Multiple sequence alignment - TraesCS3D01G497300

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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 TraesCS3D01G497300 chr3D 100.000 6965 0 0 1 6965 588490685 588483721 0.000000e+00 12863.0
1 TraesCS3D01G497300 chr3D 85.479 365 41 11 4387 4746 423644826 423644469 3.070000e-98 370.0
2 TraesCS3D01G497300 chr3D 85.153 229 23 5 5334 5561 552667041 552666823 2.530000e-54 224.0
3 TraesCS3D01G497300 chr3D 89.437 142 15 0 4739 4880 552683300 552683159 5.550000e-41 180.0
4 TraesCS3D01G497300 chr3D 78.358 268 26 19 4739 4989 583147350 583147098 2.020000e-30 145.0
5 TraesCS3D01G497300 chr3D 87.324 71 6 3 3772 3840 423645118 423645049 2.080000e-10 78.7
6 TraesCS3D01G497300 chr3A 91.376 4360 216 62 1194 5472 718837037 718832757 0.000000e+00 5821.0
7 TraesCS3D01G497300 chr3A 94.675 770 38 3 5543 6311 718832655 718831888 0.000000e+00 1192.0
8 TraesCS3D01G497300 chr3A 87.558 217 9 11 336 543 718838414 718838207 1.170000e-57 235.0
9 TraesCS3D01G497300 chr3A 83.636 165 3 6 1 157 718838731 718838583 4.380000e-27 134.0
10 TraesCS3D01G497300 chr3B 93.668 3411 137 34 2423 5782 786969594 786966212 0.000000e+00 5029.0
11 TraesCS3D01G497300 chr3B 89.233 2387 92 62 56 2374 786971882 786969593 0.000000e+00 2832.0
12 TraesCS3D01G497300 chr3B 94.808 520 20 5 5779 6291 786966140 786965621 0.000000e+00 804.0
13 TraesCS3D01G497300 chr3B 90.503 537 51 0 6429 6965 786960379 786959843 0.000000e+00 710.0
14 TraesCS3D01G497300 chr3B 81.759 307 31 11 4739 5041 62721676 62721391 4.200000e-57 233.0
15 TraesCS3D01G497300 chr3B 85.542 166 13 5 5334 5499 550786096 550786250 5.590000e-36 163.0
16 TraesCS3D01G497300 chr3B 95.455 88 3 1 6346 6433 786965622 786965536 9.420000e-29 139.0
17 TraesCS3D01G497300 chr1D 90.096 313 24 6 4436 4746 416537237 416536930 3.910000e-107 399.0
18 TraesCS3D01G497300 chr1D 85.912 362 41 8 4387 4741 71620097 71619739 1.830000e-100 377.0
19 TraesCS3D01G497300 chr1D 83.908 348 25 12 2568 2911 416536470 416536150 3.160000e-78 303.0
20 TraesCS3D01G497300 chr1D 83.483 333 28 9 2568 2899 71619281 71618975 1.140000e-72 285.0
21 TraesCS3D01G497300 chr1D 84.034 119 13 5 3765 3879 416537603 416537487 7.390000e-20 110.0
22 TraesCS3D01G497300 chr1D 92.857 70 3 1 2623 2690 416537709 416537640 4.450000e-17 100.0
23 TraesCS3D01G497300 chr6A 89.032 310 29 4 4434 4741 525286313 525286007 5.100000e-101 379.0
24 TraesCS3D01G497300 chr6A 94.118 68 2 1 2625 2690 525286775 525286708 1.240000e-17 102.0
25 TraesCS3D01G497300 chr2D 88.636 308 29 5 4436 4741 607796741 607797044 3.070000e-98 370.0
26 TraesCS3D01G497300 chr2D 88.274 307 31 4 4437 4741 34676459 34676156 5.130000e-96 363.0
27 TraesCS3D01G497300 chr2D 86.496 274 27 8 4061 4331 47628188 47627922 6.830000e-75 292.0
28 TraesCS3D01G497300 chr2D 94.286 70 2 1 2623 2690 34676892 34676823 9.550000e-19 106.0
29 TraesCS3D01G497300 chr2D 91.667 72 4 1 2622 2691 607796278 607796349 1.600000e-16 99.0
30 TraesCS3D01G497300 chr5D 88.599 307 30 4 4437 4741 125180576 125180879 1.100000e-97 368.0
31 TraesCS3D01G497300 chr5D 83.483 333 26 13 2568 2899 125181346 125181650 4.110000e-72 283.0
32 TraesCS3D01G497300 chr5D 87.162 148 17 2 1411 1557 417040864 417040718 4.320000e-37 167.0
33 TraesCS3D01G497300 chr5D 83.019 106 12 3 3774 3876 527394000 527393898 2.680000e-14 91.6
34 TraesCS3D01G497300 chr1B 88.103 311 31 4 4434 4741 589520889 589520582 1.430000e-96 364.0
35 TraesCS3D01G497300 chr1B 86.900 229 29 1 5334 5561 169950369 169950141 8.970000e-64 255.0
36 TraesCS3D01G497300 chr1B 88.725 204 21 2 4123 4325 102655763 102655561 1.500000e-61 248.0
37 TraesCS3D01G497300 chr1B 88.725 204 21 2 4123 4325 133672638 133672840 1.500000e-61 248.0
38 TraesCS3D01G497300 chr1B 80.357 168 10 5 5395 5561 133694871 133695016 9.550000e-19 106.0
39 TraesCS3D01G497300 chr1B 79.167 168 12 5 5395 5561 163674192 163674047 2.070000e-15 95.3
40 TraesCS3D01G497300 chr6D 87.912 273 25 6 4061 4331 84296025 84295759 1.460000e-81 315.0
41 TraesCS3D01G497300 chr6D 82.083 240 21 4 5334 5561 84292724 84292495 1.190000e-42 185.0
42 TraesCS3D01G497300 chr6D 85.897 156 21 1 5334 5488 431002679 431002834 1.550000e-36 165.0
43 TraesCS3D01G497300 chr5A 84.802 329 23 9 2568 2895 654420156 654419854 8.780000e-79 305.0
44 TraesCS3D01G497300 chr5A 85.401 274 29 8 4061 4331 426472345 426472080 2.480000e-69 274.0
45 TraesCS3D01G497300 chr5A 87.838 148 16 2 1411 1557 530302403 530302257 9.290000e-39 172.0
46 TraesCS3D01G497300 chr1A 83.815 346 24 18 2570 2911 513850741 513850424 4.080000e-77 300.0
47 TraesCS3D01G497300 chr1A 94.203 69 2 1 2623 2689 513851930 513851862 3.440000e-18 104.0
48 TraesCS3D01G497300 chr7B 86.813 273 25 7 4061 4328 692188312 692188578 1.900000e-75 294.0
49 TraesCS3D01G497300 chr7B 85.560 277 29 9 4061 4331 677711791 677711520 5.320000e-71 279.0
50 TraesCS3D01G497300 chr7B 90.260 154 15 0 1406 1559 239362957 239363110 1.180000e-47 202.0
51 TraesCS3D01G497300 chr7B 90.090 111 8 2 2564 2673 692189204 692189312 2.620000e-29 141.0
52 TraesCS3D01G497300 chr2B 83.784 333 26 12 2568 2899 41328101 41328406 2.460000e-74 291.0
