Multiple sequence alignment - TraesCS7D01G502200

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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 TraesCS7D01G502200 chr7D 100.000 3182 0 0 1 3182 607932269 607935450 0.000000e+00 5877
1 TraesCS7D01G502200 chr7D 98.891 1172 12 1 2011 3182 609952571 609951401 0.000000e+00 2091
2 TraesCS7D01G502200 chr7D 98.635 1172 15 1 2011 3182 609955920 609954750 0.000000e+00 2074
3 TraesCS7D01G502200 chr7D 98.635 1172 15 1 2011 3182 609957595 609956425 0.000000e+00 2074
4 TraesCS7D01G502200 chr7D 98.635 1172 15 1 2011 3182 609959270 609958100 0.000000e+00 2074
5 TraesCS7D01G502200 chr7D 98.635 1172 15 1 2011 3182 609965190 609964020 0.000000e+00 2074
6 TraesCS7D01G502200 chr7D 98.635 1172 15 1 2011 3182 609970214 609969044 0.000000e+00 2074
7 TraesCS7D01G502200 chr7D 98.549 1172 15 2 2011 3182 609954245 609953076 0.000000e+00 2069
8 TraesCS7D01G502200 chr7D 98.379 1172 18 1 2011 3182 609963515 609962345 0.000000e+00 2058
9 TraesCS7D01G502200 chr7D 97.696 651 12 2 3 653 609946220 609945573 0.000000e+00 1116
10 TraesCS7D01G502200 chr7D 79.310 1392 245 35 886 2255 608727418 608728788 0.000000e+00 935
11 TraesCS7D01G502200 chr7D 77.114 1171 210 34 956 2101 609899984 609901121 2.690000e-175 625
12 TraesCS7D01G502200 chr7D 77.969 640 100 32 37 653 608104126 608103505 2.330000e-96 363
13 TraesCS7D01G502200 chr7D 77.294 643 106 29 34 653 610652496 610653121 3.040000e-90 342
14 TraesCS7D01G502200 chr7D 76.452 637 113 26 34 653 609649010 609649626 8.570000e-81 311
15 TraesCS7D01G502200 chr7D 76.382 597 127 11 1018 1604 608422559 608423151 3.080000e-80 309
16 TraesCS7D01G502200 chr7D 76.901 342 56 12 271 595 131620224 131620559 4.220000e-39 172
17 TraesCS7D01G502200 chr7D 85.616 146 20 1 34 179 609466855 609466711 5.500000e-33 152
18 TraesCS7D01G502200 chr7D 85.616 146 20 1 34 179 609497357 609497213 5.500000e-33 152
19 TraesCS7D01G502200 chr7B 90.631 2124 139 21 1000 3089 697402209 697404306 0.000000e+00 2765
20 TraesCS7D01G502200 chr7B 89.385 1366 109 26 1691 3042 685021610 685022953 0.000000e+00 1687
21 TraesCS7D01G502200 chr7B 88.571 875 82 10 835 1696 685013073 685013942 0.000000e+00 1046
22 TraesCS7D01G502200 chr7B 79.065 1433 255 33 795 2190 697422619 697424043 0.000000e+00 942
23 TraesCS7D01G502200 chr7B 79.552 1384 228 31 884 2238 685048463 685049820 0.000000e+00 937
24 TraesCS7D01G502200 chr7B 80.078 1285 224 27 1003 2266 697120256 697118983 0.000000e+00 926
25 TraesCS7D01G502200 chr7B 79.232 1276 233 28 1003 2266 697034027 697035282 0.000000e+00 859
26 TraesCS7D01G502200 chr7B 78.781 1296 230 34 1003 2266 695908495 695909777 0.000000e+00 828
27 TraesCS7D01G502200 chr7B 79.917 961 160 26 1375 2313 694194598 694195547 0.000000e+00 675
28 TraesCS7D01G502200 chr7B 95.819 287 11 1 3 289 697101630 697101345 2.240000e-126 462
29 TraesCS7D01G502200 chr7B 87.332 371 38 4 32 402 695708024 695708385 1.770000e-112 416
30 TraesCS7D01G502200 chr7B 86.721 369 43 4 7 374 697161413 697161050 3.820000e-109 405
31 TraesCS7D01G502200 chr7B 78.987 533 92 15 1690 2208 697161755 697161229 2.350000e-91 346
32 TraesCS7D01G502200 chr7B 81.907 409 64 10 1693 2097 695331154 695331556 1.410000e-88 337
33 TraesCS7D01G502200 chr7B 75.987 633 117 26 37 653 695501225 695500612 8.630000e-76 294
34 TraesCS7D01G502200 chr7B 75.207 605 130 13 1527 2118 694254004 694254601 5.230000e-68 268
35 TraesCS7D01G502200 chr7B 74.118 595 98 28 34 595 92960562 92961133 9.010000e-46 195
36 TraesCS7D01G502200 chr7B 82.500 200 26 6 332 530 697101340 697101149 1.960000e-37 167
37 TraesCS7D01G502200 chr7B 88.235 85 9 1 115 198 693843587 693843503 2.020000e-17 100
38 TraesCS7D01G502200 chrUn 98.720 1172 14 1 2011 3182 373725041 373723871 0.000000e+00 2080
39 TraesCS7D01G502200 chrUn 79.762 168 25 8 35 198 83440087 83439925 2.590000e-21 113
40 TraesCS7D01G502200 chrUn 79.747 158 31 1 35 192 317941127 317941283 2.590000e-21 113
41 TraesCS7D01G502200 chr7A 79.308 1416 253 35 875 2269 700160864 700159468 0.000000e+00 955
42 TraesCS7D01G502200 chr7A 79.070 774 116 30 1499 2233 700941191 700940425 1.030000e-134 490
43 TraesCS7D01G502200 chr7A 78.891 649 108 18 1687 2313 699925415 699926056 2.280000e-111 412
44 TraesCS7D01G502200 chr7A 76.923 637 115 23 33 653 699922943 699923563 1.830000e-87 333


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 TraesCS7D01G502200 chr7D 607932269 607935450 3181 False 5877.0 5877 100.00000 1 3182 1 chr7D.!!$F2 3181
