Multiple sequence alignment - TraesCS1B01G465500

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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 TraesCS1B01G465500 chr1B 100.000 5755 0 0 1 5755 676199366 676205120 0.000000e+00 10628.0
1 TraesCS1B01G465500 chr1B 74.574 1821 353 74 2249 4033 676196264 676194518 0.000000e+00 697.0
2 TraesCS1B01G465500 chr1B 91.429 140 11 1 1096 1234 676197628 676197489 2.120000e-44 191.0
3 TraesCS1B01G465500 chr1B 74.270 548 93 24 3400 3933 570273448 570273961 2.740000e-43 187.0
4 TraesCS1B01G465500 chr1B 81.481 216 33 5 2669 2881 676458447 676458236 2.760000e-38 171.0
5 TraesCS1B01G465500 chr1B 80.660 212 40 1 2670 2881 676391093 676390883 4.610000e-36 163.0
6 TraesCS1B01G465500 chr1B 81.699 153 28 0 4510 4662 676466615 676466463 1.680000e-25 128.0
7 TraesCS1B01G465500 chr1D 91.234 2407 129 36 549 2903 485713815 485716191 0.000000e+00 3201.0
8 TraesCS1B01G465500 chr1D 92.447 2158 122 19 2913 5047 485716384 485718523 0.000000e+00 3044.0
9 TraesCS1B01G465500 chr1D 75.782 1503 256 66 2249 3713 485712231 485710799 0.000000e+00 660.0
10 TraesCS1B01G465500 chr1D 86.957 207 20 6 1067 1269 485713774 485713571 5.800000e-55 226.0
11 TraesCS1B01G465500 chr1D 74.727 550 88 27 3400 3933 421034393 421034907 1.260000e-46 198.0
12 TraesCS1B01G465500 chr1D 86.905 168 22 0 1068 1235 421031467 421031634 7.610000e-44 189.0
13 TraesCS1B01G465500 chr1D 85.207 169 21 3 1080 1244 485573722 485573554 2.760000e-38 171.0
14 TraesCS1B01G465500 chr1D 93.578 109 6 1 5043 5151 485718550 485718657 1.660000e-35 161.0
15 TraesCS1B01G465500 chr1D 79.812 213 42 1 2669 2881 485818773 485818562 2.780000e-33 154.0
16 TraesCS1B01G465500 chr1D 94.030 67 3 1 5219 5284 113846601 113846535 3.670000e-17 100.0
17 TraesCS1B01G465500 chr1D 95.082 61 3 0 5224 5284 401142990 401143050 4.750000e-16 97.1
18 TraesCS1B01G465500 chr1A 93.705 1811 82 12 2256 4042 583302834 583304636 0.000000e+00 2684.0
19 TraesCS1B01G465500 chr1A 88.980 1824 121 31 461 2258 583300985 583302754 0.000000e+00 2182.0
20 TraesCS1B01G465500 chr1A 90.590 882 48 11 4039 4903 583304724 583305587 0.000000e+00 1136.0
21 TraesCS1B01G465500 chr1A 76.066 1876 335 76 2249 4075 583297503 583295693 0.000000e+00 872.0
22 TraesCS1B01G465500 chr1A 82.174 460 57 11 3 459 583300364 583300801 7.040000e-99 372.0
23 TraesCS1B01G465500 chr1A 75.000 548 87 26 3400 3933 517411937 517412448 2.100000e-49 207.0
24 TraesCS1B01G465500 chr1A 86.826 167 22 0 1069 1235 517408958 517409124 2.740000e-43 187.0
25 TraesCS1B01G465500 chr1A 85.714 182 16 7 1096 1269 583299353 583299174 3.540000e-42 183.0
26 TraesCS1B01G465500 chr1A 85.965 171 20 3 1078 1244 583132526 583132356 4.580000e-41 180.0
27 TraesCS1B01G465500 chr1A 81.046 153 29 0 4510 4662 583463121 583462969 7.830000e-24 122.0
28 TraesCS1B01G465500 chr7B 96.992 532 15 1 5225 5755 57202250 57201719 0.000000e+00 893.0
29 TraesCS1B01G465500 chr7D 87.523 537 55 5 5229 5755 473484737 473485271 1.370000e-170 610.0
30 TraesCS1B01G465500 chr5B 75.793 599 129 11 2294 2882 585006097 585006689 7.300000e-74 289.0
31 TraesCS1B01G465500 chr5A 75.125 599 133 12 2294 2882 596566177 596566769 3.420000e-67 267.0
32 TraesCS1B01G465500 chr3D 93.056 72 3 2 5215 5284 497712651 497712580 2.840000e-18 104.0
33 TraesCS1B01G465500 chr3D 96.774 62 2 0 5225 5286 615026719 615026658 2.840000e-18 104.0
34 TraesCS1B01G465500 chr2D 95.312 64 3 0 5221 5284 287841440 287841377 1.020000e-17 102.0
35 TraesCS1B01G465500 chr5D 95.082 61 3 0 5224 5284 443810127 443810067 4.750000e-16 97.1
36 TraesCS1B01G465500 chr6D 91.429 70 5 1 5220 5288 264675897 264675828 1.710000e-15 95.3
37 TraesCS1B01G465500 chr4D 93.750 64 2 2 5222 5284 216526522 216526584 1.710000e-15 95.3


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 TraesCS1B01G465500 chr1B 676199366 676205120 5754 False 10628.000000 10628 100.000000 1 5755 1 chr1B.!!$F2 5754
1 TraesCS1B01G465500 chr1B 676194518 676197628 3110 True 444.000000 697 83.001500 1096 4033 2 chr1B.!!$R4 2937
2 TraesCS1B01G465500 chr1D 485713815 485718657 4842 False 2135.333333 3201 92.419667 549 5151 3 chr1D.!!$F3 4602
3 TraesCS1B01G465500 chr1D 485710799 485713774 2975 True 443.000000 660 81.369500 1067 3713 2 chr1D.!!$R4 2646
4 TraesCS1B01G465500 chr1A 583300364 583305587 5223 False 1593.500000 2684 88.862250 3 4903 4 chr1A.!!$F2 4900
5 TraesCS1B01G465500 chr1A 583295693 583299353 3660 True 527.500000 872 80.890000 1096 4075 2 chr1A.!!$R3 2979
6 TraesCS1B01G465500 chr7B 57201719 57202250 531 True 893.000000 893 96.992000 5225 5755 1 chr7B.!!$R1 530
7 TraesCS1B01G465500 chr7D 473484737 473485271 534 False 610.000000 610 87.523000 5229 5755 1 chr7D.!!$F1 526
8 TraesCS1B01G465500 chr5B 585006097 585006689 592 False 289.000000 289 75.793000 2294 2882 1 chr5B.!!$F1 588
9 TraesCS1B01G465500 chr5A 596566177 596566769 592 False 267.000000 267 75.125000 2294 2882 1 chr5A.!!$F1 588

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
284 288 0.031817 CTCCCCCTGCCCATTCAAAT 60.032 55.000 0.00 0.00 0.00 2.32 F
285 289 0.032217 TCCCCCTGCCCATTCAAATC 60.032 55.000 0.00 0.00 0.00 2.17 F