53 TraesCS3D01G497300 chr2B 81.223 229 33 3 5334 5561 603172199 603172418 7.180000e-40 176.0
54 TraesCS3D01G497300 chr2B 91.429 70 4 1 2624 2691 41326688 41326757 2.070000e-15 95.3
55 TraesCS3D01G497300 chr5B 83.784 333 25 15 2568 2899 663638211 663637907 8.840000e-74 289.0
56 TraesCS3D01G497300 chr5B 87.838 148 16 2 1411 1557 504307103 504306957 9.290000e-39 172.0
57 TraesCS3D01G497300 chr5B 79.703 202 25 10 3774 3968 618771221 618771413 1.580000e-26 132.0
58 TraesCS3D01G497300 chr5B 77.949 195 25 10 3774 3960 663639510 663639326 9.550000e-19 106.0
59 TraesCS3D01G497300 chr7D 83.036 336 23 13 2568 2899 45485965 45485660 2.480000e-69 274.0
60 TraesCS3D01G497300 chr7D 90.909 154 14 0 1406 1559 259840852 259840699 2.550000e-49 207.0
61 TraesCS3D01G497300 chrUn 80.984 305 35 12 4739 5041 41659089 41659372 3.270000e-53 220.0
62 TraesCS3D01G497300 chr7A 90.260 154 15 0 1406 1559 282369263 282369110 1.180000e-47 202.0
63 TraesCS3D01G497300 chr4D 77.841 176 21 11 3791 3960 195847456 195847619 7.440000e-15 93.5
64 TraesCS3D01G497300 chr4A 88.406 69 4 4 3774 3840 657247231 657247165 5.790000e-11 80.5


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 TraesCS3D01G497300 chr3D 588483721 588490685 6964 True 12863.00 12863 100.00000 1 6965 1 chr3D.!!$R4 6964
1 TraesCS3D01G497300 chr3D 423644469 423645118 649 True 224.35 370 86.40150 3772 4746 2 chr3D.!!$R5 974
2 TraesCS3D01G497300 chr3A 718831888 718838731 6843 True 1845.50 5821 89.31125 1 6311 4 chr3A.!!$R1 6310
3 TraesCS3D01G497300 chr3B 786965536 786971882 6346 True 2201.00 5029 93.29100 56 6433 4 chr3B.!!$R3 6377
4 TraesCS3D01G497300 chr3B 786959843 786960379 536 True 710.00 710 90.50300 6429 6965 1 chr3B.!!$R2 536
5 TraesCS3D01G497300 chr1D 71618975 71620097 1122 True 331.00 377 84.69750 2568 4741 2 chr1D.!!$R1 2173
6 TraesCS3D01G497300 chr1D 416536150 416537709 1559 True 228.00 399 87.72375 2568 4746 4 chr1D.!!$R2 2178
7 TraesCS3D01G497300 chr6A 525286007 525286775 768 True 240.50 379 91.57500 2625 4741 2 chr6A.!!$R1 2116
8 TraesCS3D01G497300 chr2D 34676156 34676892 736 True 234.50 363 91.28000 2623 4741 2 chr2D.!!$R2 2118
9 TraesCS3D01G497300 chr2D 607796278 607797044 766 False 234.50 370 90.15150 2622 4741 2 chr2D.!!$F1 2119
10 TraesCS3D01G497300 chr5D 125180576 125181650 1074 False 325.50 368 86.04100 2568 4741 2 chr5D.!!$F1 2173
11 TraesCS3D01G497300 chr6D 84292495 84296025 3530 True 250.00 315 84.99750 4061 5561 2 chr6D.!!$R1 1500
12 TraesCS3D01G497300 chr1A 513850424 513851930 1506 True 202.00 300 89.00900 2570 2911 2 chr1A.!!$R1 341
13 TraesCS3D01G497300 chr7B 692188312 692189312 1000 False 217.50 294 88.45150 2564 4328 2 chr7B.!!$F2 1764

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
571 647 0.099791 GCGACTCTCTTTCGAGGAGG 59.900 60.000 14.56 9.54 38.85 4.30 F
595 671 0.539518 GAGAAGAAGCTCCCAGTCCC 59.460 60.000 0.00 0.00 0.00 4.46 F
2169 2965 0.105778 GAGGAGGCCAGCACATACTC 59.894 60.000 5.01 0.00 0.00 2.59 F
3197 4011 2.040939 AGAGGTGATGCATGAGGAGAG 58.959 52.381 2.46 0.00 0.00 3.20 F
4188 5178 1.171308 AATGTGGACATGTGCTGCTC 58.829 50.000 18.75 7.10 36.56 4.26 F
5105 6143 2.134789 ACTTTGCCTAGCCATTCTGG 57.865 50.000 0.00 0.00 41.55 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1647 2425 0.896940 TGGAGGTGGAGGTGTACGAC 60.897 60.000 0.00 0.00 0.00 4.34 R
2402 3198 1.063867 GGTGCTACTAGGAGGACTGGA 60.064 57.143 24.22 0.00 37.86 3.86 R
3476 4297 0.178984 CCATGTGCATGATGCCCCTA 60.179 55.000 15.70 0.00 44.23 3.53 R
4858 5873 2.844122 TCGACCACTCGTGTCATATG 57.156 50.000 0.00 0.00 41.02 1.78 R
5695 9582 2.353109 GCAAGACAAGGGGCTCATTTTC 60.353 50.000 0.00 0.00 0.00 2.29 R
6317 10285 0.110238 CAAACGATGCAACGTCCCTG 60.110 55.000 22.67 15.44 45.83 4.45 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
32 33 2.552373 GGAAGCGGGGAGAAAAGAAGAA 60.552 50.000 0.00 0.00 0.00 2.52
33 34 2.481289 AGCGGGGAGAAAAGAAGAAG 57.519 50.000 0.00 0.00 0.00 2.85
34 35 1.978580 AGCGGGGAGAAAAGAAGAAGA 59.021 47.619 0.00 0.00 0.00 2.87
116 124 1.115467 TCCAGAAGCGAAGATCTCCC 58.885 55.000 0.00 0.00 0.00 4.30
149 157 1.428912 ACAGGAATTTTCAGAGCCCCA 59.571 47.619 0.00 0.00 0.00 4.96
150 158 1.821136 CAGGAATTTTCAGAGCCCCAC 59.179 52.381 0.00 0.00 0.00 4.61
151 159 1.428912 AGGAATTTTCAGAGCCCCACA 59.571 47.619 0.00 0.00 0.00 4.17
152 160 1.546029 GGAATTTTCAGAGCCCCACAC 59.454 52.381 0.00 0.00 0.00 3.82
154 162 0.609131 ATTTTCAGAGCCCCACACCG 60.609 55.000 0.00 0.00 0.00 4.94
171 179 3.670377 GCACCCCCAACGCAAGAC 61.670 66.667 0.00 0.00 43.62 3.01
172 180 2.113139 CACCCCCAACGCAAGACT 59.887 61.111 0.00 0.00 43.62 3.24
173 181 1.528309 CACCCCCAACGCAAGACTT 60.528 57.895 0.00 0.00 43.62 3.01
174 182 0.250553 CACCCCCAACGCAAGACTTA 60.251 55.000 0.00 0.00 43.62 2.24
175 183 0.475044 ACCCCCAACGCAAGACTTAA 59.525 50.000 0.00 0.00 43.62 1.85
176 184 1.133730 ACCCCCAACGCAAGACTTAAA 60.134 47.619 0.00 0.00 43.62 1.52
184 192 4.766404 ACGCAAGACTTAAAAATCCCTG 57.234 40.909 0.00 0.00 43.62 4.45
192 200 1.089123 TAAAAATCCCTGTGCCCCCT 58.911 50.000 0.00 0.00 0.00 4.79
193 201 0.252239 AAAAATCCCTGTGCCCCCTC 60.252 55.000 0.00 0.00 0.00 4.30
199 207 3.402681 CTGTGCCCCCTCCGTCAT 61.403 66.667 0.00 0.00 0.00 3.06
