191 37.500 0.00 0.00 0.00 1.73
544 545 5.584251 TCTGTTGCACGCTGATATTTGATAA 59.416 36.000 0.00 0.00 0.00 1.75
548 549 3.745332 TCTGTTGCACGCTGATATTTG 57.255 42.857 0.00 0.00 0.00 2.32
549 550 7.821359 AGATATATCTGTTGCACGCTGATATTT 59.179 33.333 22.77 18.34 38.02 1.40
551 552 6.871844 AGATATATCTGTTGCACGCTGATAT 58.128 36.000 14.60 21.96 39.31 1.63
553 554 5.144692 AGATATATCTGTTGCACGCTGAT 57.855 39.130 14.60 12.29 35.42 2.90
554 555 4.590850 AGATATATCTGTTGCACGCTGA 57.409 40.909 14.60 0.00 35.42 4.26
555 556 5.119279 GGTAAGATATATCTGTTGCACGCTG 59.881 44.000 16.01 0.00 37.19 5.18
556 557 5.011125 AGGTAAGATATATCTGTTGCACGCT 59.989 40.000 16.01 0.00 37.19 5.07
557 558 5.230942 AGGTAAGATATATCTGTTGCACGC 58.769 41.667 16.01 4.79 37.19 5.34
558 559 8.988064 ATTAGGTAAGATATATCTGTTGCACG 57.012 34.615 16.01 0.00 37.19 5.34
602 603 6.987404 TGCAATGCACGTTTATATTAGGTAGA 59.013 34.615 2.72 0.00 31.71 2.59
603 604 7.184800 TGCAATGCACGTTTATATTAGGTAG 57.815 36.000 2.72 0.00 31.71 3.18
620 621 7.169308 AGACTAGTAATAATGTACGTGCAATGC 59.831 37.037 11.22 0.00 0.00 3.56
649 650 9.333724 AGATTTTCATTTTGTGCAGAGATTTTT 57.666 25.926 0.00 0.00 0.00 1.94
650 651 8.897872 AGATTTTCATTTTGTGCAGAGATTTT 57.102 26.923 0.00 0.00 0.00 1.82
651 652 8.365647 AGAGATTTTCATTTTGTGCAGAGATTT 58.634 29.630 0.00 0.00 0.00 2.17
652 653 7.893658 AGAGATTTTCATTTTGTGCAGAGATT 58.106 30.769 0.00 0.00 0.00 2.40
653 654 7.393796 AGAGAGATTTTCATTTTGTGCAGAGAT 59.606 33.333 0.00 0.00 0.00 2.75
654 655 6.713903 AGAGAGATTTTCATTTTGTGCAGAGA 59.286 34.615 0.00 0.00 0.00 3.10
655 656 6.910995 AGAGAGATTTTCATTTTGTGCAGAG 58.089 36.000 0.00 0.00 0.00 3.35
656 657 6.889301 AGAGAGATTTTCATTTTGTGCAGA 57.111 33.333 0.00 0.00 0.00 4.26
657 658 7.220300 GCATAGAGAGATTTTCATTTTGTGCAG 59.780 37.037 0.00 0.00 0.00 4.41
658 659 7.031372 GCATAGAGAGATTTTCATTTTGTGCA 58.969 34.615 0.00 0.00 0.00 4.57
660 661 7.246311 ACGCATAGAGAGATTTTCATTTTGTG 58.754 34.615 0.00 0.00 0.00 3.33
661 662 7.383102 ACGCATAGAGAGATTTTCATTTTGT 57.617 32.000 0.00 0.00 0.00 2.83
667 668 6.656632 AGGATACGCATAGAGAGATTTTCA 57.343 37.500 0.00 0.00 46.39 2.69
1443 4286 1.351017 TGGATGGTCTTCGGCTTCTTT 59.649 47.619 0.00 0.00 0.00 2.52
1553 7725 7.063308 CCCATTTCCATTAACGAAACATCAAAG 59.937 37.037 0.00 0.00 32.30 2.77
1679 7970 6.124088 AGTTACAAACACAGCTTTCTGAAG 57.876 37.500 0.00 0.00 42.95 3.02
1872 8383 9.676861 GGTGGAAAAAGTAACACTATATACCTT 57.323 33.333 0.00 0.00 34.42 3.50
2002 8514 8.945057 CCTATATGGGAAAAACAACAATTTTGG 58.055 33.333 0.00 0.00 32.12 3.28
2054 8566 1.270625 TGCTCCGACAAGTACCTTTGG 60.271 52.381 0.55 0.00 32.32 3.28
2055 8567 2.069273 CTGCTCCGACAAGTACCTTTG 58.931 52.381 0.00 0.00 0.00 2.77
2056 8568 1.968493 TCTGCTCCGACAAGTACCTTT 59.032 47.619 0.00 0.00 0.00 3.11
2057 8569 1.546476 CTCTGCTCCGACAAGTACCTT 59.454 52.381 0.00 0.00 0.00 3.50
2058 8570 1.178276 CTCTGCTCCGACAAGTACCT 58.822 55.000 0.00 0.00 0.00 3.08
2059 8571 0.889306 ACTCTGCTCCGACAAGTACC 59.111 55.000 0.00 0.00 0.00 3.34
2069 8581 4.836125 TTTCATTTGTTCACTCTGCTCC 57.164 40.909 0.00 0.00 0.00 4.70
2174 8709 3.930336 CTTGACTACCACAAGCATCAGA 58.070 45.455 0.00 0.00 38.28 3.27
2238 8777 9.981114 CCTTTCGGGCTTTATCATTAATTTTAT 57.019 29.630 0.00 0.00 0.00 1.40
2263 8802 5.344933 CCTTTGCTTTTAATCGTGTTTAGCC 59.655 40.000 0.00 0.00 0.00 3.93
2308 8848 8.761575 TTGAAGCATAAAAATCCATGTCTTTC 57.238 30.769 0.00 0.00 0.00 2.62
2330 8870 2.951642 CAACCCTGAAGTTTGAGCTTGA 59.048 45.455 0.00 0.00 0.00 3.02
2401 8952 6.970484 AGAACCAAACACACATCATAACTTC 58.030 36.000 0.00 0.00 0.00 3.01
2408 8959 2.100584 GGCAAGAACCAAACACACATCA 59.899 45.455 0.00 0.00 0.00 3.07


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

AutoCloner maintained by Alex Coulton.