Multiple sequence alignment - TraesCS4A01G274400

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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 TraesCS4A01G274400 chr4A 100.000 2348 0 0 1 2348 584309760 584307413 0.000000e+00 4337
1 TraesCS4A01G274400 chr3B 95.473 729 25 3 1357 2079 793129527 793130253 0.000000e+00 1157
2 TraesCS4A01G274400 chr3B 95.359 237 10 1 2113 2348 793130239 793130475 2.200000e-100 375
3 TraesCS4A01G274400 chr1B 94.505 728 35 2 1357 2079 15533520 15534247 0.000000e+00 1118
4 TraesCS4A01G274400 chr1B 94.399 732 34 4 1357 2082 618316032 618315302 0.000000e+00 1118
5 TraesCS4A01G274400 chr1B 95.781 237 9 1 2113 2348 15534233 15534469 4.740000e-102 381
6 TraesCS4A01G274400 chr1B 95.359 237 10 1 2113 2348 618315319 618315083 2.200000e-100 375
7 TraesCS4A01G274400 chr2A 91.117 743 34 15 1357 2082 651915209 651914482 0.000000e+00 977
8 TraesCS4A01G274400 chr2A 94.134 358 14 5 1726 2082 737345636 737345285 2.660000e-149 538
9 TraesCS4A01G274400 chr2A 97.458 236 6 0 2113 2348 651914499 651914264 1.010000e-108 403
10 TraesCS4A01G274400 chr2A 90.444 293 18 6 1433 1715 737376166 737375874 6.130000e-101 377
11 TraesCS4A01G274400 chr2A 95.339 236 11 0 2113 2348 737345302 737345067 2.200000e-100 375
12 TraesCS4A01G274400 chr6A 94.539 586 31 1 1498 2082 4469249 4468664 0.000000e+00 904
13 TraesCS4A01G274400 chr6A 93.515 586 37 1 1498 2082 4508921 4508336 0.000000e+00 870
14 TraesCS4A01G274400 chr6A 94.915 236 10 1 2113 2348 4508353 4508120 3.690000e-98 368
15 TraesCS4A01G274400 chr6A 94.515 237 10 2 2113 2348 4468681 4468447 1.720000e-96 363
16 TraesCS4A01G274400 chr3A 93.587 499 20 2 1584 2079 565776551 565777040 0.000000e+00 734
17 TraesCS4A01G274400 chr3A 95.359 237 9 2 2113 2348 565777026 565777261 2.200000e-100 375
18 TraesCS4A01G274400 chr3D 75.054 1379 236 51 2 1351 554361017 554359718 2.050000e-150 542
19 TraesCS4A01G274400 chr3D 78.983 590 96 15 781 1348 583477516 583478099 6.130000e-101 377
20 TraesCS4A01G274400 chrUn 95.473 243 11 0 1840 2082 479806325 479806083 2.830000e-104 388
21 TraesCS4A01G274400 chrUn 95.181 166 8 0 2113 2278 479806100 479805935 1.790000e-66 263
22 TraesCS4A01G274400 chr5D 85.561 187 19 7 1518 1698 560525606 560525790 3.080000e-44 189
23 TraesCS4A01G274400 chr2D 84.896 192 24 4 1520 1707 513037542 513037732 3.080000e-44 189


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 TraesCS4A01G274400 chr4A 584307413 584309760 2347 True 4337.0 4337 100.0000 1 2348 1 chr4A.!!$R1 2347
1 TraesCS4A01G274400 chr3B 793129527 793130475 948 False 766.0 1157 95.4160 1357 2348 2 chr3B.!!$F1 991
2 TraesCS4A01G274400 chr1B 15533520 15534469 949 False 749.5 1118 95.1430 1357 2348 2 chr1B.!!$F1 991
3 TraesCS4A01G274400 chr1B 618315083 618316032 949 True 746.5 1118 94.8790 1357 2348 2 chr1B.!!$R1 991
4 TraesCS4A01G274400 chr2A 651914264 651915209 945 True 690.0 977 94.2875 1357 2348 2 chr2A.!!$R2 991