200 208 3.687321 CTGTGCCCCCTCCGTCATG 62.687 68.421 0.00 0.00 0.00 3.07
201 209 4.489771 GTGCCCCCTCCGTCATGG 62.490 72.222 0.00 0.00 40.09 3.66
205 237 2.140792 CCCCCTCCGTCATGGTAGG 61.141 68.421 0.00 0.00 39.52 3.18
258 315 5.762711 GGAAAACAAAATAAAGGTGCCATGT 59.237 36.000 0.00 0.00 0.00 3.21
273 330 2.950418 GCCATGTAAAGGAAAGGGGGAG 60.950 54.545 0.00 0.00 0.00 4.30
285 342 1.522900 AGGGGGAGAGAGAGAGAGAG 58.477 60.000 0.00 0.00 0.00 3.20
286 343 1.010793 AGGGGGAGAGAGAGAGAGAGA 59.989 57.143 0.00 0.00 0.00 3.10
287 344 1.421646 GGGGGAGAGAGAGAGAGAGAG 59.578 61.905 0.00 0.00 0.00 3.20
288 345 2.408565 GGGGAGAGAGAGAGAGAGAGA 58.591 57.143 0.00 0.00 0.00 3.10
289 346 2.370189 GGGGAGAGAGAGAGAGAGAGAG 59.630 59.091 0.00 0.00 0.00 3.20
290 347 3.309296 GGGAGAGAGAGAGAGAGAGAGA 58.691 54.545 0.00 0.00 0.00 3.10
291 348 3.323403 GGGAGAGAGAGAGAGAGAGAGAG 59.677 56.522 0.00 0.00 0.00 3.20
292 349 4.219115 GGAGAGAGAGAGAGAGAGAGAGA 58.781 52.174 0.00 0.00 0.00 3.10
293 350 4.280677 GGAGAGAGAGAGAGAGAGAGAGAG 59.719 54.167 0.00 0.00 0.00 3.20
294 351 5.136068 AGAGAGAGAGAGAGAGAGAGAGA 57.864 47.826 0.00 0.00 0.00 3.10
295 352 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
296 353 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
297 354 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
298 355 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
299 356 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
300 357 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
301 358 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
302 359 3.640967 AGAGAGAGAGAGAGAGAGAGAGC 59.359 52.174 0.00 0.00 0.00 4.09
303 360 2.363680 AGAGAGAGAGAGAGAGAGAGCG 59.636 54.545 0.00 0.00 0.00 5.03
304 361 2.362397 GAGAGAGAGAGAGAGAGAGCGA 59.638 54.545 0.00 0.00 0.00 4.93
305 362 2.363680 AGAGAGAGAGAGAGAGAGCGAG 59.636 54.545 0.00 0.00 0.00 5.03
306 363 2.362397 GAGAGAGAGAGAGAGAGCGAGA 59.638 54.545 0.00 0.00 0.00 4.04
314 371 1.202580 AGAGAGAGCGAGAGAGAGAGC 60.203 57.143 0.00 0.00 0.00 4.09
320 377 0.884704 GCGAGAGAGAGAGCGGAGAT 60.885 60.000 0.00 0.00 0.00 2.75
322 379 1.238439 GAGAGAGAGAGCGGAGATGG 58.762 60.000 0.00 0.00 0.00 3.51
329 386 2.444706 AGCGGAGATGGGCTAGCA 60.445 61.111 18.24 0.00 37.83 3.49
416 476 1.600485 GTAGAGGTAGAGTGAGCTCGC 59.400 57.143 19.76 19.76 46.39 5.03
417 477 1.092921 AGAGGTAGAGTGAGCTCGCG 61.093 60.000 21.01 0.00 46.39 5.87
419 479 2.408241 GGTAGAGTGAGCTCGCGGT 61.408 63.158 21.01 14.54 46.03 5.68
420 480 1.226435 GTAGAGTGAGCTCGCGGTG 60.226 63.158 21.01 0.07 46.03 4.94
421 481 3.052620 TAGAGTGAGCTCGCGGTGC 62.053 63.158 21.01 11.84 46.03 5.01
422 482 4.427661 GAGTGAGCTCGCGGTGCT 62.428 66.667 23.11 23.11 44.24 4.40
427 488 4.314440 AGCTCGCGGTGCTTGGAA 62.314 61.111 18.82 0.00 37.52 3.53
512 584 3.900892 GACGCCGCAGCCTAGCTA 61.901 66.667 0.00 0.00 36.40 3.32
513 585 3.832720 GACGCCGCAGCCTAGCTAG 62.833 68.421 14.20 14.20 36.40 3.42
517 589 2.496341 CGCAGCCTAGCTAGTGCA 59.504 61.111 26.78 0.00 42.74 4.57
540 616 2.431454 CCATCCATCCGTCCGTCCA 61.431 63.158 0.00 0.00 0.00 4.02
543 619 1.472662 ATCCATCCGTCCGTCCATCC 61.473 60.000 0.00 0.00 0.00 3.51
544 620 2.431454 CCATCCGTCCGTCCATCCA 61.431 63.158 0.00 0.00 0.00 3.41
545 621 1.748403 CATCCGTCCGTCCATCCAT 59.252 57.895 0.00 0.00 0.00 3.41
546 622 0.319900 CATCCGTCCGTCCATCCATC 60.320 60.000 0.00 0.00 0.00 3.51
547 623 1.472662 ATCCGTCCGTCCATCCATCC 61.473 60.000 0.00 0.00 0.00 3.51
548 624 2.027605 CGTCCGTCCATCCATCCG 59.972 66.667 0.00 0.00 0.00 4.18
550 626 1.067582 GTCCGTCCATCCATCCGTC 59.932 63.158 0.00 0.00 0.00 4.79
552 628 1.068083 CCGTCCATCCATCCGTCTG 59.932 63.158 0.00 0.00 0.00 3.51
553 629 1.592669 CGTCCATCCATCCGTCTGC 60.593 63.158 0.00 0.00 0.00 4.26
554 630 1.592669 GTCCATCCATCCGTCTGCG 60.593 63.158 0.00 0.00 37.95 5.18
555 631 1.756561 TCCATCCATCCGTCTGCGA 60.757 57.895 0.00 0.00 41.33 5.10
557 633 1.439228 CATCCATCCGTCTGCGACT 59.561 57.895 7.03 0.00 41.33 4.18
558 634 0.596083 CATCCATCCGTCTGCGACTC 60.596 60.000 7.03 0.00 41.33 3.36
559 635 0.753479 ATCCATCCGTCTGCGACTCT 60.753 55.000 7.03 0.00 41.33 3.24
560 636 1.064946 CCATCCGTCTGCGACTCTC 59.935 63.158 7.03 0.00 41.33 3.20
561 637 1.380403 CCATCCGTCTGCGACTCTCT 61.380 60.000 7.03 0.00 41.33 3.10
562 638 0.453793 CATCCGTCTGCGACTCTCTT 59.546 55.000 7.03 0.00 41.33 2.85
563 639 1.135257 CATCCGTCTGCGACTCTCTTT 60.135 52.381 7.03 0.00 41.33 2.52
564 640 0.522180 TCCGTCTGCGACTCTCTTTC 59.478 55.000 7.03 0.00 41.33 2.62
565 641 0.794981 CCGTCTGCGACTCTCTTTCG 60.795 60.000 7.03 0.00 41.33 3.46
566 642 0.166161 CGTCTGCGACTCTCTTTCGA 59.834 55.000 7.03 0.00 38.85 3.71
571 647 0.099791 GCGACTCTCTTTCGAGGAGG 59.900 60.000 14.56 9.54 38.85 4.30
595 671 0.539518 GAGAAGAAGCTCCCAGTCCC 59.460 60.000 0.00 0.00 0.00 4.46
722 813 2.202892 GCAGCCACTACGGGTAGC 60.203 66.667 5.78 0.00 46.49 3.58
875 970 4.131088 GGACTGGGTCGCGTCCTC 62.131 72.222 21.44 11.43 44.90 3.71
876 971 4.131088 GACTGGGTCGCGTCCTCC 62.131 72.222 21.44 12.14 0.00 4.30
1378 2156 2.721167 CCCTTCCCGATGCTCGACA 61.721 63.158 7.07 0.00 43.74 4.35
1721 2504 2.890311 CCAGCCATCAAGGTTTGTAACA 59.110 45.455 0.00 0.00 40.61 2.41