1 TraesCS7D01G502200 chr7D 609951401 609970214 18813 True 2073.5 2091 98.62425 2011 3182 8 chr7D.!!$R5 1171
2 TraesCS7D01G502200 chr7D 609945573 609946220 647 True 1116.0 1116 97.69600 3 653 1 chr7D.!!$R4 650
3 TraesCS7D01G502200 chr7D 608727418 608728788 1370 False 935.0 935 79.31000 886 2255 1 chr7D.!!$F4 1369
4 TraesCS7D01G502200 chr7D 609899984 609901121 1137 False 625.0 625 77.11400 956 2101 1 chr7D.!!$F6 1145
5 TraesCS7D01G502200 chr7D 608103505 608104126 621 True 363.0 363 77.96900 37 653 1 chr7D.!!$R1 616
6 TraesCS7D01G502200 chr7D 610652496 610653121 625 False 342.0 342 77.29400 34 653 1 chr7D.!!$F7 619
7 TraesCS7D01G502200 chr7D 609649010 609649626 616 False 311.0 311 76.45200 34 653 1 chr7D.!!$F5 619
8 TraesCS7D01G502200 chr7D 608422559 608423151 592 False 309.0 309 76.38200 1018 1604 1 chr7D.!!$F3 586
9 TraesCS7D01G502200 chr7B 697402209 697404306 2097 False 2765.0 2765 90.63100 1000 3089 1 chr7B.!!$F11 2089
10 TraesCS7D01G502200 chr7B 685021610 685022953 1343 False 1687.0 1687 89.38500 1691 3042 1 chr7B.!!$F3 1351
11 TraesCS7D01G502200 chr7B 685013073 685013942 869 False 1046.0 1046 88.57100 835 1696 1 chr7B.!!$F2 861
12 TraesCS7D01G502200 chr7B 697422619 697424043 1424 False 942.0 942 79.06500 795 2190 1 chr7B.!!$F12 1395
13 TraesCS7D01G502200 chr7B 685048463 685049820 1357 False 937.0 937 79.55200 884 2238 1 chr7B.!!$F4 1354
14 TraesCS7D01G502200 chr7B 697118983 697120256 1273 True 926.0 926 80.07800 1003 2266 1 chr7B.!!$R3 1263
15 TraesCS7D01G502200 chr7B 697034027 697035282 1255 False 859.0 859 79.23200 1003 2266 1 chr7B.!!$F10 1263
16 TraesCS7D01G502200 chr7B 695908495 695909777 1282 False 828.0 828 78.78100 1003 2266 1 chr7B.!!$F9 1263
17 TraesCS7D01G502200 chr7B 694194598 694195547 949 False 675.0 675 79.91700 1375 2313 1 chr7B.!!$F5 938
18 TraesCS7D01G502200 chr7B 697161050 697161755 705 True 375.5 405 82.85400 7 2208 2 chr7B.!!$R5 2201
19 TraesCS7D01G502200 chr7B 695500612 695501225 613 True 294.0 294 75.98700 37 653 1 chr7B.!!$R2 616
20 TraesCS7D01G502200 chr7B 694254004 694254601 597 False 268.0 268 75.20700 1527 2118 1 chr7B.!!$F6 591
21 TraesCS7D01G502200 chrUn 373723871 373725041 1170 True 2080.0 2080 98.72000 2011 3182 1 chrUn.!!$R2 1171
22 TraesCS7D01G502200 chr7A 700159468 700160864 1396 True 955.0 955 79.30800 875 2269 1 chr7A.!!$R1 1394
23 TraesCS7D01G502200 chr7A 700940425 700941191 766 True 490.0 490 79.07000 1499 2233 1 chr7A.!!$R2 734
24 TraesCS7D01G502200 chr7A 699922943 699926056 3113 False 372.5 412 77.90700 33 2313 2 chr7A.!!$F1 2280

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
548 571 0.037232 GGGAGTGTTTCACCTCGAGG 60.037 60.0 30.11 30.11 42.17 4.63 F
766 793 0.172578 TTCAGATCGTGGCGTAGTGG 59.827 55.0 0.00 0.00 0.00 4.00 F
1132 1356 0.695803 ATCCTTCCCCCGCAGATTCT 60.696 55.0 0.00 0.00 0.00 2.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1678 2820 0.036732 TGGCGCCTCTGACAAGAAAT 59.963 50.000 29.7 0.0 30.03 2.17 R
1829 2974 1.065410 TTCCCCTGCCTCCACAAAGA 61.065 55.000 0.0 0.0 0.00 2.52 R
2386 21250 3.564644 AGGACAACTATGATACGAGGACG 59.435 47.826 0.0 0.0 45.75 4.79 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
104 105 1.483415 GAAACAATGCCAGCCCATGAT 59.517 47.619 0.00 0.00 0.00 2.45
105 106 0.828022 AACAATGCCAGCCCATGATG 59.172 50.000 0.00 0.00 0.00 3.07
106 107 1.069090 CAATGCCAGCCCATGATGC 59.931 57.895 0.00 0.00 0.00 3.91
107 108 1.075525 AATGCCAGCCCATGATGCT 60.076 52.632 4.10 4.10 40.41 3.79
108 109 1.113517 AATGCCAGCCCATGATGCTC 61.114 55.000 6.72 0.00 36.81 4.26
119 120 0.543277 ATGATGCTCGGGACACACAT 59.457 50.000 0.00 0.00 0.00 3.21
156 157 3.057315 CCACCATCATTGTTGTCTTCACC 60.057 47.826 0.00 0.00 0.00 4.02
161 162 1.336440 CATTGTTGTCTTCACCGGCAA 59.664 47.619 0.00 0.00 0.00 4.52
175 176 3.809832 CACCGGCAATATGAAGAGGTAAG 59.190 47.826 0.00 0.00 0.00 2.34
176 177 2.808543 CCGGCAATATGAAGAGGTAAGC 59.191 50.000 0.00 0.00 0.00 3.09
179 180 4.212214 CGGCAATATGAAGAGGTAAGCTTC 59.788 45.833 0.00 0.00 41.57 3.86
184 185 7.663493 GCAATATGAAGAGGTAAGCTTCCTATT 59.337 37.037 18.64 18.64 40.55 1.73
185 186 8.997323 CAATATGAAGAGGTAAGCTTCCTATTG 58.003 37.037 21.70 17.74 44.56 1.90
186 187 4.770795 TGAAGAGGTAAGCTTCCTATTGC 58.229 43.478 21.70 15.57 40.73 3.56
204 225 8.217111 TCCTATTGCATCCTTATTATCACACAA 58.783 33.333 0.00 0.00 0.00 3.33
225 246 3.674997 ACTTGTGTAATGGTTGATCGCT 58.325 40.909 0.00 0.00 0.00 4.93
226 247 3.684788 ACTTGTGTAATGGTTGATCGCTC 59.315 43.478 0.00 0.00 0.00 5.03