290 294 0.031817 CTGCCCATTCAAATCCCCCT 60.032 55.000 0.00 0.00 0.00 4.79 F
1437 1697 0.167908 GTTTGCATTGCCGATCGACA 59.832 50.000 18.66 8.80 0.00 4.35 F
1987 3023 0.389426 GCCTAGAAACTCGGCGTCAA 60.389 55.000 6.85 0.00 32.84 3.18 F
3705 5269 1.070309 GCCGCTAGAGATTCAATTGCG 60.070 52.381 0.00 8.99 41.30 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1699 2731 1.078426 CCCCACCATGAACTCGGAC 60.078 63.158 0.00 0.0 0.00 4.79 R
1987 3023 2.446435 CCATCAAATCCACGAAACCCT 58.554 47.619 0.00 0.0 0.00 4.34 R
2125 3161 5.064452 GGTTGAGAAGTAGAGCATGTTGATG 59.936 44.000 0.00 0.0 0.00 3.07 R
3424 4972 1.189446 GCCGAACTGTATATCGCAACG 59.811 52.381 0.00 0.0 37.73 4.10 R
3946 5516 0.041090 CCAAGGGCCCAAATGTAGGT 59.959 55.000 27.56 0.0 0.00 3.08 R
4975 6657 0.605589 AACAGTCCTCGAAGCCAGAG 59.394 55.000 0.00 0.0 35.60 3.35 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
37 38 3.926616 TGAAGAGGAAGAACGTCATTCC 58.073 45.455 19.21 19.21 44.49 3.01
38 39 3.323691 TGAAGAGGAAGAACGTCATTCCA 59.676 43.478 25.33 8.77 46.21 3.53
56 57 3.536158 CCACATGTGGTAAAGTCGTTG 57.464 47.619 32.94 6.34 45.53 4.10
80 81 9.627123 TTGGGTGAGGTGAAAATAATATCTTAG 57.373 33.333 0.00 0.00 0.00 2.18
83 84 8.218488 GGTGAGGTGAAAATAATATCTTAGGGT 58.782 37.037 0.00 0.00 0.00 4.34
98 99 1.120530 AGGGTATCTTCAACGCCGAT 58.879 50.000 0.00 0.00 0.00 4.18
99 100 1.068741 AGGGTATCTTCAACGCCGATC 59.931 52.381 0.00 0.00 0.00 3.69
110 111 1.445871 ACGCCGATCCTTAAAACACC 58.554 50.000 0.00 0.00 0.00 4.16
111 112 0.730840 CGCCGATCCTTAAAACACCC 59.269 55.000 0.00 0.00 0.00 4.61
112 113 1.828979 GCCGATCCTTAAAACACCCA 58.171 50.000 0.00 0.00 0.00 4.51
113 114 1.471287 GCCGATCCTTAAAACACCCAC 59.529 52.381 0.00 0.00 0.00 4.61
115 116 3.150767 CCGATCCTTAAAACACCCACAA 58.849 45.455 0.00 0.00 0.00 3.33
117 118 4.219725 CCGATCCTTAAAACACCCACAAAT 59.780 41.667 0.00 0.00 0.00 2.32
120 121 5.523438 TCCTTAAAACACCCACAAATGTC 57.477 39.130 0.00 0.00 0.00 3.06
126 127 1.203001 ACACCCACAAATGTCCGGATT 60.203 47.619 7.81 0.00 0.00 3.01
127 128 2.040545 ACACCCACAAATGTCCGGATTA 59.959 45.455 7.81 0.00 0.00 1.75
129 130 3.508012 CACCCACAAATGTCCGGATTAAA 59.492 43.478 7.81 0.00 0.00 1.52
130 131 3.508402 ACCCACAAATGTCCGGATTAAAC 59.492 43.478 7.81 0.00 0.00 2.01
138 139 2.027561 TGTCCGGATTAAACTGTCCAGG 60.028 50.000 7.81 0.00 34.05 4.45
139 140 2.027469 GTCCGGATTAAACTGTCCAGGT 60.027 50.000 7.81 0.00 34.05 4.00
143 144 4.563993 CCGGATTAAACTGTCCAGGTGTAA 60.564 45.833 0.00 0.00 34.05 2.41
144 145 5.183228 CGGATTAAACTGTCCAGGTGTAAT 58.817 41.667 0.00 0.59 34.05 1.89
146 147 6.150474 CGGATTAAACTGTCCAGGTGTAATTT 59.850 38.462 0.00 0.00 34.05 1.82
158 159 5.469479 CAGGTGTAATTTTCCATCCAACAC 58.531 41.667 0.00 0.00 36.02 3.32
159 160 4.217550 AGGTGTAATTTTCCATCCAACACG 59.782 41.667 0.00 0.00 37.27 4.49
172 173 0.580104 CAACACGGACCGTCTTTGTC 59.420 55.000 18.72 0.00 38.32 3.18
176 177 3.946907 GGACCGTCTTTGTCCGTG 58.053 61.111 0.00 0.00 42.63 4.94
178 179 1.364901 GACCGTCTTTGTCCGTGGA 59.635 57.895 0.00 0.00 0.00 4.02
194 195 0.245266 TGGACGCATTCGCTTGTCTA 59.755 50.000 0.00 0.00 39.84 2.59
202 203 4.029308 CGCATTCGCTTGTCTAAATTTTCG 60.029 41.667 0.00 0.00 35.30 3.46
209 213 6.419413 TCGCTTGTCTAAATTTTCGCAAAAAT 59.581 30.769 0.00 0.00 44.97 1.82
217 221 9.035607 TCTAAATTTTCGCAAAAATGCAAACTA 57.964 25.926 0.00 0.00 42.82 2.24
222 226 3.057596 TCGCAAAAATGCAAACTAGAGGG 60.058 43.478 0.00 0.00 34.41 4.30
223 227 3.588955 GCAAAAATGCAAACTAGAGGGG 58.411 45.455 0.00 0.00 34.41 4.79
224 228 3.617288 GCAAAAATGCAAACTAGAGGGGG 60.617 47.826 0.00 0.00 34.41 5.40
226 230 3.372440 AAATGCAAACTAGAGGGGGAG 57.628 47.619 0.00 0.00 0.00 4.30
231 235 3.082548 GCAAACTAGAGGGGGAGTTTTC 58.917 50.000 0.00 0.00 41.93 2.29
236 240 2.856988 AGGGGGAGTTTTCGGGCA 60.857 61.111 0.00 0.00 0.00 5.36
262 266 1.251527 CCACTGCCACGTAGGACTCT 61.252 60.000 8.04 0.00 41.22 3.24
266 270 0.251209 TGCCACGTAGGACTCTGACT 60.251 55.000 8.04 0.00 41.22 3.41
269 273 1.096416 CACGTAGGACTCTGACTCCC 58.904 60.000 0.00 0.00 0.00 4.30
272 276 0.632294 GTAGGACTCTGACTCCCCCT 59.368 60.000 0.37 0.00 0.00 4.79
273 277 0.631753 TAGGACTCTGACTCCCCCTG 59.368 60.000 0.00 0.00 0.00 4.45
274 278 2.363172 GGACTCTGACTCCCCCTGC 61.363 68.421 0.00 0.00 0.00 4.85
275 279 2.284995 ACTCTGACTCCCCCTGCC 60.285 66.667 0.00 0.00 0.00 4.85
276 280 3.086600 CTCTGACTCCCCCTGCCC 61.087 72.222 0.00 0.00 0.00 5.36
277 281 3.931631 CTCTGACTCCCCCTGCCCA 62.932 68.421 0.00 0.00 0.00 5.36
278 282 2.693864 CTGACTCCCCCTGCCCAT 60.694 66.667 0.00 0.00 0.00 4.00
279 283 2.204291 TGACTCCCCCTGCCCATT 60.204 61.111 0.00 0.00 0.00 3.16
280 284 2.276309 CTGACTCCCCCTGCCCATTC 62.276 65.000 0.00 0.00 0.00 2.67
281 285 2.204291 ACTCCCCCTGCCCATTCA 60.204 61.111 0.00 0.00 0.00 2.57
282 286 1.856873 ACTCCCCCTGCCCATTCAA 60.857 57.895 0.00 0.00 0.00 2.69
283 287 1.387737 CTCCCCCTGCCCATTCAAA 59.612 57.895 0.00 0.00 0.00 2.69
284 288 0.031817 CTCCCCCTGCCCATTCAAAT 60.032 55.000 0.00 0.00 0.00 2.32
285 289 0.032217 TCCCCCTGCCCATTCAAATC 60.032 55.000 0.00 0.00 0.00 2.17
286 290 1.050421 CCCCCTGCCCATTCAAATCC 61.050 60.000 0.00 0.00 0.00 3.01