1754 2537 3.253416 GGCGACGTATCCTCTTCAC 57.747 57.895 0.00 0.00 0.00 3.18
1755 2538 0.591741 GGCGACGTATCCTCTTCACG 60.592 60.000 0.00 0.00 41.32 4.35
1756 2539 1.201098 GCGACGTATCCTCTTCACGC 61.201 60.000 0.00 0.00 39.23 5.34
1757 2540 0.377554 CGACGTATCCTCTTCACGCT 59.622 55.000 0.00 0.00 39.23 5.07
1758 2541 1.595003 CGACGTATCCTCTTCACGCTC 60.595 57.143 0.00 0.00 39.23 5.03
1759 2542 1.400846 GACGTATCCTCTTCACGCTCA 59.599 52.381 0.00 0.00 39.23 4.26
1789 2572 2.724977 ATTCGAGACAGTTCGCTCAA 57.275 45.000 0.00 0.00 40.29 3.02
1797 2580 0.445436 CAGTTCGCTCAACATCTGCC 59.555 55.000 0.00 0.00 37.48 4.85
1974 2761 2.490217 CTCTACGACCAGGGCGTG 59.510 66.667 31.86 19.73 42.62 5.34
2169 2965 0.105778 GAGGAGGCCAGCACATACTC 59.894 60.000 5.01 0.00 0.00 2.59
2388 3184 7.817478 TGTATGACATCAAGTGTTAATCGTTCT 59.183 33.333 0.00 0.00 42.36 3.01
2402 3198 7.392673 TGTTAATCGTTCTTAGTCTAGTCCAGT 59.607 37.037 0.00 0.00 0.00 4.00
2581 3377 3.312146 GCTGGTTTTGTCCAATTGGTTTG 59.688 43.478 23.76 0.00 37.01 2.93
2582 3378 3.274288 TGGTTTTGTCCAATTGGTTTGC 58.726 40.909 23.76 12.88 34.24 3.68
2785 3588 6.038356 CAGAAAAGTTTGACTCTTGCAACAT 58.962 36.000 0.00 0.00 0.00 2.71
2902 3706 4.323868 CCTTTTCCTGTTTGTTTTCCCCAA 60.324 41.667 0.00 0.00 0.00 4.12
3182 3996 3.892588 GCATGTTAGTAGAGGCTAGAGGT 59.107 47.826 0.00 0.00 0.00 3.85
3196 4010 2.171568 AGAGGTGATGCATGAGGAGA 57.828 50.000 2.46 0.00 0.00 3.71
3197 4011 2.040939 AGAGGTGATGCATGAGGAGAG 58.959 52.381 2.46 0.00 0.00 3.20
3747 4568 4.203618 GGCTTCGTAGGCCTTGAC 57.796 61.111 12.58 2.12 45.57 3.18
3748 4569 1.597461 GGCTTCGTAGGCCTTGACT 59.403 57.895 12.58 0.00 45.57 3.41
3768 4592 2.165234 CTCTCTCCTTGAATCGTGCTGA 59.835 50.000 0.00 0.00 0.00 4.26
3784 4608 4.269603 CGTGCTGATCCTTGACTAATTGAG 59.730 45.833 0.00 0.00 0.00 3.02
3789 4613 3.350219 TCCTTGACTAATTGAGCACCC 57.650 47.619 0.00 0.00 0.00 4.61
3821 4645 2.623416 CTGTTGGACAAGGTTTCCTTCC 59.377 50.000 0.00 0.00 42.67 3.46
3830 4655 3.527507 AGGTTTCCTTCCTTTCTTCCC 57.472 47.619 0.00 0.00 30.18 3.97
4057 4897 6.479660 GCACAATAAATTGGGTTGATATGTGG 59.520 38.462 6.79 0.00 43.03 4.17
4188 5178 1.171308 AATGTGGACATGTGCTGCTC 58.829 50.000 18.75 7.10 36.56 4.26
4873 5888 4.183865 ACATGTTCATATGACACGAGTGG 58.816 43.478 4.48 0.58 34.19 4.00
4965 5993 5.388408 AACAGACCTAGTACTTGTGTAGC 57.612 43.478 0.00 0.00 0.00 3.58
5014 6042 7.040062 TCCTTAACTTTTTGGTGATATGTGTGG 60.040 37.037 0.00 0.00 0.00 4.17
5105 6143 2.134789 ACTTTGCCTAGCCATTCTGG 57.865 50.000 0.00 0.00 41.55 3.86
5142 6187 2.222819 GCAATCGTTGAGCTTCTAACGG 60.223 50.000 22.76 13.25 46.87 4.44
5154 6199 3.362693 GCTTCTAACGGCATATTGCGTAC 60.363 47.826 0.00 0.00 46.21 3.67
5165 6210 6.087522 GGCATATTGCGTACAAGTTTGTTTA 58.912 36.000 2.46 0.00 46.21 2.01
5167 6212 7.274686 GGCATATTGCGTACAAGTTTGTTTAAT 59.725 33.333 2.46 2.96 46.21 1.40
5416 9238 5.586243 CACTGATGGTTAGGTTTCCATACAG 59.414 44.000 15.13 15.13 43.45 2.74
5504 9390 5.990120 AGCCAAAATTTGCTACTTCTGAT 57.010 34.783 0.00 0.00 35.69 2.90
5667 9554 8.623903 TCCACATTCTTCAATGCTGTATATTTC 58.376 33.333 0.00 0.00 43.03 2.17
5677 9564 4.769688 TGCTGTATATTTCCCTGACACAG 58.230 43.478 0.00 0.00 36.01 3.66
5694 9581 4.905429 ACACAGGTATGATGTTTGTGCTA 58.095 39.130 3.09 0.00 42.05 3.49
5695 9582 4.937620 ACACAGGTATGATGTTTGTGCTAG 59.062 41.667 3.09 0.00 42.05 3.42
5714 9601 3.532641 AGAAAATGAGCCCCTTGTCTT 57.467 42.857 0.00 0.00 0.00 3.01
5716 9603 1.260544 AAATGAGCCCCTTGTCTTGC 58.739 50.000 0.00 0.00 0.00 4.01
5746 9633 1.217882 CTGGAGTTGCTTTCGAACGT 58.782 50.000 0.00 0.00 0.00 3.99
5772 9659 4.377022 CGAACGCACTGCTTTGTAAATAGT 60.377 41.667 0.00 0.00 0.00 2.12
5783 9744 9.303537 CTGCTTTGTAAATAGTACTCCTACTTC 57.696 37.037 0.00 0.00 34.79 3.01
5793 9754 5.020132 AGTACTCCTACTTCAGATGCACTT 58.980 41.667 0.00 0.00 27.62 3.16
5986 9947 5.064962 CCGTAACTGTTGTGTTGGTTAAAGA 59.935 40.000 2.69 0.00 0.00 2.52
6107 10070 1.960689 TCTTTTCTTCTTTTGCCCCCG 59.039 47.619 0.00 0.00 0.00 5.73
6217 10181 5.121811 AGCTGTCCTGATGATCATTACAAC 58.878 41.667 10.14 7.90 0.00 3.32
6262 10230 1.189524 TGAGGGGTGTCGTGTTAGGG 61.190 60.000 0.00 0.00 0.00 3.53
6274 10242 2.744823 CGTGTTAGGGCATGCCTATTGA 60.745 50.000 34.70 15.50 36.10 2.57
6287 10255 2.684927 GCCTATTGACTCCAGTGCCAAT 60.685 50.000 0.00 0.00 34.16 3.16
6318 10286 6.438186 TGACCATCATCAATCTATAAGCCA 57.562 37.500 0.00 0.00 0.00 4.75
6319 10287 6.470278 TGACCATCATCAATCTATAAGCCAG 58.530 40.000 0.00 0.00 0.00 4.85
6320 10288 5.813383 ACCATCATCAATCTATAAGCCAGG 58.187 41.667 0.00 0.00 0.00 4.45
6321 10289 5.191426 CCATCATCAATCTATAAGCCAGGG 58.809 45.833 0.00 0.00 0.00 4.45
6322 10290 5.045359 CCATCATCAATCTATAAGCCAGGGA 60.045 44.000 0.00 0.00 0.00 4.20
6323 10291 5.489792 TCATCAATCTATAAGCCAGGGAC 57.510 43.478 0.00 0.00 0.00 4.46
6324 10292 4.021104 TCATCAATCTATAAGCCAGGGACG 60.021 45.833 0.00 0.00 0.00 4.79
6325 10293 3.305720 TCAATCTATAAGCCAGGGACGT 58.694 45.455 0.00 0.00 0.00 4.34
6326 10294 3.709653 TCAATCTATAAGCCAGGGACGTT 59.290 43.478 0.00 0.00 0.00 3.99
6327 10295 3.753294 ATCTATAAGCCAGGGACGTTG 57.247 47.619 0.00 0.00 0.00 4.10
6328 10296 1.138266 TCTATAAGCCAGGGACGTTGC 59.862 52.381 0.00 0.00 0.00 4.17