227 248 3.326836 TGTGTAATGGTTGATCGCTCA 57.673 42.857 0.00 0.00 0.00 4.26
228 249 3.872696 TGTGTAATGGTTGATCGCTCAT 58.127 40.909 0.00 0.00 0.00 2.90
229 250 4.260985 TGTGTAATGGTTGATCGCTCATT 58.739 39.130 10.56 10.56 34.65 2.57
230 251 4.094739 TGTGTAATGGTTGATCGCTCATTG 59.905 41.667 13.81 0.00 32.81 2.82
231 252 4.094887 GTGTAATGGTTGATCGCTCATTGT 59.905 41.667 13.81 0.00 32.81 2.71
232 253 4.699735 TGTAATGGTTGATCGCTCATTGTT 59.300 37.500 13.81 0.00 32.81 2.83
233 254 5.877564 TGTAATGGTTGATCGCTCATTGTTA 59.122 36.000 13.81 2.61 32.81 2.41
234 255 4.882671 ATGGTTGATCGCTCATTGTTAC 57.117 40.909 0.00 0.00 0.00 2.50
235 256 3.669536 TGGTTGATCGCTCATTGTTACA 58.330 40.909 0.00 0.00 0.00 2.41
236 257 4.260985 TGGTTGATCGCTCATTGTTACAT 58.739 39.130 0.00 0.00 0.00 2.29
259 280 7.981225 ACATTTGATAATTCTTGGTTACATGGC 59.019 33.333 0.00 0.00 0.00 4.40
261 282 6.698008 TGATAATTCTTGGTTACATGGCTG 57.302 37.500 0.00 0.00 0.00 4.85
262 283 5.593909 TGATAATTCTTGGTTACATGGCTGG 59.406 40.000 0.00 0.00 0.00 4.85
267 288 1.663911 TGGTTACATGGCTGGGTAGT 58.336 50.000 0.00 0.00 0.00 2.73
268 289 1.557832 TGGTTACATGGCTGGGTAGTC 59.442 52.381 0.00 0.00 0.00 2.59
269 290 1.838077 GGTTACATGGCTGGGTAGTCT 59.162 52.381 0.00 0.00 0.00 3.24
281 302 5.475564 GGCTGGGTAGTCTTGTTTATTTTCA 59.524 40.000 0.00 0.00 0.00 2.69
285 306 7.881142 TGGGTAGTCTTGTTTATTTTCATGTG 58.119 34.615 0.00 0.00 0.00 3.21
292 313 7.434897 GTCTTGTTTATTTTCATGTGCTTGTGA 59.565 33.333 0.00 0.00 0.00 3.58
297 318 8.482429 GTTTATTTTCATGTGCTTGTGAGAAAG 58.518 33.333 0.00 0.00 0.00 2.62
318 339 1.838112 CAAGCCAGCTTGGGAACATA 58.162 50.000 21.98 0.00 46.88 2.29
324 345 3.055891 GCCAGCTTGGGAACATAATTGTT 60.056 43.478 0.00 0.00 42.63 2.83
360 382 6.586344 TGTTTGTTCCAATTGCCATTTAAGA 58.414 32.000 0.00 0.00 0.00 2.10
363 385 6.662865 TGTTCCAATTGCCATTTAAGAGAA 57.337 33.333 0.00 0.00 0.00 2.87
376 398 7.415653 GCCATTTAAGAGAATGAGGTTGGTAAG 60.416 40.741 0.00 0.00 38.93 2.34
417 439 4.993584 GCACACTATGACTAGCTTATGCAT 59.006 41.667 3.79 3.79 42.74 3.96
422 444 6.585702 CACTATGACTAGCTTATGCATGAGTC 59.414 42.308 18.68 16.59 41.69 3.36
432 454 3.657398 ATGCATGAGTCCTGATGGAAA 57.343 42.857 0.00 0.00 45.18 3.13
434 456 2.040145 TGCATGAGTCCTGATGGAAACA 59.960 45.455 0.00 0.00 45.18 2.83
452 475 8.177119 TGGAAACATTAAAAACAGCTAGTCAT 57.823 30.769 0.00 0.00 33.40 3.06
453 476 8.637986 TGGAAACATTAAAAACAGCTAGTCATT 58.362 29.630 0.00 0.00 33.40 2.57
454 477 8.915654 GGAAACATTAAAAACAGCTAGTCATTG 58.084 33.333 0.00 0.00 0.00 2.82
466 489 9.988350 AACAGCTAGTCATTGTAATTATTTTCG 57.012 29.630 0.00 0.00 0.00 3.46
469 492 9.601217 AGCTAGTCATTGTAATTATTTTCGAGT 57.399 29.630 0.00 0.00 0.00 4.18
489 512 8.051901 TCGAGTAGTAGTTTTGATGATCAAGA 57.948 34.615 8.01 0.75 37.70 3.02
504 527 9.823647 TGATGATCAAGATAAAGTAGAAGGAAC 57.176 33.333 0.00 0.00 0.00 3.62
506 529 9.829507 ATGATCAAGATAAAGTAGAAGGAACAG 57.170 33.333 0.00 0.00 0.00 3.16
509 532 9.660180 ATCAAGATAAAGTAGAAGGAACAGAAC 57.340 33.333 0.00 0.00 0.00 3.01
511 534 9.495572 CAAGATAAAGTAGAAGGAACAGAACTT 57.504 33.333 0.00 0.00 0.00 2.66
519 542 9.268282 AGTAGAAGGAACAGAACTTTATATCCA 57.732 33.333 0.00 0.00 0.00 3.41
525 548 9.668497 AGGAACAGAACTTTATATCCAGTTTAC 57.332 33.333 1.91 0.00 33.22 2.01
526 549 8.890718 GGAACAGAACTTTATATCCAGTTTACC 58.109 37.037 1.91 0.00 33.22 2.85
529 552 9.449719 ACAGAACTTTATATCCAGTTTACCTTG 57.550 33.333 1.91 0.89 33.22 3.61
533 556 7.574607 ACTTTATATCCAGTTTACCTTGGGAG 58.425 38.462 0.00 0.00 35.13 4.30
544 567 1.143073 ACCTTGGGAGTGTTTCACCTC 59.857 52.381 0.00 0.00 34.49 3.85
548 571 0.037232 GGGAGTGTTTCACCTCGAGG 60.037 60.000 30.11 30.11 42.17 4.63
566 593 6.072508 CCTCGAGGAAATTCATTCAAGTCAAA 60.073 38.462 28.21 0.00 39.98 2.69
567 594 6.902341 TCGAGGAAATTCATTCAAGTCAAAG 58.098 36.000 0.00 0.00 39.98 2.77
569 596 7.228507 TCGAGGAAATTCATTCAAGTCAAAGAA 59.771 33.333 0.00 0.00 39.98 2.52
571 598 9.189723 GAGGAAATTCATTCAAGTCAAAGAAAG 57.810 33.333 0.00 0.00 39.98 2.62
573 600 7.095481 GGAAATTCATTCAAGTCAAAGAAAGCC 60.095 37.037 0.00 0.00 39.98 4.35
575 602 3.253188 TCATTCAAGTCAAAGAAAGCCCG 59.747 43.478 0.00 0.00 0.00 6.13
577 604 2.650322 TCAAGTCAAAGAAAGCCCGTT 58.350 42.857 0.00 0.00 0.00 4.44
578 605 3.020984 TCAAGTCAAAGAAAGCCCGTTT 58.979 40.909 0.00 0.00 0.00 3.60
586 613 2.927028 AGAAAGCCCGTTTTGTACACT 58.073 42.857 0.00 0.00 0.00 3.55
587 614 3.284617 AGAAAGCCCGTTTTGTACACTT 58.715 40.909 0.00 0.00 0.00 3.16
615 642 7.141758 TCTTTTGATAGATGTAAGGAGGCAT 57.858 36.000 0.00 0.00 0.00 4.40