287 291 1.050421 CCCCTGCCCATTCAAATCCC 61.050 60.000 0.00 0.00 0.00 3.85
288 292 1.050421 CCCTGCCCATTCAAATCCCC 61.050 60.000 0.00 0.00 0.00 4.81
289 293 1.050421 CCTGCCCATTCAAATCCCCC 61.050 60.000 0.00 0.00 0.00 5.40
290 294 0.031817 CTGCCCATTCAAATCCCCCT 60.032 55.000 0.00 0.00 0.00 4.79
291 295 0.417035 TGCCCATTCAAATCCCCCTT 59.583 50.000 0.00 0.00 0.00 3.95
292 296 1.648568 TGCCCATTCAAATCCCCCTTA 59.351 47.619 0.00 0.00 0.00 2.69
293 297 2.249743 TGCCCATTCAAATCCCCCTTAT 59.750 45.455 0.00 0.00 0.00 1.73
294 298 2.634453 GCCCATTCAAATCCCCCTTATG 59.366 50.000 0.00 0.00 0.00 1.90
295 299 3.242011 CCCATTCAAATCCCCCTTATGG 58.758 50.000 0.00 0.00 0.00 2.74
309 313 2.107031 CCTTATGGGTCTGCATCCATCA 59.893 50.000 16.44 8.08 42.28 3.07
325 329 7.772292 TGCATCCATCAATATAGATAGAAAGCC 59.228 37.037 0.00 0.00 0.00 4.35
349 353 6.148948 CCAAGATTTTACACGATGAAAGCAA 58.851 36.000 0.00 0.00 0.00 3.91
352 356 7.202016 AGATTTTACACGATGAAAGCAAGAA 57.798 32.000 0.00 0.00 0.00 2.52
366 370 7.202526 TGAAAGCAAGAATTACAAGTTTGAGG 58.797 34.615 0.00 0.00 0.00 3.86
380 384 1.707106 TTGAGGTTCGGGTCTACACA 58.293 50.000 0.00 0.00 0.00 3.72
383 387 2.036733 TGAGGTTCGGGTCTACACAAAG 59.963 50.000 0.00 0.00 0.00 2.77
422 426 5.255687 TCAAAACATCACATGATACCTGCT 58.744 37.500 0.00 0.00 32.63 4.24
475 661 8.246180 AGTATTCTTTGGCATTCATGTACTTTG 58.754 33.333 0.00 0.00 0.00 2.77
477 663 6.647334 TCTTTGGCATTCATGTACTTTGAA 57.353 33.333 12.26 12.26 37.49 2.69
486 672 7.410728 GCATTCATGTACTTTGAAAAATCACCG 60.411 37.037 13.42 0.00 36.72 4.94
491 677 8.638565 CATGTACTTTGAAAAATCACCGATTTC 58.361 33.333 2.62 0.00 40.77 2.17
547 733 8.154203 TCATATAACCTTGATTAAAGCGATGGA 58.846 33.333 0.00 0.00 34.24 3.41
552 738 5.066505 ACCTTGATTAAAGCGATGGATTCAC 59.933 40.000 0.00 0.00 34.24 3.18
570 756 8.637986 TGGATTCACCAATGCCTATATTTTTAC 58.362 33.333 0.00 0.00 46.75 2.01
606 793 9.260002 AGATTTAAATGTCGAAGCAAAAATTGT 57.740 25.926 5.17 0.00 0.00 2.71
815 1007 4.007659 GGGGATTAGAAGCAGAAAAACGA 58.992 43.478 0.00 0.00 0.00 3.85
824 1016 6.564328 AGAAGCAGAAAAACGAAAGAACAAT 58.436 32.000 0.00 0.00 0.00 2.71
853 1045 2.731571 CGGATTCTCCTTGGGCCGA 61.732 63.158 0.00 0.00 41.11 5.54
905 1097 2.106683 GCCCAACATCTCCCGTTCG 61.107 63.158 0.00 0.00 0.00 3.95
909 1101 2.589157 AACATCTCCCGTTCGGCCA 61.589 57.895 2.24 0.00 0.00 5.36
918 1110 1.738099 CGTTCGGCCACTTCTCCTG 60.738 63.158 2.24 0.00 0.00 3.86
927 1119 1.066573 CCACTTCTCCTGCACGATCTT 60.067 52.381 0.00 0.00 0.00 2.40
1008 1205 0.680921 AAGGCCGATCAATGGTGGTG 60.681 55.000 0.00 0.00 0.00 4.17
1071 1268 0.627986 AGGGATGCCAAGGAAAGGAG 59.372 55.000 5.86 0.00 0.00 3.69
1072 1269 0.396278 GGGATGCCAAGGAAAGGAGG 60.396 60.000 0.00 0.00 0.00 4.30
1073 1270 0.625849 GGATGCCAAGGAAAGGAGGA 59.374 55.000 0.00 0.00 0.00 3.71
1074 1271 1.409381 GGATGCCAAGGAAAGGAGGAG 60.409 57.143 0.00 0.00 0.00 3.69
1075 1272 0.627986 ATGCCAAGGAAAGGAGGAGG 59.372 55.000 0.00 0.00 0.00 4.30
1076 1273 1.379176 GCCAAGGAAAGGAGGAGGC 60.379 63.158 0.00 0.00 0.00 4.70
1284 1503 2.146724 CCCTCCATGCCCCGTATGA 61.147 63.158 0.00 0.00 0.00 2.15
1288 1507 0.692756 TCCATGCCCCGTATGAAGGA 60.693 55.000 0.00 0.00 0.00 3.36
1289 1508 0.182537 CCATGCCCCGTATGAAGGAA 59.817 55.000 0.00 0.00 0.00 3.36
1292 1511 1.208706 TGCCCCGTATGAAGGAATGA 58.791 50.000 0.00 0.00 0.00 2.57
1293 1512 1.134220 TGCCCCGTATGAAGGAATGAC 60.134 52.381 0.00 0.00 0.00 3.06
1335 1585 1.012086 CATGTCAAGCTGGATCGTGG 58.988 55.000 0.00 0.00 0.00 4.94
1377 1627 9.644993 GAAGTGCAAAATTTACCATTTTGTAAC 57.355 29.630 17.19 15.47 45.63 2.50
1437 1697 0.167908 GTTTGCATTGCCGATCGACA 59.832 50.000 18.66 8.80 0.00 4.35
1482 1911 4.724279 AATGTCCCCCTGTGGAATATAC 57.276 45.455 0.00 0.00 35.80 1.47
1483 1912 3.431411 TGTCCCCCTGTGGAATATACT 57.569 47.619 0.00 0.00 35.80 2.12
1484 1913 3.045634 TGTCCCCCTGTGGAATATACTG 58.954 50.000 0.00 0.00 35.80 2.74
1518 2538 6.528537 ACATGTTTCTGCTAAATGCCAATA 57.471 33.333 0.00 0.00 42.00 1.90
1521 2541 8.694540 ACATGTTTCTGCTAAATGCCAATATTA 58.305 29.630 0.00 0.00 42.00 0.98
1537 2560 6.747280 GCCAATATTATTGTCACAGTGTTGAC 59.253 38.462 13.87 14.99 45.34 3.18
1547 2570 2.351888 GTGTTGACGTGGTTGCGC 60.352 61.111 0.00 0.00 34.88 6.09
1569 2592 4.919754 GCTCAAATCCTTTTCATGTGTCAC 59.080 41.667 0.00 0.00 0.00 3.67
1583 2615 7.781548 TCATGTGTCACTTTGATATGATCTG 57.218 36.000 4.27 0.00 0.00 2.90
1586 2618 5.876460 TGTGTCACTTTGATATGATCTGGTG 59.124 40.000 4.27 0.00 0.00 4.17
1672 2704 2.362632 ACCCGGCTTCTCTACGCT 60.363 61.111 0.00 0.00 0.00 5.07
1987 3023 0.389426 GCCTAGAAACTCGGCGTCAA 60.389 55.000 6.85 0.00 32.84 3.18
2122 3158 6.732896 TTCTATCTAAGTTGATCAGTCCCC 57.267 41.667 0.00 0.00 0.00 4.81
2123 3159 5.777449 TCTATCTAAGTTGATCAGTCCCCA 58.223 41.667 0.00 0.00 0.00 4.96
2124 3160 6.202331 TCTATCTAAGTTGATCAGTCCCCAA 58.798 40.000 0.00 0.00 0.00 4.12
2125 3161 4.553330 TCTAAGTTGATCAGTCCCCAAC 57.447 45.455 0.00 0.00 40.14 3.77
2126 3162 3.907474 TCTAAGTTGATCAGTCCCCAACA 59.093 43.478 0.00 0.00 41.72 3.33
2139 3175 2.575735 TCCCCAACATCAACATGCTCTA 59.424 45.455 0.00 0.00 32.57 2.43
2160 3196 6.692486 TCTACTTCTCAACCAATGTTCTCTC 58.308 40.000 0.00 0.00 30.42 3.20