6329 10297 0.906066 TATAAGCCAGGGACGTTGCA 59.094 50.000 0.00 0.00 0.00 4.08
6330 10298 0.255890 ATAAGCCAGGGACGTTGCAT 59.744 50.000 0.00 0.00 0.00 3.96
6331 10299 0.392461 TAAGCCAGGGACGTTGCATC 60.392 55.000 0.00 0.00 0.00 3.91
6332 10300 3.499737 GCCAGGGACGTTGCATCG 61.500 66.667 15.36 15.36 0.00 3.84
6333 10301 2.047274 CCAGGGACGTTGCATCGT 60.047 61.111 21.96 21.96 46.88 3.73
6334 10302 1.671054 CCAGGGACGTTGCATCGTT 60.671 57.895 22.58 5.76 44.21 3.85
6335 10303 1.234615 CCAGGGACGTTGCATCGTTT 61.235 55.000 22.58 10.00 44.21 3.60
6336 10304 0.110238 CAGGGACGTTGCATCGTTTG 60.110 55.000 22.58 16.78 44.21 2.93
6337 10305 1.209127 GGGACGTTGCATCGTTTGG 59.791 57.895 22.58 0.00 44.21 3.28
6338 10306 1.231958 GGGACGTTGCATCGTTTGGA 61.232 55.000 22.58 0.00 44.21 3.53
6339 10307 0.165944 GGACGTTGCATCGTTTGGAG 59.834 55.000 22.58 0.00 44.21 3.86
6340 10308 1.144969 GACGTTGCATCGTTTGGAGA 58.855 50.000 22.58 0.00 44.21 3.71
6341 10309 1.529438 GACGTTGCATCGTTTGGAGAA 59.471 47.619 22.58 0.00 44.21 2.87
6342 10310 1.531149 ACGTTGCATCGTTTGGAGAAG 59.469 47.619 16.76 0.00 41.37 2.85
6343 10311 1.135972 CGTTGCATCGTTTGGAGAAGG 60.136 52.381 9.02 0.00 0.00 3.46
6344 10312 2.151202 GTTGCATCGTTTGGAGAAGGA 58.849 47.619 0.00 0.00 0.00 3.36
6345 10313 2.552315 GTTGCATCGTTTGGAGAAGGAA 59.448 45.455 0.00 0.00 0.00 3.36
6346 10314 2.857483 TGCATCGTTTGGAGAAGGAAA 58.143 42.857 0.00 0.00 0.00 3.13
6347 10315 3.218453 TGCATCGTTTGGAGAAGGAAAA 58.782 40.909 0.00 0.00 0.00 2.29
6348 10316 3.634448 TGCATCGTTTGGAGAAGGAAAAA 59.366 39.130 0.00 0.00 0.00 1.94
6349 10317 4.229876 GCATCGTTTGGAGAAGGAAAAAG 58.770 43.478 0.00 0.00 0.00 2.27
6350 10318 4.023193 GCATCGTTTGGAGAAGGAAAAAGA 60.023 41.667 0.00 0.00 0.00 2.52
6351 10319 5.507315 GCATCGTTTGGAGAAGGAAAAAGAA 60.507 40.000 0.00 0.00 0.00 2.52
6380 10348 7.503549 AGAAACTATATGATGTGTCATGCTCA 58.496 34.615 1.37 0.00 44.62 4.26
6427 10395 7.276658 CACTATGAATCTCAACCTACTTGTGAC 59.723 40.741 0.00 0.00 35.67 3.67
6447 10415 2.750166 ACTGAGTGTCGTGTGGAGATAG 59.250 50.000 0.00 0.00 0.00 2.08
6480 10448 2.768527 CTCCCAATCTCTAGTGAGCCAA 59.231 50.000 0.50 0.00 40.03 4.52
6498 10466 1.347707 CAAGCTCACTTGTCACCCCTA 59.652 52.381 0.00 0.00 46.84 3.53
6505 10473 5.652452 GCTCACTTGTCACCCCTAAATTATT 59.348 40.000 0.00 0.00 0.00 1.40
6507 10475 5.949354 TCACTTGTCACCCCTAAATTATTGG 59.051 40.000 0.00 0.00 0.00 3.16
6516 10484 7.004086 CACCCCTAAATTATTGGCTTATCTCA 58.996 38.462 0.00 0.00 0.00 3.27
6529 10497 4.158394 GGCTTATCTCACTTTTCATGGCAA 59.842 41.667 0.00 0.00 0.00 4.52
6534 10502 4.592942 TCTCACTTTTCATGGCAAGCTAT 58.407 39.130 0.00 0.00 0.00 2.97
6550 10518 2.827921 AGCTATTTTTGGGGCTCACTTG 59.172 45.455 0.00 0.00 0.00 3.16
6551 10519 2.094026 GCTATTTTTGGGGCTCACTTGG 60.094 50.000 0.00 0.00 0.00 3.61
6552 10520 2.101640 ATTTTTGGGGCTCACTTGGT 57.898 45.000 0.00 0.00 0.00 3.67
6636 10604 8.993121 CCACATATTATGAGAACTTGGACATAC 58.007 37.037 10.62 0.00 0.00 2.39
6713 10681 7.948357 TGATACGCTGTACAAGTATAGGAAAT 58.052 34.615 18.18 3.10 31.93 2.17
6720 10688 6.567050 TGTACAAGTATAGGAAATGACGACC 58.433 40.000 0.00 0.00 0.00 4.79
6752 10720 5.655090 AGATTGATTTCATGGATTGAGCACA 59.345 36.000 0.00 0.00 35.27 4.57
6765 10733 4.640771 TTGAGCACAAAGTTCTATCCCT 57.359 40.909 0.00 0.00 32.73 4.20
6767 10735 5.344743 TGAGCACAAAGTTCTATCCCTAG 57.655 43.478 0.00 0.00 0.00 3.02
6771 10739 5.128008 AGCACAAAGTTCTATCCCTAGAGTC 59.872 44.000 0.00 0.00 35.43 3.36
6787 10755 0.541863 AGTCACAATTCTAGGCCCCG 59.458 55.000 0.00 0.00 0.00 5.73
6790 10758 0.394352 CACAATTCTAGGCCCCGCTT 60.394 55.000 0.00 0.00 0.00 4.68
6804 10772 2.432444 CCCGCTTGTGAATGAGGTTAA 58.568 47.619 0.00 0.00 0.00 2.01
6818 10786 3.908103 TGAGGTTAAGGTTCTGGCTAGTT 59.092 43.478 0.00 0.00 0.00 2.24
6821 10789 3.259902 GTTAAGGTTCTGGCTAGTTCGG 58.740 50.000 0.00 0.00 0.00 4.30
6822 10790 1.349067 AAGGTTCTGGCTAGTTCGGT 58.651 50.000 0.00 0.00 0.00 4.69
6823 10791 0.608640 AGGTTCTGGCTAGTTCGGTG 59.391 55.000 0.00 0.00 0.00 4.94
6824 10792 0.391263 GGTTCTGGCTAGTTCGGTGG 60.391 60.000 0.00 0.00 0.00 4.61
6863 10831 3.833559 ATTGGTCCAACTTTCCCATCT 57.166 42.857 6.41 0.00 0.00 2.90
6872 10840 4.637534 CCAACTTTCCCATCTACACATCTG 59.362 45.833 0.00 0.00 0.00 2.90
6892 10860 2.564504 TGCCTAGATCCAATCCATCTCG 59.435 50.000 0.00 0.00 32.61 4.04
6900 10868 4.672587 TCCAATCCATCTCGGTCTTTAG 57.327 45.455 0.00 0.00 35.57 1.85
6901 10869 3.134458 CCAATCCATCTCGGTCTTTAGC 58.866 50.000 0.00 0.00 35.57 3.09
6923 10891 5.041287 GCTTAGTTTTGGGTTGAGTTGAAC 58.959 41.667 0.00 0.00 0.00 3.18
6935 10903 4.081322 TGAGTTGAACCAGAAACCTACC 57.919 45.455 0.00 0.00 0.00 3.18
6938 10906 2.882761 GTTGAACCAGAAACCTACCCAC 59.117 50.000 0.00 0.00 0.00 4.61
6959 10928 5.207768 CACACTGTGTTTCTTCTGCATTAC 58.792 41.667 11.40 0.00 0.00 1.89
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
32 33 3.764466 CCGGCCGCTTCTCTGTCT 61.764 66.667 22.85 0.00 0.00 3.41
52 53 2.123726 ATCCATCTTTGCCCGGCC 60.124 61.111 7.03 0.00 0.00 6.13
53 54 2.492773 CCATCCATCTTTGCCCGGC 61.493 63.158 1.04 1.04 0.00 6.13
54 55 0.178981 ATCCATCCATCTTTGCCCGG 60.179 55.000 0.00 0.00 0.00 5.73
55 56 2.038952 TCTATCCATCCATCTTTGCCCG 59.961 50.000 0.00 0.00 0.00 6.13