619 646 9.693739 TTTTGATAGATGTAAGGAGGCATAAAA 57.306 29.630 0.00 0.00 0.00 1.52
623 650 8.910351 ATAGATGTAAGGAGGCATAAAAGTTC 57.090 34.615 0.00 0.00 0.00 3.01
625 652 7.051000 AGATGTAAGGAGGCATAAAAGTTCTC 58.949 38.462 0.00 0.00 0.00 2.87
667 694 9.831737 GATGTATAATTTGAAATTCCGATCAGG 57.168 33.333 6.40 0.00 42.97 3.86
668 695 8.746052 TGTATAATTTGAAATTCCGATCAGGT 57.254 30.769 6.40 0.00 41.99 4.00
670 697 3.848272 TTTGAAATTCCGATCAGGTGC 57.152 42.857 0.00 0.00 41.99 5.01
671 698 1.368641 TGAAATTCCGATCAGGTGCG 58.631 50.000 0.00 0.00 41.99 5.34
677 704 1.876714 CCGATCAGGTGCGGTTACG 60.877 63.158 0.00 0.00 42.49 3.18
678 705 1.138036 CGATCAGGTGCGGTTACGA 59.862 57.895 0.00 0.00 44.60 3.43
679 706 0.248907 CGATCAGGTGCGGTTACGAT 60.249 55.000 0.00 0.00 44.60 3.73
680 707 1.801395 CGATCAGGTGCGGTTACGATT 60.801 52.381 0.00 0.00 44.60 3.34
681 708 2.542205 CGATCAGGTGCGGTTACGATTA 60.542 50.000 0.00 0.00 44.60 1.75
682 709 2.572191 TCAGGTGCGGTTACGATTAG 57.428 50.000 0.00 0.00 44.60 1.73
684 711 2.691526 TCAGGTGCGGTTACGATTAGAT 59.308 45.455 0.00 0.00 44.60 1.98
685 712 2.794910 CAGGTGCGGTTACGATTAGATG 59.205 50.000 0.00 0.00 44.60 2.90
687 714 1.525619 GTGCGGTTACGATTAGATGGC 59.474 52.381 0.00 0.00 44.60 4.40
688 715 1.137282 TGCGGTTACGATTAGATGGCA 59.863 47.619 0.00 0.00 44.60 4.92
689 716 1.792949 GCGGTTACGATTAGATGGCAG 59.207 52.381 0.00 0.00 44.60 4.85
690 717 2.802057 GCGGTTACGATTAGATGGCAGT 60.802 50.000 0.00 0.00 44.60 4.40
691 718 3.050619 CGGTTACGATTAGATGGCAGTC 58.949 50.000 0.00 0.00 44.60 3.51
693 720 3.243301 GGTTACGATTAGATGGCAGTCGA 60.243 47.826 13.29 0.00 36.28 4.20
694 721 2.783828 ACGATTAGATGGCAGTCGAG 57.216 50.000 13.29 0.00 36.28 4.04
695 722 2.025155 ACGATTAGATGGCAGTCGAGT 58.975 47.619 13.29 0.00 36.28 4.18
697 724 3.046390 CGATTAGATGGCAGTCGAGTTC 58.954 50.000 0.00 0.00 34.46 3.01
698 725 2.961526 TTAGATGGCAGTCGAGTTCC 57.038 50.000 1.48 1.48 0.00 3.62
699 726 0.738975 TAGATGGCAGTCGAGTTCCG 59.261 55.000 4.42 0.00 40.25 4.30
700 727 0.965866 AGATGGCAGTCGAGTTCCGA 60.966 55.000 4.42 0.00 46.35 4.55
707 734 3.744719 TCGAGTTCCGACCGCAGG 61.745 66.667 0.00 0.00 46.95 4.85
719 746 2.494445 CGCAGGTATCCGACAGCA 59.506 61.111 0.00 0.00 32.52 4.41
720 747 1.153647 CGCAGGTATCCGACAGCAA 60.154 57.895 0.00 0.00 32.52 3.91
721 748 0.739462 CGCAGGTATCCGACAGCAAA 60.739 55.000 0.00 0.00 32.52 3.68
723 750 1.130561 GCAGGTATCCGACAGCAAAAC 59.869 52.381 0.00 0.00 32.52 2.43
724 751 1.393539 CAGGTATCCGACAGCAAAACG 59.606 52.381 0.00 0.00 0.00 3.60
725 752 1.274167 AGGTATCCGACAGCAAAACGA 59.726 47.619 0.00 0.00 0.00 3.85
728 755 3.866910 GGTATCCGACAGCAAAACGATAA 59.133 43.478 0.00 0.00 0.00 1.75
729 756 4.260091 GGTATCCGACAGCAAAACGATAAC 60.260 45.833 0.00 0.00 0.00 1.89
730 757 1.722464 TCCGACAGCAAAACGATAACG 59.278 47.619 0.00 0.00 45.75 3.18
745 772 5.817616 CGATAACGTTTAGATGCGGTTAT 57.182 39.130 5.91 0.00 34.56 1.89
746 773 5.829681 CGATAACGTTTAGATGCGGTTATC 58.170 41.667 5.91 10.59 33.39 1.75
747 774 5.628193 CGATAACGTTTAGATGCGGTTATCT 59.372 40.000 5.91 0.00 36.75 1.98
748 775 6.143438 CGATAACGTTTAGATGCGGTTATCTT 59.857 38.462 5.91 0.00 35.59 2.40
749 776 5.713822 AACGTTTAGATGCGGTTATCTTC 57.286 39.130 0.00 0.00 38.35 2.87
750 777 4.751060 ACGTTTAGATGCGGTTATCTTCA 58.249 39.130 0.00 0.00 38.35 3.02
752 779 5.041287 CGTTTAGATGCGGTTATCTTCAGA 58.959 41.667 0.00 0.00 38.35 3.27
755 782 3.906998 AGATGCGGTTATCTTCAGATCG 58.093 45.455 0.00 0.00 33.74 3.69
756 783 3.319405 AGATGCGGTTATCTTCAGATCGT 59.681 43.478 0.00 0.00 33.74 3.73
757 784 2.809446 TGCGGTTATCTTCAGATCGTG 58.191 47.619 0.00 0.00 36.05 4.35
758 785 2.128035 GCGGTTATCTTCAGATCGTGG 58.872 52.381 0.00 0.00 36.05 4.94
759 786 2.128035 CGGTTATCTTCAGATCGTGGC 58.872 52.381 0.00 0.00 36.05 5.01
760 787 2.128035 GGTTATCTTCAGATCGTGGCG 58.872 52.381 0.00 0.00 36.05 5.69
761 788 2.481449 GGTTATCTTCAGATCGTGGCGT 60.481 50.000 0.00 0.00 36.05 5.68
762 789 3.243301 GGTTATCTTCAGATCGTGGCGTA 60.243 47.826 0.00 0.00 36.05 4.42
763 790 2.783828 ATCTTCAGATCGTGGCGTAG 57.216 50.000 0.00 0.00 0.00 3.51
764 791 1.460504 TCTTCAGATCGTGGCGTAGT 58.539 50.000 0.00 0.00 0.00 2.73
765 792 1.132453 TCTTCAGATCGTGGCGTAGTG 59.868 52.381 0.00 0.00 0.00 2.74
766 793 0.172578 TTCAGATCGTGGCGTAGTGG 59.827 55.000 0.00 0.00 0.00 4.00
767 794 1.878522 CAGATCGTGGCGTAGTGGC 60.879 63.158 0.00 0.00 45.12 5.01
769 796 1.878522 GATCGTGGCGTAGTGGCTG 60.879 63.158 0.00 0.00 45.14 4.85
770 797 2.279502 GATCGTGGCGTAGTGGCTGA 62.280 60.000 0.00 0.00 45.14 4.26