2161 3197 5.559148 ACTTCTCAACCAATGTTCTCTCT 57.441 39.130 0.00 0.00 30.42 3.10
2169 3209 3.118261 ACCAATGTTCTCTCTGTGTGTGT 60.118 43.478 0.00 0.00 0.00 3.72
2186 3245 9.639601 CTGTGTGTGTTACTTCTAATAAGATCA 57.360 33.333 0.00 0.00 0.00 2.92
2289 3614 7.572814 TGATATGAATGACCACCTCACATTTA 58.427 34.615 0.00 0.00 34.94 1.40
2299 3624 7.998383 TGACCACCTCACATTTATTATGCTTAT 59.002 33.333 0.00 0.00 0.00 1.73
2372 3705 5.009010 GGTGGTAATATTTGACATGGCTCTG 59.991 44.000 0.00 0.00 0.00 3.35
2448 3781 4.499040 GCATATCGTGTTCCAATTTTTCCG 59.501 41.667 0.00 0.00 0.00 4.30
2566 3899 6.966021 TGAACACTCTTTGGCAATACTTTAC 58.034 36.000 0.00 0.00 0.00 2.01
2590 3923 1.405105 GGAGCGCCTTATGATTGCAAA 59.595 47.619 1.71 0.00 0.00 3.68
2715 4057 3.054139 TGGCTGGTTGCTTGATATCTTCT 60.054 43.478 3.98 0.00 42.39 2.85
2771 4113 1.593196 TGGAACTTCTGTTTGCTCCG 58.407 50.000 0.00 0.00 36.39 4.63
2903 4245 9.955102 ATATGACCTCGTGATGTTACTAGTATA 57.045 33.333 2.79 0.00 0.00 1.47
2904 4246 7.488187 TGACCTCGTGATGTTACTAGTATAC 57.512 40.000 2.79 5.94 0.00 1.47
2905 4247 6.201615 TGACCTCGTGATGTTACTAGTATACG 59.798 42.308 2.79 9.83 0.00 3.06
2906 4248 5.049818 ACCTCGTGATGTTACTAGTATACGC 60.050 44.000 2.79 2.31 0.00 4.42
2907 4249 5.049886 CCTCGTGATGTTACTAGTATACGCA 60.050 44.000 2.79 1.91 0.00 5.24
2908 4250 5.982324 TCGTGATGTTACTAGTATACGCAG 58.018 41.667 2.79 1.80 0.00 5.18
3017 4544 3.386726 TCCACCGTAACCATATTCAGGAG 59.613 47.826 0.00 0.00 0.00 3.69
3152 4685 9.613428 TTCCCATTAGATATCAAGTAAGTTGTG 57.387 33.333 5.32 0.00 37.43 3.33
3296 4844 1.560860 GCCACGAAGCTATGCCGATC 61.561 60.000 0.00 0.00 0.00 3.69
3331 4879 6.019640 GTGTTTTCATTGTGTGGTTTCTCATG 60.020 38.462 0.00 0.00 0.00 3.07
3364 4912 5.321927 TCTACAGTCACATACCTTGAGTCA 58.678 41.667 0.00 0.00 0.00 3.41
3375 4923 6.665680 ACATACCTTGAGTCACTAGTGAAGAT 59.334 38.462 26.74 15.66 41.85 2.40
3424 4972 2.690778 GGTGCTTGCATGGTCGACC 61.691 63.158 28.17 28.17 0.00 4.79
3584 5145 3.678548 ACTTCCTTCGTAAGCAAATCGAC 59.321 43.478 0.00 0.00 33.38 4.20
3684 5248 6.934056 TGGCATCATATTAACCATTATTGCC 58.066 36.000 0.00 0.00 44.70 4.52
3688 5252 4.155099 TCATATTAACCATTATTGCCGCCG 59.845 41.667 0.00 0.00 0.00 6.46
3705 5269 1.070309 GCCGCTAGAGATTCAATTGCG 60.070 52.381 0.00 8.99 41.30 4.85
3713 5277 6.018751 GCTAGAGATTCAATTGCGTACATGAA 60.019 38.462 0.00 3.27 36.35 2.57
3715 5279 6.722301 AGAGATTCAATTGCGTACATGAATG 58.278 36.000 14.79 0.00 41.29 2.67
3717 5281 3.419264 TCAATTGCGTACATGAATGGC 57.581 42.857 0.00 0.00 0.00 4.40
3788 5352 2.353406 GGGTGAGCTACTTAACTTGCGA 60.353 50.000 0.00 0.00 0.00 5.10
3794 5358 3.933332 AGCTACTTAACTTGCGATGGTTC 59.067 43.478 0.00 0.00 0.00 3.62
3796 5360 3.134574 ACTTAACTTGCGATGGTTCCA 57.865 42.857 0.00 0.00 0.00 3.53
3801 5365 1.818674 ACTTGCGATGGTTCCATTTCC 59.181 47.619 5.77 0.00 0.00 3.13
3802 5366 1.818060 CTTGCGATGGTTCCATTTCCA 59.182 47.619 5.77 1.77 38.14 3.53
3803 5367 2.142356 TGCGATGGTTCCATTTCCAT 57.858 45.000 5.77 0.00 45.69 3.41
3804 5368 3.289407 TGCGATGGTTCCATTTCCATA 57.711 42.857 5.77 0.00 43.45 2.74
3826 5396 8.944029 CCATATATTTTCTCTATTCTGTGCTGG 58.056 37.037 0.00 0.00 0.00 4.85
3946 5516 0.672091 TGCTGACGGCGCTTCATTAA 60.672 50.000 6.90 0.00 45.43 1.40
3972 5542 0.030603 TTTGGGCCCTTGGGTTTCTT 60.031 50.000 25.70 0.00 0.00 2.52
3988 5558 7.010160 TGGGTTTCTTTTTATGAGAATCTGGT 58.990 34.615 0.00 0.00 33.48 4.00
4104 5769 2.287788 GGGAATGATTTGCTACATGGCG 60.288 50.000 0.00 0.00 34.52 5.69
4117 5782 2.710377 ACATGGCGCTCAAACTATTCA 58.290 42.857 7.64 0.00 0.00 2.57
4146 5811 8.186178 AGTCGTGTCTCATTTCATATTGTTAC 57.814 34.615 0.00 0.00 0.00 2.50
4149 5814 7.969508 TCGTGTCTCATTTCATATTGTTACGTA 59.030 33.333 0.00 0.00 0.00 3.57
4150 5815 8.048436 CGTGTCTCATTTCATATTGTTACGTAC 58.952 37.037 0.00 0.00 0.00 3.67
4151 5816 8.048436 GTGTCTCATTTCATATTGTTACGTACG 58.952 37.037 15.01 15.01 0.00 3.67
4152 5817 7.756272 TGTCTCATTTCATATTGTTACGTACGT 59.244 33.333 25.98 25.98 0.00 3.57
4161 5826 3.201726 TGTTACGTACGTTAGTCAGGC 57.798 47.619 27.92 4.87 0.00 4.85
4198 5863 8.533569 AGTTCAGTTTTCTTCTTTATTCCCAA 57.466 30.769 0.00 0.00 0.00 4.12
4297 5977 3.416151 TTGGGTAGCATGCAGCCAATTT 61.416 45.455 31.78 11.91 45.93 1.82
4368 6048 5.441709 TTTAACTCACCGGATTTTTGTCC 57.558 39.130 9.46 0.00 34.82 4.02
4400 6080 1.561542 CAGATAAGGGCCAGACCTGTT 59.438 52.381 6.18 0.00 40.87 3.16
4415 6095 5.931146 CAGACCTGTTCTTGCCTATATCATC 59.069 44.000 0.00 0.00 28.96 2.92
4500 6180 4.843220 ATGTTCTGGTTCTTGCAAGAAG 57.157 40.909 36.07 26.23 45.01 2.85
4626 6306 0.747255 AGTCTATCGCTTCGCATGGT 59.253 50.000 0.00 0.00 0.00 3.55
4668 6348 4.022603 TGAGCTCTGCTATCTCTTCAAGT 58.977 43.478 16.19 0.00 39.88 3.16
4679 6359 4.944962 TCTCTTCAAGTTGTTGTGTGTG 57.055 40.909 2.11 0.00 34.98 3.82
4691 6371 3.376859 TGTTGTGTGTGAAACTCCATGAC 59.623 43.478 0.00 0.00 38.04 3.06
4715 6395 3.060615 AGGGACGAGCGCTACGTT 61.061 61.111 27.11 14.63 43.97 3.99
4764 6445 0.179000 CCATAGCTGAAGGCCGACTT 59.821 55.000 0.00 0.00 43.65 3.01
4768 6449 0.951040 AGCTGAAGGCCGACTTTTCG 60.951 55.000 0.00 0.00 45.44 3.46
4780 6461 2.222596 CGACTTTTCGCGGAGAATTCTG 60.223 50.000 14.00 0.00 38.71 3.02