56 57 3.795688 TCTATCCATCCATCTTTGCCC 57.204 47.619 0.00 0.00 0.00 5.36
57 58 4.880696 GCTATCTATCCATCCATCTTTGCC 59.119 45.833 0.00 0.00 0.00 4.52
58 59 4.569966 CGCTATCTATCCATCCATCTTTGC 59.430 45.833 0.00 0.00 0.00 3.68
116 124 3.077556 CCTGTGGGACGGAGGGAG 61.078 72.222 0.00 0.00 33.58 4.30
154 162 3.670377 GTCTTGCGTTGGGGGTGC 61.670 66.667 0.00 0.00 0.00 5.01
156 164 0.475044 TTAAGTCTTGCGTTGGGGGT 59.525 50.000 0.00 0.00 0.00 4.95
157 165 1.611519 TTTAAGTCTTGCGTTGGGGG 58.388 50.000 0.00 0.00 0.00 5.40
160 168 4.022329 AGGGATTTTTAAGTCTTGCGTTGG 60.022 41.667 0.00 0.00 0.00 3.77
162 170 4.583073 ACAGGGATTTTTAAGTCTTGCGTT 59.417 37.500 0.00 0.00 0.00 4.84
163 171 4.023193 CACAGGGATTTTTAAGTCTTGCGT 60.023 41.667 0.00 0.00 0.00 5.24
164 172 4.475944 CACAGGGATTTTTAAGTCTTGCG 58.524 43.478 0.00 0.00 0.00 4.85
165 173 4.237724 GCACAGGGATTTTTAAGTCTTGC 58.762 43.478 0.00 0.00 0.00 4.01
166 174 4.321974 GGGCACAGGGATTTTTAAGTCTTG 60.322 45.833 0.00 0.00 0.00 3.02
169 177 2.496070 GGGGCACAGGGATTTTTAAGTC 59.504 50.000 0.00 0.00 0.00 3.01
171 179 1.831106 GGGGGCACAGGGATTTTTAAG 59.169 52.381 0.00 0.00 0.00 1.85
172 180 1.435168 AGGGGGCACAGGGATTTTTAA 59.565 47.619 0.00 0.00 0.00 1.52
173 181 1.006639 GAGGGGGCACAGGGATTTTTA 59.993 52.381 0.00 0.00 0.00 1.52
174 182 0.252239 GAGGGGGCACAGGGATTTTT 60.252 55.000 0.00 0.00 0.00 1.94
175 183 1.388133 GAGGGGGCACAGGGATTTT 59.612 57.895 0.00 0.00 0.00 1.82
176 184 2.626467 GGAGGGGGCACAGGGATTT 61.626 63.158 0.00 0.00 0.00 2.17
184 192 4.489771 CCATGACGGAGGGGGCAC 62.490 72.222 0.00 0.00 36.56 5.01
192 200 2.112190 TGTAATGCCTACCATGACGGA 58.888 47.619 0.00 0.00 38.03 4.69
193 201 2.613026 TGTAATGCCTACCATGACGG 57.387 50.000 0.00 0.00 38.03 4.79
195 203 5.640732 CACTTTTGTAATGCCTACCATGAC 58.359 41.667 0.00 0.00 36.05 3.06
196 204 4.157656 GCACTTTTGTAATGCCTACCATGA 59.842 41.667 0.00 0.00 33.49 3.07
197 205 4.158394 AGCACTTTTGTAATGCCTACCATG 59.842 41.667 0.00 0.00 40.33 3.66
198 206 4.344104 AGCACTTTTGTAATGCCTACCAT 58.656 39.130 0.00 0.00 40.33 3.55
199 207 3.761897 AGCACTTTTGTAATGCCTACCA 58.238 40.909 0.00 0.00 40.33 3.25
200 208 5.183228 TCTAGCACTTTTGTAATGCCTACC 58.817 41.667 0.00 0.00 40.33 3.18
201 209 6.737254 TTCTAGCACTTTTGTAATGCCTAC 57.263 37.500 0.00 0.00 40.33 3.18
205 237 7.062255 GGTGATTTTCTAGCACTTTTGTAATGC 59.938 37.037 0.00 0.00 39.74 3.56
258 315 3.340049 TCTCTCTCTCCCCCTTTCCTTTA 59.660 47.826 0.00 0.00 0.00 1.85
273 330 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
285 342 2.362397 TCTCGCTCTCTCTCTCTCTCTC 59.638 54.545 0.00 0.00 0.00 3.20
286 343 2.363680 CTCTCGCTCTCTCTCTCTCTCT 59.636 54.545 0.00 0.00 0.00 3.10
287 344 2.362397 TCTCTCGCTCTCTCTCTCTCTC 59.638 54.545 0.00 0.00 0.00 3.20
288 345 2.363680 CTCTCTCGCTCTCTCTCTCTCT 59.636 54.545 0.00 0.00 0.00 3.10
289 346 2.362397 TCTCTCTCGCTCTCTCTCTCTC 59.638 54.545 0.00 0.00 0.00 3.20
290 347 2.363680 CTCTCTCTCGCTCTCTCTCTCT 59.636 54.545 0.00 0.00 0.00 3.10
291 348 2.362397 TCTCTCTCTCGCTCTCTCTCTC 59.638 54.545 0.00 0.00 0.00 3.20
292 349 2.363680 CTCTCTCTCTCGCTCTCTCTCT 59.636 54.545 0.00 0.00 0.00 3.10
293 350 2.748605 CTCTCTCTCTCGCTCTCTCTC 58.251 57.143 0.00 0.00 0.00 3.20
294 351 1.202580 GCTCTCTCTCTCGCTCTCTCT 60.203 57.143 0.00 0.00 0.00 3.10
295 352 1.221414 GCTCTCTCTCTCGCTCTCTC 58.779 60.000 0.00 0.00 0.00 3.20
296 353 0.530650 CGCTCTCTCTCTCGCTCTCT 60.531 60.000 0.00 0.00 0.00 3.10
297 354 1.498865 CCGCTCTCTCTCTCGCTCTC 61.499 65.000 0.00 0.00 0.00 3.20
298 355 1.523711 CCGCTCTCTCTCTCGCTCT 60.524 63.158 0.00 0.00 0.00 4.09
299 356 1.498865 CTCCGCTCTCTCTCTCGCTC 61.499 65.000 0.00 0.00 0.00 5.03
300 357 1.523711 CTCCGCTCTCTCTCTCGCT 60.524 63.158 0.00 0.00 0.00 4.93
301 358 0.884704 ATCTCCGCTCTCTCTCTCGC 60.885 60.000 0.00 0.00 0.00 5.03
302 359 0.867746 CATCTCCGCTCTCTCTCTCG 59.132 60.000 0.00 0.00 0.00 4.04
303 360 1.238439 CCATCTCCGCTCTCTCTCTC 58.762 60.000 0.00 0.00 0.00 3.20
304 361 0.178992 CCCATCTCCGCTCTCTCTCT 60.179 60.000 0.00 0.00 0.00 3.10
305 362 1.805428 GCCCATCTCCGCTCTCTCTC 61.805 65.000 0.00 0.00 0.00 3.20
306 363 1.832167 GCCCATCTCCGCTCTCTCT 60.832 63.158 0.00 0.00 0.00 3.10
314 371 2.030262 GCTGCTAGCCCATCTCCG 59.970 66.667 13.29 0.00 34.48 4.63
397 457 1.807000 CGCGAGCTCACTCTACCTCTA 60.807 57.143 15.40 0.00 41.09 2.43
400 460 2.115911 CCGCGAGCTCACTCTACCT 61.116 63.158 15.40 0.00 41.09 3.08
416 476 0.250295 TCCAACTCTTCCAAGCACCG 60.250 55.000 0.00 0.00 0.00 4.94
417 477 1.072331 TCTCCAACTCTTCCAAGCACC 59.928 52.381 0.00 0.00 0.00 5.01
419 479 3.369892 GCTATCTCCAACTCTTCCAAGCA 60.370 47.826 0.00 0.00 0.00 3.91
420 480 3.202097 GCTATCTCCAACTCTTCCAAGC 58.798 50.000 0.00 0.00 0.00 4.01
421 481 3.131223 TCGCTATCTCCAACTCTTCCAAG 59.869 47.826 0.00 0.00 0.00 3.61
422 482 3.096852 TCGCTATCTCCAACTCTTCCAA 58.903 45.455 0.00 0.00 0.00 3.53
427 488 2.582052 CCTCTCGCTATCTCCAACTCT 58.418 52.381 0.00 0.00 0.00 3.24
473 542 2.438021 TCTATCGCCCCAATTGCTACTT 59.562 45.455 0.00 0.00 0.00 2.24
479 551 1.502231 CGTCTCTATCGCCCCAATTG 58.498 55.000 0.00 0.00 0.00 2.32
510 582 0.105593 ATGGATGGCGAGTGCACTAG 59.894 55.000 21.73 21.47 45.35 2.57
511 583 0.104855 GATGGATGGCGAGTGCACTA 59.895 55.000 21.73 4.02 45.35 2.74