771 798 2.284798 ATCGTGGCGTAGTGGCTGAG 62.285 60.000 0.00 0.00 45.14 3.35
772 799 2.815647 GTGGCGTAGTGGCTGAGC 60.816 66.667 0.00 0.00 45.14 4.26
773 800 3.310307 TGGCGTAGTGGCTGAGCA 61.310 61.111 6.82 0.00 45.14 4.26
774 801 2.510238 GGCGTAGTGGCTGAGCAG 60.510 66.667 6.82 0.00 40.72 4.24
775 802 2.510238 GCGTAGTGGCTGAGCAGG 60.510 66.667 6.82 0.00 0.00 4.85
776 803 2.185350 CGTAGTGGCTGAGCAGGG 59.815 66.667 6.82 0.00 0.00 4.45
777 804 2.124942 GTAGTGGCTGAGCAGGGC 60.125 66.667 6.82 0.00 0.00 5.19
782 809 4.486503 GGCTGAGCAGGGCCTGAG 62.487 72.222 37.07 24.97 44.48 3.35
796 823 1.681793 GCCTGAGCCACTACGATTAGA 59.318 52.381 0.00 0.00 0.00 2.10
808 835 3.724508 ACGATTAGATGGCAGTCTGAG 57.275 47.619 3.32 2.52 0.00 3.35
810 837 2.402305 GATTAGATGGCAGTCTGAGCG 58.598 52.381 3.32 0.00 0.00 5.03
834 861 2.711542 CCTGAAAACTGGGCTCGTTAT 58.288 47.619 0.00 0.00 0.00 1.89
839 866 3.706600 AAACTGGGCTCGTTATTACCA 57.293 42.857 0.00 0.00 0.00 3.25
871 898 2.659016 CAGCTTCGAGTGCCCTCA 59.341 61.111 8.54 0.00 37.59 3.86
882 1090 4.767255 GCCCTCACTCACAGCCGG 62.767 72.222 0.00 0.00 0.00 6.13
910 1120 1.486310 TCCCAATTCCATCTCGTCCAG 59.514 52.381 0.00 0.00 0.00 3.86
913 1123 1.210478 CAATTCCATCTCGTCCAGGGT 59.790 52.381 0.00 0.00 0.00 4.34
997 1213 2.412870 GACCCGCAAAAAGAAAATGGG 58.587 47.619 0.00 0.00 41.06 4.00
998 1214 2.036604 GACCCGCAAAAAGAAAATGGGA 59.963 45.455 0.61 0.00 38.56 4.37
1001 1225 3.055891 CCCGCAAAAAGAAAATGGGAGAT 60.056 43.478 0.00 0.00 37.35 2.75
1025 1249 4.753662 CCCCGACCACCTCCTCGA 62.754 72.222 0.00 0.00 31.24 4.04
1026 1250 2.678934 CCCGACCACCTCCTCGAA 60.679 66.667 0.00 0.00 31.24 3.71
1027 1251 2.572284 CCGACCACCTCCTCGAAC 59.428 66.667 0.00 0.00 31.24 3.95
1106 1330 4.514577 CTTCCGCCGACTCGCCAT 62.515 66.667 0.00 0.00 0.00 4.40
1113 1337 2.180769 CGACTCGCCATTGACGGA 59.819 61.111 0.00 0.00 0.00 4.69
1121 1345 0.819666 GCCATTGACGGATCCTTCCC 60.820 60.000 15.24 0.00 39.01 3.97
1132 1356 0.695803 ATCCTTCCCCCGCAGATTCT 60.696 55.000 0.00 0.00 0.00 2.40
1181 1408 2.203252 CCTCGATCCGGACGGGTA 60.203 66.667 20.08 6.05 37.00 3.69
1266 1839 1.687493 CTCCTTCGCCTTCCTCCCT 60.687 63.158 0.00 0.00 0.00 4.20
1486 2609 2.436109 GGTGCAAGCCCTTCCTCA 59.564 61.111 0.00 0.00 0.00 3.86
1606 2744 1.523154 GAGCACCGGACAATGGCAAA 61.523 55.000 9.46 0.00 0.00 3.68
1610 2748 2.091541 CACCGGACAATGGCAAACTAT 58.908 47.619 9.46 0.00 0.00 2.12
1644 2786 2.905415 TGAGTGATTTGGGCCTTGAT 57.095 45.000 4.53 0.00 0.00 2.57
1678 2820 2.359797 CCATGTCACATGGCCCCA 59.640 61.111 24.12 0.00 31.75 4.96
1814 2956 2.696864 TCCCACCTGGAGATTGGAC 58.303 57.895 0.00 0.00 38.61 4.02
1829 2974 1.145571 TGGACTGGGCAAGGTTTAGT 58.854 50.000 0.00 0.00 0.00 2.24
1954 3105 1.757306 CAGTGGCAGGTGGAGAAGT 59.243 57.895 0.00 0.00 0.00 3.01
2190 21023 4.776349 TGCCGACAATATGAAGTGGTAAT 58.224 39.130 0.00 0.00 0.00 1.89
2342 21206 4.940463 GAATGCTTATCATTGCACCACAT 58.060 39.130 0.00 0.00 44.95 3.21
2386 21250 2.564947 AGTCAATCTCCACCACTCTGAC 59.435 50.000 0.00 0.00 33.51 3.51
2947 21994 7.944729 ATTTTCAGGTGATTGTGTATTAGCT 57.055 32.000 0.00 0.00 31.42 3.32
3103 22150 9.503427 CCTTGTTTTCTAGTTAGAAGTTTGTTG 57.497 33.333 2.21 0.00 42.66 3.33
3112 22159 7.948278 AGTTAGAAGTTTGTTGTACTGCTAG 57.052 36.000 0.00 0.00 35.64 3.42
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.960957 CTAGAGATGGGCGTGGCACG 62.961 65.000 33.96 33.96 45.88 5.34
25 26 9.403110 GTCCATTGAGAAATATTCATATTGTGC 57.597 33.333 0.00 0.00 33.51 4.57
104 105 4.262292 GGTATATAATGTGTGTCCCGAGCA 60.262 45.833 0.00 0.00 0.00 4.26
105 106 4.243270 GGTATATAATGTGTGTCCCGAGC 58.757 47.826 0.00 0.00 0.00 5.03
106 107 5.462530 TGGTATATAATGTGTGTCCCGAG 57.537 43.478 0.00 0.00 0.00 4.63
107 108 5.364446 AGTTGGTATATAATGTGTGTCCCGA 59.636 40.000 0.00 0.00 0.00 5.14
108 109 5.607477 AGTTGGTATATAATGTGTGTCCCG 58.393 41.667 0.00 0.00 0.00 5.14
119 120 6.833346 TGATGGTGGGAAGTTGGTATATAA 57.167 37.500 0.00 0.00 0.00 0.98
156 157 3.733337 AGCTTACCTCTTCATATTGCCG 58.267 45.455 0.00 0.00 0.00 5.69
161 162 7.164803 GCAATAGGAAGCTTACCTCTTCATAT 58.835 38.462 17.42 4.66 44.46 1.78
169 170 3.718956 AGGATGCAATAGGAAGCTTACCT 59.281 43.478 17.83 17.83 41.05 3.08
175 176 7.391554 TGTGATAATAAGGATGCAATAGGAAGC 59.608 37.037 0.00 0.00 0.00 3.86
176 177 8.725148 GTGTGATAATAAGGATGCAATAGGAAG 58.275 37.037 0.00 0.00 0.00 3.46
179 180 7.984422 TGTGTGATAATAAGGATGCAATAGG 57.016 36.000 0.00 0.00 0.00 2.57
184 185 6.658816 ACAAGTTGTGTGATAATAAGGATGCA 59.341 34.615 7.96 0.00 39.72 3.96