5 TraesCS4A01G274400 chr2A 737345067 737345636 569 True 456.5 538 94.7365 1726 2348 2 chr2A.!!$R3 622
6 TraesCS4A01G274400 chr6A 4468447 4469249 802 True 633.5 904 94.5270 1498 2348 2 chr6A.!!$R1 850
7 TraesCS4A01G274400 chr6A 4508120 4508921 801 True 619.0 870 94.2150 1498 2348 2 chr6A.!!$R2 850
8 TraesCS4A01G274400 chr3A 565776551 565777261 710 False 554.5 734 94.4730 1584 2348 2 chr3A.!!$F1 764
9 TraesCS4A01G274400 chr3D 554359718 554361017 1299 True 542.0 542 75.0540 2 1351 1 chr3D.!!$R1 1349
10 TraesCS4A01G274400 chr3D 583477516 583478099 583 False 377.0 377 78.9830 781 1348 1 chr3D.!!$F1 567

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
589 605 0.038526 ACGGTGACAACGACATCCTC 60.039 55.0 21.82 0.0 34.93 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2080 2135 0.111446 TGAAGGGACAAAATGGGCGA 59.889 50.0 0.0 0.0 0.0 5.54 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
18 19 4.154347 GGAGCTCACGGAGGGCAG 62.154 72.222 17.19 0.00 0.00 4.85
21 22 4.704833 GCTCACGGAGGGCAGCAA 62.705 66.667 0.00 0.00 0.00 3.91
22 23 2.270205 CTCACGGAGGGCAGCAAT 59.730 61.111 0.00 0.00 0.00 3.56
88 89 1.370414 CAAGCGCAAAACGGACAGG 60.370 57.895 11.47 0.00 43.93 4.00
92 93 1.501741 CGCAAAACGGACAGGATGG 59.498 57.895 0.00 0.00 38.39 3.51
100 101 4.864334 GACAGGATGGCCCGGCTG 62.864 72.222 9.86 1.33 39.24 4.85
137 138 2.395690 GCGTCCGCAAGTTCATCG 59.604 61.111 6.82 0.00 41.49 3.84
139 140 1.074319 GCGTCCGCAAGTTCATCGTA 61.074 55.000 6.82 0.00 41.49 3.43
141 142 1.278238 GTCCGCAAGTTCATCGTAGG 58.722 55.000 0.00 0.00 0.00 3.18
143 144 0.810031 CCGCAAGTTCATCGTAGGGG 60.810 60.000 0.00 0.00 0.00 4.79
147 148 0.620700 AAGTTCATCGTAGGGGGCCT 60.621 55.000 0.84 0.00 37.71 5.19
148 149 1.146263 GTTCATCGTAGGGGGCCTG 59.854 63.158 0.84 0.00 34.61 4.85
150 151 3.479203 CATCGTAGGGGGCCTGCA 61.479 66.667 0.84 0.00 35.99 4.41
151 152 3.480133 ATCGTAGGGGGCCTGCAC 61.480 66.667 0.84 0.00 35.99 4.57
163 164 4.655647 CTGCACCCACCTGCTGCT 62.656 66.667 0.00 0.00 38.07 4.24
164 165 4.960866 TGCACCCACCTGCTGCTG 62.961 66.667 0.00 0.00 38.07 4.41
174 175 4.783621 TGCTGCTGCCGGGACATC 62.784 66.667 13.47 0.00 38.71 3.06
184 185 1.730487 CGGGACATCGGAGTCAGAG 59.270 63.158 9.73 0.00 40.29 3.35
186 187 1.439644 GGACATCGGAGTCAGAGGC 59.560 63.158 4.81 0.00 40.29 4.70
228 229 2.406401 GCTGCTTCGCGAATGCAT 59.594 55.556 31.42 0.00 42.97 3.96
229 230 1.937846 GCTGCTTCGCGAATGCATG 60.938 57.895 31.42 26.35 42.97 4.06
230 231 1.298116 CTGCTTCGCGAATGCATGG 60.298 57.895 31.42 22.45 42.97 3.66
231 232 1.708193 CTGCTTCGCGAATGCATGGA 61.708 55.000 31.42 18.52 42.97 3.41
234 235 0.247814 CTTCGCGAATGCATGGACAC 60.248 55.000 23.67 0.00 42.97 3.67
240 241 1.004610 CGAATGCATGGACACGATGAC 60.005 52.381 0.00 0.00 0.00 3.06
244 245 2.202743 ATGGACACGATGACGCGG 60.203 61.111 12.47 0.00 43.96 6.46
248 249 4.796231 ACACGATGACGCGGCTCC 62.796 66.667 15.80 3.35 43.96 4.70