4803 6484 5.050227 TGTTTCCAATAGTTTTGTACGGACG 60.050 40.000 0.00 0.00 0.00 4.79
4819 6500 2.671351 CGGACGTGGATATGGTGATAGC 60.671 54.545 0.00 0.00 0.00 2.97
4926 6608 6.554334 GAAGTTATTGACTGCCACTGTTTA 57.446 37.500 0.00 0.00 39.00 2.01
4928 6610 7.524717 AAGTTATTGACTGCCACTGTTTAAT 57.475 32.000 0.00 0.00 39.00 1.40
4957 6639 5.376854 TTTCTGCCTTTTATGCTCACTTC 57.623 39.130 0.00 0.00 0.00 3.01
4958 6640 4.292186 TCTGCCTTTTATGCTCACTTCT 57.708 40.909 0.00 0.00 0.00 2.85
4961 6643 6.237901 TCTGCCTTTTATGCTCACTTCTTTA 58.762 36.000 0.00 0.00 0.00 1.85
4962 6644 6.886459 TCTGCCTTTTATGCTCACTTCTTTAT 59.114 34.615 0.00 0.00 0.00 1.40
4963 6645 8.046708 TCTGCCTTTTATGCTCACTTCTTTATA 58.953 33.333 0.00 0.00 0.00 0.98
4986 6668 1.964223 ACAGTTCTTCTCTGGCTTCGA 59.036 47.619 0.00 0.00 37.25 3.71
4991 6673 1.181786 CTTCTCTGGCTTCGAGGACT 58.818 55.000 0.67 0.00 0.00 3.85
5017 6701 5.813513 ATCCTCATCAAGGCAAAGTTTTT 57.186 34.783 0.00 0.00 45.78 1.94
5039 6723 8.450578 TTTTTGGGTAGTCATCATATGATCAC 57.549 34.615 15.49 13.43 42.04 3.06
5043 6727 8.613922 TGGGTAGTCATCATATGATCACATAT 57.386 34.615 20.22 4.16 46.66 1.78
5059 6774 7.550196 TGATCACATATATTCATTGGGTCATCG 59.450 37.037 0.00 0.00 0.00 3.84
5090 6805 3.837146 ACCATGTCTGTCTGAATGTCTCT 59.163 43.478 0.00 0.00 0.00 3.10
5096 6811 5.157781 GTCTGTCTGAATGTCTCTGTACAC 58.842 45.833 0.00 0.00 30.75 2.90
5101 6816 4.584743 TCTGAATGTCTCTGTACACACTGT 59.415 41.667 0.00 0.00 30.75 3.55
5128 6843 0.320247 ACTCTTGAACTGCCTCAGCG 60.320 55.000 0.00 0.00 44.31 5.18
5129 6844 0.037882 CTCTTGAACTGCCTCAGCGA 60.038 55.000 0.00 0.00 44.31 4.93
5151 6866 4.697514 AGTCAGCATGCACTACGAAATAT 58.302 39.130 21.98 0.00 34.76 1.28
5152 6867 4.509230 AGTCAGCATGCACTACGAAATATG 59.491 41.667 21.98 4.58 34.76 1.78
5153 6868 4.271049 GTCAGCATGCACTACGAAATATGT 59.729 41.667 21.98 0.00 34.76 2.29
5154 6869 4.875536 TCAGCATGCACTACGAAATATGTT 59.124 37.500 21.98 0.00 34.76 2.71
5155 6870 5.006649 TCAGCATGCACTACGAAATATGTTC 59.993 40.000 21.98 0.00 34.76 3.18
5156 6871 5.007039 CAGCATGCACTACGAAATATGTTCT 59.993 40.000 21.98 0.00 0.00 3.01
5157 6872 5.586243 AGCATGCACTACGAAATATGTTCTT 59.414 36.000 21.98 0.00 0.00 2.52
5158 6873 6.094048 AGCATGCACTACGAAATATGTTCTTT 59.906 34.615 21.98 0.00 0.00 2.52
5159 6874 6.747280 GCATGCACTACGAAATATGTTCTTTT 59.253 34.615 14.21 0.00 0.00 2.27
5160 6875 7.273381 GCATGCACTACGAAATATGTTCTTTTT 59.727 33.333 14.21 0.00 0.00 1.94
5179 6894 3.730215 TTTAGCACCAATAGGGAAGCA 57.270 42.857 0.00 0.00 41.52 3.91
5180 6895 3.951563 TTAGCACCAATAGGGAAGCAT 57.048 42.857 0.00 0.00 41.52 3.79
5181 6896 2.355010 AGCACCAATAGGGAAGCATC 57.645 50.000 0.00 0.00 41.52 3.91
5182 6897 1.849039 AGCACCAATAGGGAAGCATCT 59.151 47.619 0.00 0.00 41.52 2.90
5183 6898 3.048600 AGCACCAATAGGGAAGCATCTA 58.951 45.455 0.00 0.00 41.52 1.98
5184 6899 3.142174 GCACCAATAGGGAAGCATCTAC 58.858 50.000 0.00 0.00 41.15 2.59
5185 6900 3.744660 CACCAATAGGGAAGCATCTACC 58.255 50.000 0.00 0.00 41.15 3.18
5186 6901 3.392616 CACCAATAGGGAAGCATCTACCT 59.607 47.826 0.00 0.00 41.15 3.08
5187 6902 4.593206 CACCAATAGGGAAGCATCTACCTA 59.407 45.833 0.00 0.00 41.15 3.08
5188 6903 5.249393 CACCAATAGGGAAGCATCTACCTAT 59.751 44.000 2.09 2.09 45.66 2.57
5195 6910 7.821134 AGGGAAGCATCTACCTATTCATATT 57.179 36.000 0.00 0.00 0.00 1.28
5196 6911 8.917414 AGGGAAGCATCTACCTATTCATATTA 57.083 34.615 0.00 0.00 0.00 0.98
5197 6912 9.512748 AGGGAAGCATCTACCTATTCATATTAT 57.487 33.333 0.00 0.00 0.00 1.28
5223 6938 9.507329 TTTTTAGAAAGTGTGCTTATCATCTCT 57.493 29.630 0.00 0.00 33.95 3.10
5380 7096 2.355244 GGTATCTCTCGCGCTGCC 60.355 66.667 5.56 0.00 0.00 4.85
5478 7195 3.965379 ACATCAAAATCCAAGCATGCA 57.035 38.095 21.98 0.00 0.00 3.96
5554 7277 4.101448 GGTGAGCCACGGCCTCAT 62.101 66.667 3.95 0.00 43.17 2.90
5561 7284 4.529219 CACGGCCTCATGCGCCTA 62.529 66.667 18.17 0.00 44.73 3.93
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 7.444183 TGACGTTCTTCCTCTTCATTAACAAAT 59.556 33.333 0.00 0.00 0.00 2.32
19 20 2.632996 TGTGGAATGACGTTCTTCCTCT 59.367 45.455 22.89 0.00 41.29 3.69
23 24 4.070581 CACATGTGGAATGACGTTCTTC 57.929 45.455 18.51 0.00 37.01 2.87
37 38 2.225491 CCCAACGACTTTACCACATGTG 59.775 50.000 19.31 19.31 0.00 3.21
38 39 2.158726 ACCCAACGACTTTACCACATGT 60.159 45.455 0.00 0.00 0.00 3.21
56 57 7.665974 CCCTAAGATATTATTTTCACCTCACCC 59.334 40.741 0.00 0.00 0.00 4.61
80 81 1.499049 GATCGGCGTTGAAGATACCC 58.501 55.000 6.85 0.00 0.00 3.69
83 84 4.659111 TTAAGGATCGGCGTTGAAGATA 57.341 40.909 6.85 0.00 0.00 1.98
93 94 1.471287 GTGGGTGTTTTAAGGATCGGC 59.529 52.381 0.00 0.00 0.00 5.54
98 99 4.342665 GGACATTTGTGGGTGTTTTAAGGA 59.657 41.667 0.00 0.00 0.00 3.36
99 100 4.627058 GGACATTTGTGGGTGTTTTAAGG 58.373 43.478 0.00 0.00 0.00 2.69
110 111 4.217550 ACAGTTTAATCCGGACATTTGTGG 59.782 41.667 6.12 0.00 0.00 4.17
111 112 5.371115 ACAGTTTAATCCGGACATTTGTG 57.629 39.130 6.12 3.45 0.00 3.33
112 113 4.457949 GGACAGTTTAATCCGGACATTTGT 59.542 41.667 6.12 7.10 0.00 2.83
113 114 4.457603 TGGACAGTTTAATCCGGACATTTG 59.542 41.667 6.12 3.48 37.87 2.32
115 116 4.261801 CTGGACAGTTTAATCCGGACATT 58.738 43.478 6.12 0.00 43.17 2.71