185 186 7.088589 ACAAGTTGTGTGATAATAAGGATGC 57.911 36.000 7.96 0.00 39.72 3.91
204 225 3.674997 AGCGATCAACCATTACACAAGT 58.325 40.909 0.00 0.00 0.00 3.16
210 231 4.882671 ACAATGAGCGATCAACCATTAC 57.117 40.909 7.76 0.00 0.00 1.89
216 237 6.314018 TCAAATGTAACAATGAGCGATCAAC 58.686 36.000 7.76 0.73 0.00 3.18
222 243 9.507280 AAGAATTATCAAATGTAACAATGAGCG 57.493 29.630 0.00 0.00 0.00 5.03
233 254 7.981225 GCCATGTAACCAAGAATTATCAAATGT 59.019 33.333 0.00 0.00 0.00 2.71
234 255 8.199449 AGCCATGTAACCAAGAATTATCAAATG 58.801 33.333 0.00 0.00 0.00 2.32
235 256 8.199449 CAGCCATGTAACCAAGAATTATCAAAT 58.801 33.333 0.00 0.00 0.00 2.32
236 257 7.363705 CCAGCCATGTAACCAAGAATTATCAAA 60.364 37.037 0.00 0.00 0.00 2.69
250 271 3.270877 CAAGACTACCCAGCCATGTAAC 58.729 50.000 0.00 0.00 0.00 2.50
258 279 6.569179 TGAAAATAAACAAGACTACCCAGC 57.431 37.500 0.00 0.00 0.00 4.85
259 280 8.023128 CACATGAAAATAAACAAGACTACCCAG 58.977 37.037 0.00 0.00 0.00 4.45
261 282 6.806739 GCACATGAAAATAAACAAGACTACCC 59.193 38.462 0.00 0.00 0.00 3.69
262 283 7.593825 AGCACATGAAAATAAACAAGACTACC 58.406 34.615 0.00 0.00 0.00 3.18
267 288 7.487484 TCACAAGCACATGAAAATAAACAAGA 58.513 30.769 0.00 0.00 0.00 3.02
268 289 7.648908 TCTCACAAGCACATGAAAATAAACAAG 59.351 33.333 0.00 0.00 0.00 3.16
269 290 7.487484 TCTCACAAGCACATGAAAATAAACAA 58.513 30.769 0.00 0.00 0.00 2.83
292 313 2.348665 CAAGCTGGCTTGGCTTTCT 58.651 52.632 23.00 0.00 46.24 2.52
299 320 7.304933 ACAATTATGTTCCCAAGCTGGCTTG 62.305 44.000 23.56 23.56 43.89 4.01
324 345 4.887748 TGGAACAAACAAGACAGCAAAAA 58.112 34.783 0.00 0.00 31.92 1.94
341 362 7.322664 TCATTCTCTTAAATGGCAATTGGAAC 58.677 34.615 7.72 0.00 37.27 3.62
383 405 7.386299 GCTAGTCATAGTGTGCAAGCTATATTT 59.614 37.037 9.97 3.60 0.00 1.40
384 406 6.870965 GCTAGTCATAGTGTGCAAGCTATATT 59.129 38.462 9.97 3.86 0.00 1.28
387 409 4.343526 AGCTAGTCATAGTGTGCAAGCTAT 59.656 41.667 0.52 3.38 36.08 2.97
388 410 3.701542 AGCTAGTCATAGTGTGCAAGCTA 59.298 43.478 0.52 1.10 36.08 3.32
389 411 2.499289 AGCTAGTCATAGTGTGCAAGCT 59.501 45.455 0.00 0.00 34.30 3.74
390 412 2.898705 AGCTAGTCATAGTGTGCAAGC 58.101 47.619 0.00 0.00 0.00 4.01
391 413 5.050499 GCATAAGCTAGTCATAGTGTGCAAG 60.050 44.000 0.00 0.00 37.91 4.01
392 414 4.811024 GCATAAGCTAGTCATAGTGTGCAA 59.189 41.667 0.00 0.00 37.91 4.08
399 421 6.071447 AGGACTCATGCATAAGCTAGTCATAG 60.071 42.308 18.79 0.00 42.36 2.23
405 427 4.597404 TCAGGACTCATGCATAAGCTAG 57.403 45.455 0.00 0.00 42.74 3.42
417 439 7.286546 TGTTTTTAATGTTTCCATCAGGACTCA 59.713 33.333 0.00 0.00 45.73 3.41
422 444 6.458210 AGCTGTTTTTAATGTTTCCATCAGG 58.542 36.000 0.00 0.00 0.00 3.86
442 465 9.855361 CTCGAAAATAATTACAATGACTAGCTG 57.145 33.333 0.00 0.00 0.00 4.24
465 488 8.864069 ATCTTGATCATCAAAACTACTACTCG 57.136 34.615 0.75 0.00 35.73 4.18
483 506 9.660180 GTTCTGTTCCTTCTACTTTATCTTGAT 57.340 33.333 0.00 0.00 0.00 2.57
495 518 9.268282 ACTGGATATAAAGTTCTGTTCCTTCTA 57.732 33.333 0.00 0.00 0.00 2.10
503 526 9.449719 CAAGGTAAACTGGATATAAAGTTCTGT 57.550 33.333 3.62 0.00 35.60 3.41
504 527 8.893727 CCAAGGTAAACTGGATATAAAGTTCTG 58.106 37.037 3.62 0.00 35.60 3.02
506 529 8.050930 TCCCAAGGTAAACTGGATATAAAGTTC 58.949 37.037 3.62 0.00 35.60 3.01
509 532 7.499232 CACTCCCAAGGTAAACTGGATATAAAG 59.501 40.741 0.00 0.00 0.00 1.85
511 534 6.445786 ACACTCCCAAGGTAAACTGGATATAA 59.554 38.462 0.00 0.00 0.00 0.98
514 537 4.172807 ACACTCCCAAGGTAAACTGGATA 58.827 43.478 0.00 0.00 0.00 2.59
516 539 2.414612 ACACTCCCAAGGTAAACTGGA 58.585 47.619 0.00 0.00 0.00 3.86
517 540 2.951229 ACACTCCCAAGGTAAACTGG 57.049 50.000 0.00 0.00 0.00 4.00
518 541 4.036380 GTGAAACACTCCCAAGGTAAACTG 59.964 45.833 0.00 0.00 36.32 3.16
519 542 4.204799 GTGAAACACTCCCAAGGTAAACT 58.795 43.478 0.00 0.00 36.32 2.66
525 548 1.878102 CGAGGTGAAACACTCCCAAGG 60.878 57.143 0.00 0.00 39.98 3.61
526 549 1.070134 TCGAGGTGAAACACTCCCAAG 59.930 52.381 0.00 0.00 39.98 3.61
529 552 0.037232 CCTCGAGGTGAAACACTCCC 60.037 60.000 24.04 0.00 39.98 4.30
533 556 3.813166 TGAATTTCCTCGAGGTGAAACAC 59.187 43.478 30.17 19.34 39.98 3.32
544 567 6.902341 TCTTTGACTTGAATGAATTTCCTCG 58.098 36.000 0.00 0.00 33.04 4.63
548 571 7.095481 GGGCTTTCTTTGACTTGAATGAATTTC 60.095 37.037 0.00 0.00 34.72 2.17
566 593 2.927028 AGTGTACAAAACGGGCTTTCT 58.073 42.857 0.00 0.00 0.00 2.52
567 594 3.703286 AAGTGTACAAAACGGGCTTTC 57.297 42.857 0.00 0.00 0.00 2.62
569 596 4.459390 AAAAAGTGTACAAAACGGGCTT 57.541 36.364 0.00 0.00 0.00 4.35
587 614 8.739972 GCCTCCTTACATCTATCAAAAGAAAAA 58.260 33.333 0.00 0.00 0.00 1.94