512 584 1.153289 GATGGATGGCGAGTGCACT 60.153 57.895 21.88 21.88 45.35 4.40
513 585 2.182842 GGATGGATGGCGAGTGCAC 61.183 63.158 9.40 9.40 45.35 4.57
517 589 2.797278 GGACGGATGGATGGCGAGT 61.797 63.158 0.00 0.00 0.00 4.18
559 635 1.916874 TCTCCTCTCCTCCTCGAAAGA 59.083 52.381 0.00 0.00 39.12 2.52
560 636 2.428544 TCTCCTCTCCTCCTCGAAAG 57.571 55.000 0.00 0.00 0.00 2.62
561 637 2.309162 TCTTCTCCTCTCCTCCTCGAAA 59.691 50.000 0.00 0.00 0.00 3.46
562 638 1.916874 TCTTCTCCTCTCCTCCTCGAA 59.083 52.381 0.00 0.00 0.00 3.71
563 639 1.585895 TCTTCTCCTCTCCTCCTCGA 58.414 55.000 0.00 0.00 0.00 4.04
564 640 2.297701 CTTCTTCTCCTCTCCTCCTCG 58.702 57.143 0.00 0.00 0.00 4.63
565 641 2.031870 GCTTCTTCTCCTCTCCTCCTC 58.968 57.143 0.00 0.00 0.00 3.71
566 642 1.645919 AGCTTCTTCTCCTCTCCTCCT 59.354 52.381 0.00 0.00 0.00 3.69
591 667 2.348998 CTGAGGCTGTGGTGGGAC 59.651 66.667 0.00 0.00 0.00 4.46
593 669 4.729918 GGCTGAGGCTGTGGTGGG 62.730 72.222 0.00 0.00 38.73 4.61
594 670 3.644606 AGGCTGAGGCTGTGGTGG 61.645 66.667 8.08 0.00 36.97 4.61
692 783 3.133014 GCTGCTGAGCGGATCCTA 58.867 61.111 19.07 0.00 37.02 2.94
702 793 1.304630 TACCCGTAGTGGCTGCTGA 60.305 57.895 0.00 0.00 35.87 4.26
704 795 3.617368 CTACCCGTAGTGGCTGCT 58.383 61.111 0.00 0.00 35.87 4.24
799 894 0.177141 GCCACACTTATACCCAGCGA 59.823 55.000 0.00 0.00 0.00 4.93
1101 1199 2.668550 GTGTGGTGGAACGAGGCC 60.669 66.667 0.00 0.00 38.12 5.19
1401 2179 4.704833 CAGGTGGTGGTGCCGGAG 62.705 72.222 5.05 0.00 41.21 4.63
1602 2380 1.592939 GCGAGGCTTCTTCGATCCC 60.593 63.158 2.54 0.00 0.00 3.85
1647 2425 0.896940 TGGAGGTGGAGGTGTACGAC 60.897 60.000 0.00 0.00 0.00 4.34
1651 2429 1.823169 GCGTTGGAGGTGGAGGTGTA 61.823 60.000 0.00 0.00 0.00 2.90
1739 2522 1.400846 TGAGCGTGAAGAGGATACGTC 59.599 52.381 0.00 0.00 46.39 4.34
1789 2572 1.592400 GCAGCACACATGGCAGATGT 61.592 55.000 0.00 0.79 0.00 3.06
1797 2580 2.175078 GCGTCTGCAGCACACATG 59.825 61.111 9.47 0.00 42.15 3.21
2085 2878 3.849951 GGCGCCATCGAGGAGGAA 61.850 66.667 24.80 0.00 41.22 3.36
2388 3184 3.592427 AGGACTGGACTGGACTAGACTAA 59.408 47.826 0.00 0.00 0.00 2.24
2402 3198 1.063867 GGTGCTACTAGGAGGACTGGA 60.064 57.143 24.22 0.00 37.86 3.86
2502 3298 9.862371 AGTACTACTAGTGTTGATTTCATCTTG 57.138 33.333 5.39 0.00 0.00 3.02
2508 3304 8.221766 GTGCAAAGTACTACTAGTGTTGATTTC 58.778 37.037 5.39 0.00 0.00 2.17
2581 3377 1.811359 AGCAAAGCATGAGACAAGAGC 59.189 47.619 0.00 0.00 0.00 4.09
2582 3378 5.123502 ACATAAGCAAAGCATGAGACAAGAG 59.876 40.000 0.00 0.00 0.00 2.85
2785 3588 2.358898 GAGTGAAAGCCAAGCAAGTGAA 59.641 45.455 0.00 0.00 0.00 3.18
2902 3706 4.677182 TCCTACCTACCCGTAGAAAAAGT 58.323 43.478 3.37 0.00 38.41 2.66
3182 3996 1.421480 CCTCCTCTCCTCATGCATCA 58.579 55.000 0.00 0.00 0.00 3.07
3196 4010 0.549950 CAACCATGATCCTGCCTCCT 59.450 55.000 0.00 0.00 0.00 3.69
3197 4011 1.105759 GCAACCATGATCCTGCCTCC 61.106 60.000 0.00 0.00 0.00 4.30
3473 4294 0.330941 TGTGCATGATGCCCCTAACA 59.669 50.000 15.70 9.15 44.23 2.41
3474 4295 1.338973 CATGTGCATGATGCCCCTAAC 59.661 52.381 15.70 6.42 44.23 2.34
3475 4296 1.694844 CATGTGCATGATGCCCCTAA 58.305 50.000 15.70 0.00 44.23 2.69
3476 4297 0.178984 CCATGTGCATGATGCCCCTA 60.179 55.000 15.70 0.00 44.23 3.53
3747 4568 2.165234 TCAGCACGATTCAAGGAGAGAG 59.835 50.000 0.00 0.00 0.00 3.20
3748 4569 2.171003 TCAGCACGATTCAAGGAGAGA 58.829 47.619 0.00 0.00 0.00 3.10
3768 4592 3.682718 CGGGTGCTCAATTAGTCAAGGAT 60.683 47.826 0.00 0.00 0.00 3.24
3821 4645 5.438761 AAACAGAAACATCGGGAAGAAAG 57.561 39.130 0.00 0.00 0.00 2.62
3876 4703 4.258543 CAAGTCCAAGGGCGACTAAATAA 58.741 43.478 0.00 0.00 39.69 1.40
3913 4740 9.137459 TGACAAAATTCTGGTGTTAAATCCTTA 57.863 29.630 0.00 0.00 0.00 2.69
4019 4859 7.148606 CCAATTTATTGTGCCAATTATATGCCG 60.149 37.037 5.85 0.00 36.06 5.69
4112 4958 4.379290 GGGACGTGACAGAAGTTAGTAGTC 60.379 50.000 0.00 0.00 0.00 2.59
4113 4959 3.505293 GGGACGTGACAGAAGTTAGTAGT 59.495 47.826 0.00 0.00 0.00 2.73
4188 5178 3.507786 TCACCATCGTCACAAGAATACG 58.492 45.455 0.00 0.00 37.96 3.06
4564 5577 7.506328 AACCCTACTTGAGTTGAACATAAAC 57.494 36.000 0.00 0.00 0.00 2.01
4771 5785 7.175293 ACCATAGCTAGTATACTAACACAGAGC 59.825 40.741 13.51 12.61 0.00 4.09
4772 5786 8.624367 ACCATAGCTAGTATACTAACACAGAG 57.376 38.462 13.51 3.45 0.00 3.35
4858 5873 2.844122 TCGACCACTCGTGTCATATG 57.156 50.000 0.00 0.00 41.02 1.78
4873 5888 6.569228 TCGTCAAGATACAATTTCATCGAC 57.431 37.500 0.00 0.00 0.00 4.20
4961 5989 4.273969 AGAATAGTCAGCAGTCTACGCTAC 59.726 45.833 0.00 0.00 37.72 3.58
4965 5993 6.035112 GGAAAAAGAATAGTCAGCAGTCTACG 59.965 42.308 0.00 0.00 0.00 3.51
5142 6187 7.555639 TTAAACAAACTTGTACGCAATATGC 57.444 32.000 0.00 0.00 41.31 3.14
5154 6199 9.701355 GATCCAACAAACAATTAAACAAACTTG 57.299 29.630 0.00 0.00 0.00 3.16
5165 6210 6.772716 ACTACTCAGTGATCCAACAAACAATT 59.227 34.615 0.00 0.00 32.25 2.32
5167 6212 5.680619 ACTACTCAGTGATCCAACAAACAA 58.319 37.500 0.00 0.00 32.25 2.83
5416 9238 5.399604 AAAGAACGTAAATATACCTGCGC 57.600 39.130 0.00 0.00 0.00 6.09
5677 9564 7.761409 TCATTTTCTAGCACAAACATCATACC 58.239 34.615 0.00 0.00 0.00 2.73
5694 9581 3.160269 CAAGACAAGGGGCTCATTTTCT 58.840 45.455 0.00 0.00 0.00 2.52
5695 9582 2.353109 GCAAGACAAGGGGCTCATTTTC 60.353 50.000 0.00 0.00 0.00 2.29