117 118 2.027561 CCTGGACAGTTTAATCCGGACA 60.028 50.000 6.12 0.00 43.17 4.02
120 121 2.290071 ACACCTGGACAGTTTAATCCGG 60.290 50.000 0.00 0.00 40.58 5.14
126 127 6.366340 TGGAAAATTACACCTGGACAGTTTA 58.634 36.000 0.00 0.00 0.00 2.01
127 128 5.205056 TGGAAAATTACACCTGGACAGTTT 58.795 37.500 0.00 0.00 0.00 2.66
129 130 4.447138 TGGAAAATTACACCTGGACAGT 57.553 40.909 0.00 0.00 0.00 3.55
130 131 4.399303 GGATGGAAAATTACACCTGGACAG 59.601 45.833 0.00 0.00 0.00 3.51
138 139 4.216687 TCCGTGTTGGATGGAAAATTACAC 59.783 41.667 0.00 0.00 43.74 2.90
139 140 4.399219 TCCGTGTTGGATGGAAAATTACA 58.601 39.130 0.00 0.00 43.74 2.41
166 167 0.165944 GAATGCGTCCACGGACAAAG 59.834 55.000 16.23 1.48 43.72 2.77
185 186 5.553692 TTTTGCGAAAATTTAGACAAGCG 57.446 34.783 0.00 0.00 0.00 4.68
194 195 7.914465 TCTAGTTTGCATTTTTGCGAAAATTT 58.086 26.923 19.98 0.88 42.14 1.82
202 203 3.588955 CCCCTCTAGTTTGCATTTTTGC 58.411 45.455 0.00 0.00 0.00 3.68
209 213 1.742308 AACTCCCCCTCTAGTTTGCA 58.258 50.000 0.00 0.00 32.00 4.08
217 221 2.603652 GCCCGAAAACTCCCCCTCT 61.604 63.158 0.00 0.00 0.00 3.69
222 226 2.675423 GGGTGCCCGAAAACTCCC 60.675 66.667 0.00 0.00 32.79 4.30
245 249 0.251209 TCAGAGTCCTACGTGGCAGT 60.251 55.000 0.00 0.00 35.26 4.40
249 253 1.096416 GGAGTCAGAGTCCTACGTGG 58.904 60.000 16.35 0.00 34.81 4.94
262 266 2.204291 AATGGGCAGGGGGAGTCA 60.204 61.111 0.00 0.00 0.00 3.41
266 270 0.032217 GATTTGAATGGGCAGGGGGA 60.032 55.000 0.00 0.00 0.00 4.81
269 273 1.050421 GGGGATTTGAATGGGCAGGG 61.050 60.000 0.00 0.00 0.00 4.45
272 276 0.417035 AAGGGGGATTTGAATGGGCA 59.583 50.000 0.00 0.00 0.00 5.36
273 277 2.470057 TAAGGGGGATTTGAATGGGC 57.530 50.000 0.00 0.00 0.00 5.36
274 278 3.242011 CCATAAGGGGGATTTGAATGGG 58.758 50.000 0.00 0.00 30.90 4.00
288 292 2.107031 TGATGGATGCAGACCCATAAGG 59.893 50.000 15.40 0.00 42.80 2.69
289 293 3.497103 TGATGGATGCAGACCCATAAG 57.503 47.619 15.40 0.00 42.80 1.73
290 294 3.949586 TTGATGGATGCAGACCCATAA 57.050 42.857 15.40 7.94 42.80 1.90
291 295 5.784398 ATATTGATGGATGCAGACCCATA 57.216 39.130 15.40 4.80 42.80 2.74
292 296 4.669866 ATATTGATGGATGCAGACCCAT 57.330 40.909 15.36 15.36 45.22 4.00
293 297 4.845796 TCTATATTGATGGATGCAGACCCA 59.154 41.667 7.58 7.58 36.79 4.51
294 298 5.426689 TCTATATTGATGGATGCAGACCC 57.573 43.478 9.71 3.33 0.00 4.46
295 299 8.016301 TCTATCTATATTGATGGATGCAGACC 57.984 38.462 8.70 5.86 34.40 3.85
296 300 9.881649 TTTCTATCTATATTGATGGATGCAGAC 57.118 33.333 12.55 0.00 34.40 3.51
303 307 7.813087 TGGGCTTTCTATCTATATTGATGGA 57.187 36.000 8.70 8.70 33.20 3.41
325 329 5.698832 TGCTTTCATCGTGTAAAATCTTGG 58.301 37.500 0.00 0.00 0.00 3.61
349 353 4.760204 CCCGAACCTCAAACTTGTAATTCT 59.240 41.667 0.00 0.00 0.00 2.40
352 356 4.070009 GACCCGAACCTCAAACTTGTAAT 58.930 43.478 0.00 0.00 0.00 1.89
366 370 3.725490 ACTTCTTTGTGTAGACCCGAAC 58.275 45.455 0.00 0.00 0.00 3.95
380 384 7.610305 TGTTTTGAGACCAAGAGTTACTTCTTT 59.390 33.333 0.00 0.00 35.28 2.52
383 387 6.920569 TGTTTTGAGACCAAGAGTTACTTC 57.079 37.500 0.00 0.00 36.61 3.01
450 454 8.243426 TCAAAGTACATGAATGCCAAAGAATAC 58.757 33.333 0.00 0.00 0.00 1.89
459 463 7.148590 GGTGATTTTTCAAAGTACATGAATGCC 60.149 37.037 12.99 7.37 36.72 4.40
475 661 7.850492 CCAACTTTTTGAAATCGGTGATTTTTC 59.150 33.333 6.26 0.00 41.56 2.29
477 663 6.238347 GCCAACTTTTTGAAATCGGTGATTTT 60.238 34.615 6.26 0.00 41.56 1.82
486 672 6.576551 TTAACACGCCAACTTTTTGAAATC 57.423 33.333 0.00 0.00 34.24 2.17
518 704 8.725405 TCGCTTTAATCAAGGTTATATGAACA 57.275 30.769 0.00 0.00 32.37 3.18
519 705 9.599322 CATCGCTTTAATCAAGGTTATATGAAC 57.401 33.333 0.00 0.00 32.37 3.18
520 706 8.783093 CCATCGCTTTAATCAAGGTTATATGAA 58.217 33.333 0.00 0.00 32.37 2.57
526 712 6.826231 TGAATCCATCGCTTTAATCAAGGTTA 59.174 34.615 0.00 0.00 32.37 2.85
530 716 5.066375 TGGTGAATCCATCGCTTTAATCAAG 59.934 40.000 0.00 0.00 41.93 3.02
540 726 0.031178 GGCATTGGTGAATCCATCGC 59.969 55.000 0.00 0.00 46.60 4.58
547 733 8.458573 TCGTAAAAATATAGGCATTGGTGAAT 57.541 30.769 0.00 0.00 0.00 2.57
552 738 8.918961 TTGTTTCGTAAAAATATAGGCATTGG 57.081 30.769 0.00 0.00 0.00 3.16
606 793 7.816995 GCAACAAATATTTGGATGTTCAAGGTA 59.183 33.333 27.43 0.00 42.34 3.08
638 827 8.448615 GTCACCAGCGAATACTTTTAAATTACT 58.551 33.333 0.00 0.00 0.00 2.24
639 828 8.448615 AGTCACCAGCGAATACTTTTAAATTAC 58.551 33.333 0.00 0.00 0.00 1.89
815 1007 6.767524 TCCGTGCCATTATTATTGTTCTTT 57.232 33.333 0.00 0.00 0.00 2.52
853 1045 0.829333 TCTCGTCTAGCTAGGGTCGT 59.171 55.000 20.58 0.00 0.00 4.34
905 1097 2.527951 ATCGTGCAGGAGAAGTGGCC 62.528 60.000 15.18 0.00 0.00 5.36
909 1101 2.300152 TGAAAGATCGTGCAGGAGAAGT 59.700 45.455 15.18 0.00 0.00 3.01
918 1110 0.642800 GAGCGAGTGAAAGATCGTGC 59.357 55.000 0.00 0.00 40.97 5.34
977 1174 4.493747 GGCCTTCCCGTCGTCTCG 62.494 72.222 0.00 0.00 0.00 4.04
1019 1216 3.157949 CCCCCTCTTCTCCTCCGC 61.158 72.222 0.00 0.00 0.00 5.54
1057 1254 2.078452 CCTCCTCCTTTCCTTGGCA 58.922 57.895 0.00 0.00 0.00 4.92
1276 1495 1.768870 AGGGTCATTCCTTCATACGGG 59.231 52.381 0.00 0.00 32.13 5.28
1288 1507 1.754234 GCGGCATGGAAGGGTCATT 60.754 57.895 0.00 0.00 0.00 2.57
1289 1508 2.124151 GCGGCATGGAAGGGTCAT 60.124 61.111 0.00 0.00 0.00 3.06
1292 1511 2.257409 CTACAGCGGCATGGAAGGGT 62.257 60.000 1.45 0.00 0.00 4.34