596 623 8.034313 ACTTTTATGCCTCCTTACATCTATCA 57.966 34.615 0.00 0.00 0.00 2.15
602 629 6.963322 AGAGAACTTTTATGCCTCCTTACAT 58.037 36.000 0.00 0.00 0.00 2.29
604 631 7.689446 AAAGAGAACTTTTATGCCTCCTTAC 57.311 36.000 0.00 0.00 42.79 2.34
641 668 9.831737 CCTGATCGGAATTTCAAATTATACATC 57.168 33.333 2.08 0.00 33.16 3.06
644 671 7.591426 GCACCTGATCGGAATTTCAAATTATAC 59.409 37.037 2.08 0.00 36.31 1.47
660 687 0.248907 ATCGTAACCGCACCTGATCG 60.249 55.000 0.00 0.00 0.00 3.69
664 691 2.572191 TCTAATCGTAACCGCACCTG 57.428 50.000 0.00 0.00 0.00 4.00
665 692 2.223971 CCATCTAATCGTAACCGCACCT 60.224 50.000 0.00 0.00 0.00 4.00
666 693 2.132762 CCATCTAATCGTAACCGCACC 58.867 52.381 0.00 0.00 0.00 5.01
667 694 1.525619 GCCATCTAATCGTAACCGCAC 59.474 52.381 0.00 0.00 0.00 5.34
668 695 1.137282 TGCCATCTAATCGTAACCGCA 59.863 47.619 0.00 0.00 0.00 5.69
670 697 3.050619 GACTGCCATCTAATCGTAACCG 58.949 50.000 0.00 0.00 0.00 4.44
671 698 3.050619 CGACTGCCATCTAATCGTAACC 58.949 50.000 0.00 0.00 0.00 2.85
672 699 3.961182 TCGACTGCCATCTAATCGTAAC 58.039 45.455 0.00 0.00 34.47 2.50
673 700 3.630769 ACTCGACTGCCATCTAATCGTAA 59.369 43.478 0.00 0.00 34.47 3.18
674 701 3.211865 ACTCGACTGCCATCTAATCGTA 58.788 45.455 0.00 0.00 34.47 3.43
675 702 2.025155 ACTCGACTGCCATCTAATCGT 58.975 47.619 0.00 0.00 34.47 3.73
677 704 3.385577 GGAACTCGACTGCCATCTAATC 58.614 50.000 0.00 0.00 0.00 1.75
678 705 2.223829 CGGAACTCGACTGCCATCTAAT 60.224 50.000 0.00 0.00 42.43 1.73
679 706 1.134367 CGGAACTCGACTGCCATCTAA 59.866 52.381 0.00 0.00 42.43 2.10
680 707 0.738975 CGGAACTCGACTGCCATCTA 59.261 55.000 0.00 0.00 42.43 1.98
681 708 0.965866 TCGGAACTCGACTGCCATCT 60.966 55.000 0.00 0.00 43.74 2.90
682 709 1.511305 TCGGAACTCGACTGCCATC 59.489 57.895 0.00 0.00 43.74 3.51
690 717 3.744719 CCTGCGGTCGGAACTCGA 61.745 66.667 0.00 0.00 46.77 4.04
691 718 2.001361 ATACCTGCGGTCGGAACTCG 62.001 60.000 3.45 0.00 37.09 4.18
693 720 1.673808 GGATACCTGCGGTCGGAACT 61.674 60.000 3.45 0.00 37.09 3.01
694 721 1.227176 GGATACCTGCGGTCGGAAC 60.227 63.158 3.45 0.00 37.09 3.62
695 722 2.777972 CGGATACCTGCGGTCGGAA 61.778 63.158 3.45 0.00 37.09 4.30
697 724 3.214123 TCGGATACCTGCGGTCGG 61.214 66.667 3.45 0.00 37.09 4.79
698 725 2.025727 GTCGGATACCTGCGGTCG 59.974 66.667 3.45 2.88 37.09 4.79
699 726 1.065928 CTGTCGGATACCTGCGGTC 59.934 63.158 3.45 0.00 37.09 4.79
700 727 3.077519 GCTGTCGGATACCTGCGGT 62.078 63.158 5.58 5.58 40.16 5.68
701 728 2.279517 GCTGTCGGATACCTGCGG 60.280 66.667 0.00 0.00 36.78 5.69
702 729 0.739462 TTTGCTGTCGGATACCTGCG 60.739 55.000 0.00 0.00 37.59 5.18
704 731 1.393539 CGTTTTGCTGTCGGATACCTG 59.606 52.381 0.00 0.00 0.00 4.00
705 732 1.274167 TCGTTTTGCTGTCGGATACCT 59.726 47.619 0.00 0.00 0.00 3.08
706 733 1.717194 TCGTTTTGCTGTCGGATACC 58.283 50.000 0.00 0.00 0.00 2.73
707 734 4.547587 CGTTATCGTTTTGCTGTCGGATAC 60.548 45.833 0.00 0.00 0.00 2.24
709 736 2.347452 CGTTATCGTTTTGCTGTCGGAT 59.653 45.455 0.00 0.00 0.00 4.18
710 737 1.722464 CGTTATCGTTTTGCTGTCGGA 59.278 47.619 0.00 0.00 0.00 4.55
711 738 2.139336 CGTTATCGTTTTGCTGTCGG 57.861 50.000 0.00 0.00 0.00 4.79
723 750 5.628193 AGATAACCGCATCTAAACGTTATCG 59.372 40.000 0.00 0.00 37.36 2.92
724 751 7.168637 TGAAGATAACCGCATCTAAACGTTATC 59.831 37.037 0.00 9.25 34.08 1.75
725 752 6.982141 TGAAGATAACCGCATCTAAACGTTAT 59.018 34.615 0.00 0.00 34.08 1.89
728 755 4.751060 TGAAGATAACCGCATCTAAACGT 58.249 39.130 0.00 0.00 34.08 3.99
729 756 5.041287 TCTGAAGATAACCGCATCTAAACG 58.959 41.667 0.00 0.00 34.08 3.60
730 757 6.129062 CGATCTGAAGATAACCGCATCTAAAC 60.129 42.308 0.00 0.00 34.08 2.01
731 758 5.920840 CGATCTGAAGATAACCGCATCTAAA 59.079 40.000 0.00 0.00 34.08 1.85
732 759 5.009710 ACGATCTGAAGATAACCGCATCTAA 59.990 40.000 0.00 0.00 34.08 2.10
733 760 4.519350 ACGATCTGAAGATAACCGCATCTA 59.481 41.667 0.00 0.00 34.08 1.98
734 761 3.319405 ACGATCTGAAGATAACCGCATCT 59.681 43.478 0.00 0.00 36.83 2.90
735 762 3.426859 CACGATCTGAAGATAACCGCATC 59.573 47.826 0.00 0.00 34.37 3.91
736 763 3.384668 CACGATCTGAAGATAACCGCAT 58.615 45.455 0.00 0.00 34.37 4.73
737 764 2.481276 CCACGATCTGAAGATAACCGCA 60.481 50.000 0.00 0.00 34.37 5.69
738 765 2.128035 CCACGATCTGAAGATAACCGC 58.872 52.381 0.00 0.00 34.37 5.68
739 766 2.128035 GCCACGATCTGAAGATAACCG 58.872 52.381 0.00 0.00 34.37 4.44
741 768 2.810650 ACGCCACGATCTGAAGATAAC 58.189 47.619 0.00 0.00 34.37 1.89
742 769 3.630769 ACTACGCCACGATCTGAAGATAA 59.369 43.478 0.00 0.00 34.37 1.75
743 770 3.003378 CACTACGCCACGATCTGAAGATA 59.997 47.826 0.00 0.00 34.37 1.98
744 771 2.025155 ACTACGCCACGATCTGAAGAT 58.975 47.619 0.00 0.00 37.51 2.40