5714 9601 3.018856 CAACTCCAGCATATTCCAAGCA 58.981 45.455 0.00 0.00 0.00 3.91
5716 9603 3.285484 AGCAACTCCAGCATATTCCAAG 58.715 45.455 0.00 0.00 0.00 3.61
5772 9659 5.016831 TCAAGTGCATCTGAAGTAGGAGTA 58.983 41.667 0.00 0.00 0.00 2.59
5793 9754 9.173021 AGAATGTTCGGATTAAAATGTACATCA 57.827 29.630 9.23 0.00 0.00 3.07
5986 9947 4.524802 TTTCAGGAAGCATATGGTGGAT 57.475 40.909 8.44 0.00 0.00 3.41
6040 10003 3.994204 TTCGGCTGGTTCCTTAAAAAC 57.006 42.857 0.00 0.00 0.00 2.43
6107 10070 2.454055 GAACAACAAGAGCAGCACAAC 58.546 47.619 0.00 0.00 0.00 3.32
6217 10181 4.078639 AGCAAGGGGAAATTCTATCTCG 57.921 45.455 0.00 0.00 0.00 4.04
6262 10230 1.945394 CACTGGAGTCAATAGGCATGC 59.055 52.381 9.90 9.90 0.00 4.06
6274 10242 0.606401 CCGTTCATTGGCACTGGAGT 60.606 55.000 4.92 0.00 0.00 3.85
6311 10279 0.255890 ATGCAACGTCCCTGGCTTAT 59.744 50.000 0.00 0.00 0.00 1.73
6312 10280 0.392461 GATGCAACGTCCCTGGCTTA 60.392 55.000 0.00 0.00 0.00 3.09
6313 10281 1.675641 GATGCAACGTCCCTGGCTT 60.676 57.895 0.00 0.00 0.00 4.35
6314 10282 2.045926 GATGCAACGTCCCTGGCT 60.046 61.111 0.00 0.00 0.00 4.75
6315 10283 3.499737 CGATGCAACGTCCCTGGC 61.500 66.667 8.38 0.00 0.00 4.85
6316 10284 1.234615 AAACGATGCAACGTCCCTGG 61.235 55.000 22.67 0.00 45.83 4.45
6317 10285 0.110238 CAAACGATGCAACGTCCCTG 60.110 55.000 22.67 15.44 45.83 4.45
6318 10286 1.234615 CCAAACGATGCAACGTCCCT 61.235 55.000 22.67 4.29 45.83 4.20
6319 10287 1.209127 CCAAACGATGCAACGTCCC 59.791 57.895 22.67 0.00 45.83 4.46
6320 10288 0.165944 CTCCAAACGATGCAACGTCC 59.834 55.000 22.67 0.00 45.83 4.79
6321 10289 1.144969 TCTCCAAACGATGCAACGTC 58.855 50.000 22.67 0.00 45.83 4.34
6323 10291 1.135972 CCTTCTCCAAACGATGCAACG 60.136 52.381 15.38 15.38 39.31 4.10
6324 10292 2.151202 TCCTTCTCCAAACGATGCAAC 58.849 47.619 0.00 0.00 0.00 4.17
6325 10293 2.559698 TCCTTCTCCAAACGATGCAA 57.440 45.000 0.00 0.00 0.00 4.08
6326 10294 2.559698 TTCCTTCTCCAAACGATGCA 57.440 45.000 0.00 0.00 0.00 3.96
6327 10295 3.915437 TTTTCCTTCTCCAAACGATGC 57.085 42.857 0.00 0.00 0.00 3.91
6328 10296 5.689383 TCTTTTTCCTTCTCCAAACGATG 57.311 39.130 0.00 0.00 0.00 3.84
6329 10297 6.709018 TTTCTTTTTCCTTCTCCAAACGAT 57.291 33.333 0.00 0.00 0.00 3.73
6330 10298 6.518208 TTTTCTTTTTCCTTCTCCAAACGA 57.482 33.333 0.00 0.00 0.00 3.85
6351 10319 9.793252 GCATGACACATCATATAGTTTCTTTTT 57.207 29.630 0.00 0.00 44.13 1.94
6380 10348 3.648339 CAAGGCTGCAAACACTACAAT 57.352 42.857 0.50 0.00 0.00 2.71
6427 10395 2.478709 GCTATCTCCACACGACACTCAG 60.479 54.545 0.00 0.00 0.00 3.35
6447 10415 1.237285 ATTGGGAGCCATAATCGCGC 61.237 55.000 0.00 0.00 31.53 6.86
6480 10448 1.729586 TTAGGGGTGACAAGTGAGCT 58.270 50.000 0.00 0.00 0.00 4.09
6505 10473 3.696051 GCCATGAAAAGTGAGATAAGCCA 59.304 43.478 0.00 0.00 0.00 4.75
6507 10475 4.970662 TGCCATGAAAAGTGAGATAAGC 57.029 40.909 0.00 0.00 0.00 3.09
6516 10484 5.702209 CCAAAAATAGCTTGCCATGAAAAGT 59.298 36.000 0.00 0.00 0.00 2.66
6525 10493 0.904649 AGCCCCAAAAATAGCTTGCC 59.095 50.000 0.00 0.00 29.27 4.52
6529 10497 2.827921 CAAGTGAGCCCCAAAAATAGCT 59.172 45.455 0.00 0.00 38.56 3.32
6534 10502 1.408969 GACCAAGTGAGCCCCAAAAA 58.591 50.000 0.00 0.00 0.00 1.94
6550 10518 9.311676 AGCTAATCTTAGTATAGTTTAGGGACC 57.688 37.037 0.00 0.00 32.10 4.46
6586 10554 5.111293 CCTGCACAAAACAAGAAAGTTCAT 58.889 37.500 0.00 0.00 0.00 2.57
6587 10555 4.493547 CCTGCACAAAACAAGAAAGTTCA 58.506 39.130 0.00 0.00 0.00 3.18
6604 10572 4.136796 GTTCTCATAATATGTGGCCTGCA 58.863 43.478 3.32 3.24 0.00 4.41
6636 10604 3.882288 CCCCAACTCAAACCCAAAAATTG 59.118 43.478 0.00 0.00 0.00 2.32
6639 10607 2.502130 GTCCCCAACTCAAACCCAAAAA 59.498 45.455 0.00 0.00 0.00 1.94
6752 10720 7.741554 ATTGTGACTCTAGGGATAGAACTTT 57.258 36.000 0.00 0.00 0.00 2.66
6765 10733 3.039011 GGGGCCTAGAATTGTGACTCTA 58.961 50.000 0.84 0.00 0.00 2.43
6767 10735 1.473434 CGGGGCCTAGAATTGTGACTC 60.473 57.143 0.84 0.00 0.00 3.36
6771 10739 0.394352 AAGCGGGGCCTAGAATTGTG 60.394 55.000 0.84 0.00 0.00 3.33
6787 10755 4.762251 AGAACCTTAACCTCATTCACAAGC 59.238 41.667 0.00 0.00 0.00 4.01
6790 10758 4.651778 CCAGAACCTTAACCTCATTCACA 58.348 43.478 0.00 0.00 0.00 3.58
6804 10772 0.608640 CACCGAACTAGCCAGAACCT 59.391 55.000 0.00 0.00 0.00 3.50
6849 10817 4.637534 CAGATGTGTAGATGGGAAAGTTGG 59.362 45.833 0.00 0.00 0.00 3.77
6855 10823 2.481441 AGGCAGATGTGTAGATGGGAA 58.519 47.619 0.00 0.00 0.00 3.97
6857 10825 3.234353 TCTAGGCAGATGTGTAGATGGG 58.766 50.000 0.00 0.00 0.00 4.00
6863 10831 4.284490 GGATTGGATCTAGGCAGATGTGTA 59.716 45.833 4.51 0.00 41.78 2.90
6872 10840 2.093764 CCGAGATGGATTGGATCTAGGC 60.094 54.545 0.00 0.00 42.00 3.93
6892 10860 5.533528 TCAACCCAAAACTAAGCTAAAGACC 59.466 40.000 3.13 0.00 0.00 3.85
6900 10868 4.911514 TCAACTCAACCCAAAACTAAGC 57.088 40.909 0.00 0.00 0.00 3.09
6901 10869 5.126384 TGGTTCAACTCAACCCAAAACTAAG 59.874 40.000 0.00 0.00 44.82 2.18
6923 10891 1.420138 ACAGTGTGGGTAGGTTTCTGG 59.580 52.381 0.00 0.00 0.00 3.86
6935 10903 2.016318 TGCAGAAGAAACACAGTGTGG 58.984 47.619 26.40 9.41 37.94 4.17
6938 10906 5.008019 ACAGTAATGCAGAAGAAACACAGTG 59.992 40.000 0.00 0.00 0.00 3.66


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

AutoCloner maintained by Alex Coulton.