273 274 2.004583 CGAATTCGTGCCTCCTACAA 57.995 50.000 19.67 0.00 34.11 2.41
277 278 1.334160 TTCGTGCCTCCTACAACAGA 58.666 50.000 0.00 0.00 0.00 3.41
278 279 1.334160 TCGTGCCTCCTACAACAGAA 58.666 50.000 0.00 0.00 0.00 3.02
280 281 2.002586 CGTGCCTCCTACAACAGAATG 58.997 52.381 0.00 0.00 46.00 2.67
302 318 2.125912 CCTCCAAGGACACGAGCG 60.126 66.667 0.00 0.00 37.67 5.03
304 320 1.444553 CTCCAAGGACACGAGCGAC 60.445 63.158 0.00 0.00 0.00 5.19
307 323 1.797933 CAAGGACACGAGCGACGAG 60.798 63.158 12.62 7.62 45.77 4.18
318 334 4.838486 CGACGAGGAGCTGGCGAC 62.838 72.222 0.00 0.00 0.00 5.19
319 335 4.838486 GACGAGGAGCTGGCGACG 62.838 72.222 0.00 0.00 0.00 5.12
322 338 2.496817 GAGGAGCTGGCGACGAAT 59.503 61.111 0.00 0.00 0.00 3.34
323 339 1.880340 GAGGAGCTGGCGACGAATG 60.880 63.158 0.00 0.00 0.00 2.67
328 344 2.680913 GCTGGCGACGAATGTGCTT 61.681 57.895 0.00 0.00 0.00 3.91
337 353 1.710339 GAATGTGCTTCTCGACGGC 59.290 57.895 0.00 0.00 0.00 5.68
344 360 1.080501 CTTCTCGACGGCTGCTTCA 60.081 57.895 0.00 0.00 0.00 3.02
352 368 1.078214 CGGCTGCTTCATCCTCCAA 60.078 57.895 0.00 0.00 0.00 3.53
369 385 2.027625 AACGCCTGCTCAAGTACGC 61.028 57.895 0.00 0.00 0.00 4.42
370 386 3.188786 CGCCTGCTCAAGTACGCC 61.189 66.667 0.00 0.00 0.00 5.68
373 389 2.571757 CTGCTCAAGTACGCCCGA 59.428 61.111 0.00 0.00 0.00 5.14
374 390 1.080093 CTGCTCAAGTACGCCCGAA 60.080 57.895 0.00 0.00 0.00 4.30
375 391 0.460284 CTGCTCAAGTACGCCCGAAT 60.460 55.000 0.00 0.00 0.00 3.34
376 392 0.739462 TGCTCAAGTACGCCCGAATG 60.739 55.000 0.00 0.00 0.00 2.67
388 404 1.767759 CCCGAATGGCCAAAAGATCT 58.232 50.000 10.96 0.00 0.00 2.75
389 405 2.102578 CCCGAATGGCCAAAAGATCTT 58.897 47.619 10.96 0.88 0.00 2.40
390 406 2.099756 CCCGAATGGCCAAAAGATCTTC 59.900 50.000 10.96 6.18 0.00 2.87
391 407 2.099756 CCGAATGGCCAAAAGATCTTCC 59.900 50.000 10.96 6.20 0.00 3.46
392 408 2.754552 CGAATGGCCAAAAGATCTTCCA 59.245 45.455 10.96 14.18 0.00 3.53
393 409 3.181493 CGAATGGCCAAAAGATCTTCCAG 60.181 47.826 10.96 6.90 0.00 3.86
394 410 2.220653 TGGCCAAAAGATCTTCCAGG 57.779 50.000 8.78 11.80 0.00 4.45
395 411 1.272648 TGGCCAAAAGATCTTCCAGGG 60.273 52.381 8.78 9.05 0.00 4.45
396 412 1.005924 GGCCAAAAGATCTTCCAGGGA 59.994 52.381 8.78 0.00 0.00 4.20
397 413 2.557452 GGCCAAAAGATCTTCCAGGGAA 60.557 50.000 8.78 0.09 0.00 3.97
406 422 1.809684 CTTCCAGGGAAGGAAACGAC 58.190 55.000 18.40 0.00 46.44 4.34
409 425 0.389948 CCAGGGAAGGAAACGACGAG 60.390 60.000 0.00 0.00 0.00 4.18
418 434 1.257539 GAAACGACGAGGACGATGAC 58.742 55.000 0.00 0.00 42.66 3.06
422 438 1.433879 GACGAGGACGATGACTGGG 59.566 63.158 0.00 0.00 42.66 4.45
423 439 2.105128 CGAGGACGATGACTGGGC 59.895 66.667 0.00 0.00 42.66 5.36
436 452 4.189580 TGGGCCCAGCTAATCGGC 62.190 66.667 24.45 5.03 42.23 5.54
440 456 3.546543 CCCAGCTAATCGGCCGGA 61.547 66.667 27.83 12.89 31.86 5.14
441 457 2.504032 CCAGCTAATCGGCCGGAA 59.496 61.111 27.83 7.28 31.86 4.30
442 458 1.153249 CCAGCTAATCGGCCGGAAA 60.153 57.895 27.83 6.34 31.86 3.13