745 772 1.132453 CACTACGCCACGATCTGAAGA 59.868 52.381 0.00 0.00 0.00 2.87
746 773 1.550065 CACTACGCCACGATCTGAAG 58.450 55.000 0.00 0.00 0.00 3.02
747 774 0.172578 CCACTACGCCACGATCTGAA 59.827 55.000 0.00 0.00 0.00 3.02
748 775 1.807226 CCACTACGCCACGATCTGA 59.193 57.895 0.00 0.00 0.00 3.27
749 776 1.878522 GCCACTACGCCACGATCTG 60.879 63.158 0.00 0.00 0.00 2.90
750 777 2.052690 AGCCACTACGCCACGATCT 61.053 57.895 0.00 0.00 0.00 2.75
752 779 2.184322 CAGCCACTACGCCACGAT 59.816 61.111 0.00 0.00 0.00 3.73
755 782 2.815647 GCTCAGCCACTACGCCAC 60.816 66.667 0.00 0.00 0.00 5.01
756 783 3.300934 CTGCTCAGCCACTACGCCA 62.301 63.158 0.00 0.00 0.00 5.69
757 784 2.510238 CTGCTCAGCCACTACGCC 60.510 66.667 0.00 0.00 0.00 5.68
758 785 2.510238 CCTGCTCAGCCACTACGC 60.510 66.667 0.00 0.00 0.00 4.42
759 786 2.185350 CCCTGCTCAGCCACTACG 59.815 66.667 0.00 0.00 0.00 3.51
760 787 2.124942 GCCCTGCTCAGCCACTAC 60.125 66.667 0.00 0.00 0.00 2.73
776 803 1.681793 TCTAATCGTAGTGGCTCAGGC 59.318 52.381 0.00 0.00 37.82 4.85
777 804 3.305676 CCATCTAATCGTAGTGGCTCAGG 60.306 52.174 0.00 0.00 0.00 3.86
778 805 3.858877 GCCATCTAATCGTAGTGGCTCAG 60.859 52.174 7.39 0.00 43.70 3.35
779 806 2.035961 GCCATCTAATCGTAGTGGCTCA 59.964 50.000 7.39 0.00 43.70 4.26
780 807 2.035961 TGCCATCTAATCGTAGTGGCTC 59.964 50.000 14.84 0.00 45.35 4.70
781 808 2.036475 CTGCCATCTAATCGTAGTGGCT 59.964 50.000 14.84 0.00 45.35 4.75
782 809 2.224066 ACTGCCATCTAATCGTAGTGGC 60.224 50.000 7.69 7.69 45.34 5.01
783 810 3.319405 AGACTGCCATCTAATCGTAGTGG 59.681 47.826 0.00 0.00 34.33 4.00
784 811 4.036852 TCAGACTGCCATCTAATCGTAGTG 59.963 45.833 0.00 0.00 0.00 2.74
785 812 4.207955 TCAGACTGCCATCTAATCGTAGT 58.792 43.478 0.00 0.00 0.00 2.73
786 813 4.793071 CTCAGACTGCCATCTAATCGTAG 58.207 47.826 0.00 0.00 0.00 3.51
788 815 2.223923 GCTCAGACTGCCATCTAATCGT 60.224 50.000 0.00 0.00 0.00 3.73
789 816 2.402305 GCTCAGACTGCCATCTAATCG 58.598 52.381 0.00 0.00 0.00 3.34
790 817 2.402305 CGCTCAGACTGCCATCTAATC 58.598 52.381 0.00 0.00 0.00 1.75
791 818 1.069823 CCGCTCAGACTGCCATCTAAT 59.930 52.381 0.00 0.00 0.00 1.73
792 819 0.461548 CCGCTCAGACTGCCATCTAA 59.538 55.000 0.00 0.00 0.00 2.10
796 823 3.790437 CCCCGCTCAGACTGCCAT 61.790 66.667 0.00 0.00 0.00 4.40
808 835 3.373565 CCAGTTTTCAGGCCCCGC 61.374 66.667 0.00 0.00 0.00 6.13
810 837 2.997315 GCCCAGTTTTCAGGCCCC 60.997 66.667 0.00 0.00 41.00 5.80
815 842 4.094442 GGTAATAACGAGCCCAGTTTTCAG 59.906 45.833 0.00 0.00 33.42 3.02
834 861 0.324275 GAATGGGCCTTGGCTGGTAA 60.324 55.000 11.71 0.00 0.00 2.85
839 866 2.361771 CTGGAATGGGCCTTGGCT 59.638 61.111 11.71 0.00 0.00 4.75
840 867 3.464494 GCTGGAATGGGCCTTGGC 61.464 66.667 4.53 2.49 0.00 4.52
882 1090 0.106318 ATGGAATTGGGAGGAGCTGC 60.106 55.000 0.00 0.00 0.00 5.25
910 1120 3.047735 CAACCGCCAGGAAAACCC 58.952 61.111 0.00 0.00 41.02 4.11
925 1135 3.081409 GTAGGGCGGAGGAGGCAA 61.081 66.667 0.00 0.00 38.57 4.52
986 1202 4.958581 GGATGTCCATCTCCCATTTTCTTT 59.041 41.667 7.19 0.00 37.92 2.52
997 1213 1.048724 TGGTCGGGGATGTCCATCTC 61.049 60.000 7.19 2.97 37.58 2.75
998 1214 1.002921 TGGTCGGGGATGTCCATCT 59.997 57.895 7.19 0.00 37.92 2.90
1001 1225 3.006728 GGTGGTCGGGGATGTCCA 61.007 66.667 0.86 0.00 37.91 4.02
1025 1249 0.539051 CAGGCGGAGGAAGATCTGTT 59.461 55.000 0.00 0.00 0.00 3.16
1026 1250 1.965754 GCAGGCGGAGGAAGATCTGT 61.966 60.000 0.00 0.00 0.00 3.41
1027 1251 1.227497 GCAGGCGGAGGAAGATCTG 60.227 63.158 0.00 0.00 0.00 2.90
1113 1337 0.695803 AGAATCTGCGGGGGAAGGAT 60.696 55.000 0.00 0.00 0.00 3.24
1266 1839 4.329545 GTCCAGCGGCAGTGGGAA 62.330 66.667 1.45 0.00 35.58 3.97
1606 2744 5.359009 CACTCAAATCCTTGGATGCAATAGT 59.641 40.000 0.00 1.32 33.01 2.12
1610 2748 3.765381 TCACTCAAATCCTTGGATGCAA 58.235 40.909 2.56 0.00 33.01 4.08
1644 2786 2.118313 TGGTGATCGACTCGAACCTA 57.882 50.000 18.74 6.96 39.99 3.08
1678 2820 0.036732 TGGCGCCTCTGACAAGAAAT 59.963 50.000 29.70 0.00 30.03 2.17
1711 2853 1.517832 CCCAGTCCCAGTAGAAGCG 59.482 63.158 0.00 0.00 0.00 4.68
1814 2956 3.004734 CACAAAGACTAAACCTTGCCCAG 59.995 47.826 0.00 0.00 0.00 4.45
1829 2974 1.065410 TTCCCCTGCCTCCACAAAGA 61.065 55.000 0.00 0.00 0.00 2.52
2386 21250 3.564644 AGGACAACTATGATACGAGGACG 59.435 47.826 0.00 0.00 45.75 4.79
2947 21994 5.310594 CCCCTCCAATTCATCTTACAGGATA 59.689 44.000 0.00 0.00 0.00 2.59
3112 22159 7.520614 GCAAGAAATCATATACTACAAGGCACC 60.521 40.741 0.00 0.00 0.00 5.01


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

AutoCloner maintained by Alex Coulton.