1293 1512 1.524621 CTACAGCGGCATGGAAGGG 60.525 63.158 1.45 0.00 0.00 3.95
1347 1597 7.713764 AAATGGTAAATTTTGCACTTCACTC 57.286 32.000 0.00 0.00 0.00 3.51
1377 1627 9.110617 GCATTGATATTTGAGTATTTGATCACG 57.889 33.333 0.00 0.00 0.00 4.35
1507 1936 8.965819 ACACTGTGACAATAATATTGGCATTTA 58.034 29.630 22.74 12.36 39.95 1.40
1518 2538 4.213270 CCACGTCAACACTGTGACAATAAT 59.787 41.667 15.86 0.00 46.90 1.28
1521 2541 1.939934 CCACGTCAACACTGTGACAAT 59.060 47.619 15.86 0.00 46.90 2.71
1537 2560 1.154225 GGATTTGAGCGCAACCACG 60.154 57.895 11.47 0.00 32.79 4.94
1547 2570 6.323203 AGTGACACATGAAAAGGATTTGAG 57.677 37.500 8.59 0.00 39.02 3.02
1569 2592 5.763698 AGCATCACACCAGATCATATCAAAG 59.236 40.000 0.00 0.00 0.00 2.77
1583 2615 7.094677 TGCATCAATATATGTTAGCATCACACC 60.095 37.037 0.00 0.00 36.58 4.16
1586 2618 8.037382 AGTGCATCAATATATGTTAGCATCAC 57.963 34.615 0.00 0.00 36.58 3.06
1699 2731 1.078426 CCCCACCATGAACTCGGAC 60.078 63.158 0.00 0.00 0.00 4.79
1987 3023 2.446435 CCATCAAATCCACGAAACCCT 58.554 47.619 0.00 0.00 0.00 4.34
2073 3109 9.574516 AACTAACTGATTAACCTGAACAAGATT 57.425 29.630 0.00 0.00 0.00 2.40
2122 3158 5.640783 TGAGAAGTAGAGCATGTTGATGTTG 59.359 40.000 0.00 0.00 31.50 3.33
2123 3159 5.798132 TGAGAAGTAGAGCATGTTGATGTT 58.202 37.500 0.00 0.00 31.50 2.71
2124 3160 5.411831 TGAGAAGTAGAGCATGTTGATGT 57.588 39.130 0.00 0.00 31.50 3.06
2125 3161 5.064452 GGTTGAGAAGTAGAGCATGTTGATG 59.936 44.000 0.00 0.00 0.00 3.07
2126 3162 5.181748 GGTTGAGAAGTAGAGCATGTTGAT 58.818 41.667 0.00 0.00 0.00 2.57
2139 3175 5.163258 ACAGAGAGAACATTGGTTGAGAAGT 60.163 40.000 0.00 0.00 37.36 3.01
2160 3196 9.639601 TGATCTTATTAGAAGTAACACACACAG 57.360 33.333 0.00 0.00 33.20 3.66
2204 3265 7.066284 AGGACATTAATTAGTGCTTTACTGCAG 59.934 37.037 13.48 13.48 44.20 4.41
2372 3705 4.994852 GGGAGAAAAACCAAAATACAAGCC 59.005 41.667 0.00 0.00 0.00 4.35
2448 3781 2.039084 AGGAGTTGACTTCACCCACATC 59.961 50.000 0.00 0.00 0.00 3.06
2566 3899 2.397413 AATCATAAGGCGCTCCCCCG 62.397 60.000 7.64 0.00 0.00 5.73
2715 4057 5.240891 TGTTGCACCAAACATTTTTGAAGA 58.759 33.333 5.90 0.00 44.38 2.87
2771 4113 4.274459 TGAAGAGAAGCTGAAGCAAAAGAC 59.726 41.667 4.90 0.00 45.16 3.01
2903 4245 3.838244 ATACCCATGAACATACTGCGT 57.162 42.857 0.00 0.00 0.00 5.24
2904 4246 5.931724 TGATTATACCCATGAACATACTGCG 59.068 40.000 0.00 0.00 0.00 5.18
2905 4247 6.936900 ACTGATTATACCCATGAACATACTGC 59.063 38.462 0.00 0.00 0.00 4.40
2906 4248 7.933577 ACACTGATTATACCCATGAACATACTG 59.066 37.037 0.00 0.00 0.00 2.74
2907 4249 8.034313 ACACTGATTATACCCATGAACATACT 57.966 34.615 0.00 0.00 0.00 2.12
2908 4250 8.559536 CAACACTGATTATACCCATGAACATAC 58.440 37.037 0.00 0.00 0.00 2.39
2909 4251 8.271458 ACAACACTGATTATACCCATGAACATA 58.729 33.333 0.00 0.00 0.00 2.29
2910 4252 7.118723 ACAACACTGATTATACCCATGAACAT 58.881 34.615 0.00 0.00 0.00 2.71
2911 4253 6.480763 ACAACACTGATTATACCCATGAACA 58.519 36.000 0.00 0.00 0.00 3.18
3017 4544 7.691877 CGCTTAAAATAAAATTTGTGGAATGGC 59.308 33.333 0.00 0.00 0.00 4.40
3164 4702 4.108336 CGGACAGTACACATCAGATGAAG 58.892 47.826 17.81 11.11 0.00 3.02
3285 4833 2.158449 CGAGAAATTGGATCGGCATAGC 59.842 50.000 0.00 0.00 32.93 2.97
3296 4844 5.748152 ACACAATGAAAACACGAGAAATTGG 59.252 36.000 0.00 0.00 0.00 3.16
3331 4879 2.037251 TGTGACTGTAGAAGTGCCCTTC 59.963 50.000 0.00 0.00 46.23 3.46
3364 4912 8.466617 AATACCGAGTTATCATCTTCACTAGT 57.533 34.615 0.00 0.00 0.00 2.57
3375 4923 4.278919 TGGCATACGAATACCGAGTTATCA 59.721 41.667 0.00 0.00 41.76 2.15
3424 4972 1.189446 GCCGAACTGTATATCGCAACG 59.811 52.381 0.00 0.00 37.73 4.10
3541 5089 4.098654 AGTCCGACAACCATCTCTGAATAG 59.901 45.833 0.40 0.00 0.00 1.73
3684 5248 1.070309 GCAATTGAATCTCTAGCGGCG 60.070 52.381 10.34 0.51 0.00 6.46
3688 5252 5.463392 TCATGTACGCAATTGAATCTCTAGC 59.537 40.000 10.34 0.00 0.00 3.42
3705 5269 1.583054 GTCTCCCGCCATTCATGTAC 58.417 55.000 0.00 0.00 0.00 2.90
3717 5281 2.076622 CTAGATGGCGTGGTCTCCCG 62.077 65.000 0.00 0.00 0.00 5.14
3788 5352 9.887862 AGAGAAAATATATGGAAATGGAACCAT 57.112 29.630 0.00 0.00 46.73 3.55
3801 5365 9.716531 TCCAGCACAGAATAGAGAAAATATATG 57.283 33.333 0.00 0.00 0.00 1.78
3802 5366 9.941325 CTCCAGCACAGAATAGAGAAAATATAT 57.059 33.333 0.00 0.00 0.00 0.86
3803 5367 8.928448 ACTCCAGCACAGAATAGAGAAAATATA 58.072 33.333 0.00 0.00 0.00 0.86
3804 5368 7.800092 ACTCCAGCACAGAATAGAGAAAATAT 58.200 34.615 0.00 0.00 0.00 1.28
3935 5505 4.351192 CCAAATGTAGGTTAATGAAGCGC 58.649 43.478 0.00 0.00 38.14 5.92
3938 5508 4.099419 GGGCCCAAATGTAGGTTAATGAAG 59.901 45.833 19.95 0.00 0.00 3.02
3946 5516 0.041090 CCAAGGGCCCAAATGTAGGT 59.959 55.000 27.56 0.00 0.00 3.08
3972 5542 7.669722 ACCAGCTTTAACCAGATTCTCATAAAA 59.330 33.333 0.00 0.00 0.00 1.52
3988 5558 3.287222 AGTTGCAACTCACCAGCTTTAA 58.713 40.909 26.36 0.00 32.86 1.52
4104 5769 5.634020 ACACGACTAACTGAATAGTTTGAGC 59.366 40.000 8.24 1.07 44.57 4.26
4117 5782 8.035394 ACAATATGAAATGAGACACGACTAACT 58.965 33.333 0.00 0.00 0.00 2.24
4146 5811 0.806868 TGAGGCCTGACTAACGTACG 59.193 55.000 12.00 15.01 0.00 3.67
4149 5814 2.354805 GGAAATGAGGCCTGACTAACGT 60.355 50.000 12.00 0.00 0.00 3.99
4150 5815 2.280628 GGAAATGAGGCCTGACTAACG 58.719 52.381 12.00 0.00 0.00 3.18
4151 5816 3.350219 TGGAAATGAGGCCTGACTAAC 57.650 47.619 12.00 0.00 0.00 2.34
4152 5817 4.202567 ACTTTGGAAATGAGGCCTGACTAA 60.203 41.667 12.00 0.00 0.00 2.24
4161 5826 6.809869 AGAAAACTGAACTTTGGAAATGAGG 58.190 36.000 0.00 0.00 0.00 3.86
4198 5863 6.555360 AGGAGACAAGGAAATAGACGGAATAT 59.445 38.462 0.00 0.00 0.00 1.28
4400 6080 6.014242 ACCTTTCATCGATGATATAGGCAAGA 60.014 38.462 31.44 14.92 36.56 3.02
4415 6095 0.036765 TCGGAACCCACCTTTCATCG 60.037 55.000 0.00 0.00 0.00 3.84
4668 6348 4.013050 TCATGGAGTTTCACACACAACAA 58.987 39.130 0.00 0.00 0.00 2.83
4679 6359 3.452474 CCTGATCGAGTCATGGAGTTTC 58.548 50.000 0.00 0.00 35.97 2.78
4703 6383 1.724929 CCCGATAACGTAGCGCTCG 60.725 63.158 16.34 20.10 36.05 5.03
4715 6395 3.110293 TCTTCCAACCTCTTCCCGATA 57.890 47.619 0.00 0.00 0.00 2.92
4746 6426 2.029838 AAAGTCGGCCTTCAGCTATG 57.970 50.000 0.00 0.00 43.05 2.23
4764 6445 2.482721 GGAAACAGAATTCTCCGCGAAA 59.517 45.455 8.23 0.00 34.79 3.46
4768 6449 4.636206 ACTATTGGAAACAGAATTCTCCGC 59.364 41.667 4.57 0.00 44.54 5.54
4780 6461 5.050159 ACGTCCGTACAAAACTATTGGAAAC 60.050 40.000 0.00 0.00 0.00 2.78
4860 6541 7.238486 TCCAAACAAATGCACCACTAATTAT 57.762 32.000 0.00 0.00 0.00 1.28
4933 6615 5.789643 AGTGAGCATAAAAGGCAGAAAAA 57.210 34.783 0.00 0.00 0.00 1.94
4957 6639 9.606631 AAGCCAGAGAAGAACTGTTATATAAAG 57.393 33.333 0.00 0.72 34.04 1.85
4958 6640 9.601217 GAAGCCAGAGAAGAACTGTTATATAAA 57.399 33.333 0.00 0.00 34.04 1.40
4961 6643 6.096987 TCGAAGCCAGAGAAGAACTGTTATAT 59.903 38.462 0.00 0.00 34.04 0.86
4962 6644 5.417894 TCGAAGCCAGAGAAGAACTGTTATA 59.582 40.000 0.00 0.00 34.04 0.98
4963 6645 4.220821 TCGAAGCCAGAGAAGAACTGTTAT 59.779 41.667 0.00 0.00 34.04 1.89
4968 6650 1.548269 CCTCGAAGCCAGAGAAGAACT 59.452 52.381 2.67 0.00 37.93 3.01
4969 6651 1.546476 TCCTCGAAGCCAGAGAAGAAC 59.454 52.381 2.67 0.00 37.93 3.01
4975 6657 0.605589 AACAGTCCTCGAAGCCAGAG 59.394 55.000 0.00 0.00 35.60 3.35
5017 6701 6.745794 TGTGATCATATGATGACTACCCAA 57.254 37.500 28.16 10.65 43.01 4.12
5039 6723 7.870509 ATTCCGATGACCCAATGAATATATG 57.129 36.000 0.00 0.00 0.00 1.78
5043 6727 5.221224 GCAAATTCCGATGACCCAATGAATA 60.221 40.000 0.00 0.00 0.00 1.75
5059 6774 2.821969 AGACAGACATGGTGCAAATTCC 59.178 45.455 0.00 0.00 0.00 3.01
5101 6816 5.897250 TGAGGCAGTTCAAGAGTATATGGTA 59.103 40.000 0.00 0.00 0.00 3.25
5128 6843 1.996292 TTCGTAGTGCATGCTGACTC 58.004 50.000 20.33 8.10 0.00 3.36
5129 6844 2.455674 TTTCGTAGTGCATGCTGACT 57.544 45.000 20.33 16.99 0.00 3.41
5157 6872 4.411927 TGCTTCCCTATTGGTGCTAAAAA 58.588 39.130 0.00 0.00 36.27 1.94
5158 6873 4.040936 TGCTTCCCTATTGGTGCTAAAA 57.959 40.909 0.00 0.00 36.27 1.52
5159 6874 3.730215 TGCTTCCCTATTGGTGCTAAA 57.270 42.857 0.00 0.00 36.27 1.85
5160 6875 3.459598 AGATGCTTCCCTATTGGTGCTAA 59.540 43.478 0.00 0.00 36.27 3.09
5161 6876 3.048600 AGATGCTTCCCTATTGGTGCTA 58.951 45.455 0.00 0.00 36.27 3.49
5162 6877 1.849039 AGATGCTTCCCTATTGGTGCT 59.151 47.619 0.00 0.00 36.27 4.40
5163 6878 2.355010 AGATGCTTCCCTATTGGTGC 57.645 50.000 0.00 0.00 35.99 5.01
5164 6879 3.392616 AGGTAGATGCTTCCCTATTGGTG 59.607 47.826 0.00 0.00 34.77 4.17
5165 6880 3.669949 AGGTAGATGCTTCCCTATTGGT 58.330 45.455 0.00 0.00 34.77 3.67
5166 6881 6.013379 TGAATAGGTAGATGCTTCCCTATTGG 60.013 42.308 23.29 0.00 45.68 3.16
5167 6882 7.009179 TGAATAGGTAGATGCTTCCCTATTG 57.991 40.000 23.29 0.00 45.68 1.90
5169 6884 9.512748 AATATGAATAGGTAGATGCTTCCCTAT 57.487 33.333 10.03 10.03 41.05 2.57
5170 6885 8.917414 AATATGAATAGGTAGATGCTTCCCTA 57.083 34.615 6.96 6.96 34.24 3.53
5171 6886 7.821134 AATATGAATAGGTAGATGCTTCCCT 57.179 36.000 0.00 0.00 0.00 4.20
5197 6912 9.507329 AGAGATGATAAGCACACTTTCTAAAAA 57.493 29.630 0.00 0.00 37.33 1.94
5198 6913 9.507329 AAGAGATGATAAGCACACTTTCTAAAA 57.493 29.630 0.00 0.00 37.33 1.52
5199 6914 9.155975 GAAGAGATGATAAGCACACTTTCTAAA 57.844 33.333 0.00 0.00 37.33 1.85
5200 6915 8.535335 AGAAGAGATGATAAGCACACTTTCTAA 58.465 33.333 0.00 0.00 37.33 2.10
5201 6916 8.072321 AGAAGAGATGATAAGCACACTTTCTA 57.928 34.615 0.00 0.00 37.33 2.10
5202 6917 6.945218 AGAAGAGATGATAAGCACACTTTCT 58.055 36.000 0.00 0.00 37.33 2.52
5203 6918 7.041107 AGAGAAGAGATGATAAGCACACTTTC 58.959 38.462 0.00 0.00 37.33 2.62
5204 6919 6.945218 AGAGAAGAGATGATAAGCACACTTT 58.055 36.000 0.00 0.00 37.33 2.66
5205 6920 6.543430 AGAGAAGAGATGATAAGCACACTT 57.457 37.500 0.00 0.00 40.07 3.16
5206 6921 6.833416 AGTAGAGAAGAGATGATAAGCACACT 59.167 38.462 0.00 0.00 0.00 3.55
5207 6922 7.038154 AGTAGAGAAGAGATGATAAGCACAC 57.962 40.000 0.00 0.00 0.00 3.82
5208 6923 8.932434 ATAGTAGAGAAGAGATGATAAGCACA 57.068 34.615 0.00 0.00 0.00 4.57
5209 6924 9.231297 AGATAGTAGAGAAGAGATGATAAGCAC 57.769 37.037 0.00 0.00 0.00 4.40
5249 6964 1.342175 CGTAAGAGGGGAGAGGGAACT 60.342 57.143 0.00 0.00 43.81 3.01
5380 7096 9.543018 GATTTACGTTGATTCAAAGGAAACTAG 57.457 33.333 20.36 0.00 38.15 2.57
5554 7277 3.583276 CTGAACCGTGGTAGGCGCA 62.583 63.158 10.83 0.00 33.69 6.09
5561 7284 3.637273 GGCCCTCTGAACCGTGGT 61.637 66.667 0.00 0.00 0.00 4.16


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

AutoCloner maintained by Alex Coulton.