453 469 2.275418 CCGGAAATGGGTCTGGGG 59.725 66.667 0.00 0.00 40.00 4.96
475 491 1.443872 CGTGAAGCGCGACCTACTT 60.444 57.895 12.10 2.10 39.94 2.24
476 492 1.674611 CGTGAAGCGCGACCTACTTG 61.675 60.000 12.10 0.00 39.94 3.16
481 497 2.027625 GCGCGACCTACTTGTGCTT 61.028 57.895 12.10 0.00 36.89 3.91
482 498 1.781555 CGCGACCTACTTGTGCTTG 59.218 57.895 0.00 0.00 0.00 4.01
483 499 1.626654 CGCGACCTACTTGTGCTTGG 61.627 60.000 0.00 0.00 0.00 3.61
484 500 0.320421 GCGACCTACTTGTGCTTGGA 60.320 55.000 0.00 0.00 0.00 3.53
496 512 0.469144 TGCTTGGAAACCAGGTTCCC 60.469 55.000 11.91 1.96 45.67 3.97
506 522 0.685097 CCAGGTTCCCTTCTTCGTCA 59.315 55.000 0.00 0.00 0.00 4.35
510 526 2.637872 AGGTTCCCTTCTTCGTCATTCA 59.362 45.455 0.00 0.00 0.00 2.57
514 530 4.193826 TCCCTTCTTCGTCATTCAGAAG 57.806 45.455 0.00 0.00 43.70 2.85
520 536 3.990469 TCTTCGTCATTCAGAAGCTGTTC 59.010 43.478 0.00 0.00 42.48 3.18
523 539 3.742882 TCGTCATTCAGAAGCTGTTCAAG 59.257 43.478 0.00 0.00 34.82 3.02
532 548 4.085876 CTGTTCAAGCACCTGGGG 57.914 61.111 0.00 0.00 0.00 4.96
533 549 1.455849 CTGTTCAAGCACCTGGGGA 59.544 57.895 0.00 0.00 0.00 4.81
534 550 0.607489 CTGTTCAAGCACCTGGGGAG 60.607 60.000 0.00 0.00 0.00 4.30
535 551 1.059584 TGTTCAAGCACCTGGGGAGA 61.060 55.000 0.00 0.00 0.00 3.71
536 552 0.110486 GTTCAAGCACCTGGGGAGAA 59.890 55.000 0.00 0.00 0.00 2.87
537 553 0.850100 TTCAAGCACCTGGGGAGAAA 59.150 50.000 0.00 0.00 0.00 2.52
538 554 0.401738 TCAAGCACCTGGGGAGAAAG 59.598 55.000 0.00 0.00 0.00 2.62
539 555 0.401738 CAAGCACCTGGGGAGAAAGA 59.598 55.000 0.00 0.00 0.00 2.52
540 556 0.695347 AAGCACCTGGGGAGAAAGAG 59.305 55.000 0.00 0.00 0.00 2.85
541 557 1.377856 GCACCTGGGGAGAAAGAGC 60.378 63.158 0.00 0.00 0.00 4.09
542 558 2.069776 CACCTGGGGAGAAAGAGCA 58.930 57.895 0.00 0.00 0.00 4.26
543 559 0.401738 CACCTGGGGAGAAAGAGCAA 59.598 55.000 0.00 0.00 0.00 3.91
553 569 3.126686 GGAGAAAGAGCAAGAGCAACATC 59.873 47.826 0.00 0.00 45.49 3.06
554 570 4.002316 GAGAAAGAGCAAGAGCAACATCT 58.998 43.478 0.00 0.00 45.49 2.90
555 571 3.752222 AGAAAGAGCAAGAGCAACATCTG 59.248 43.478 0.00 0.00 45.49 2.90
556 572 2.855209 AGAGCAAGAGCAACATCTGT 57.145 45.000 0.00 0.00 45.49 3.41
559 575 3.008330 GAGCAAGAGCAACATCTGTGAT 58.992 45.455 0.00 0.00 45.49 3.06
560 576 2.747989 AGCAAGAGCAACATCTGTGATG 59.252 45.455 6.06 6.06 45.49 3.07
565 581 0.376152 GCAACATCTGTGATGGCGAG 59.624 55.000 11.55 1.11 0.00 5.03
566 582 0.376152 CAACATCTGTGATGGCGAGC 59.624 55.000 11.55 0.00 0.00 5.03
567 583 1.086067 AACATCTGTGATGGCGAGCG 61.086 55.000 11.55 0.00 0.00 5.03
568 584 1.520120 CATCTGTGATGGCGAGCGT 60.520 57.895 0.00 0.00 0.00 5.07
569 585 1.520120 ATCTGTGATGGCGAGCGTG 60.520 57.895 0.00 0.00 0.00 5.34
570 586 1.948721 ATCTGTGATGGCGAGCGTGA 61.949 55.000 0.00 0.00 0.00 4.35
571 587 2.432456 TGTGATGGCGAGCGTGAC 60.432 61.111 0.00 0.00 0.00 3.67
572 588 3.545481 GTGATGGCGAGCGTGACG 61.545 66.667 0.00 0.00 0.00 4.35
573 589 4.794439 TGATGGCGAGCGTGACGG 62.794 66.667 7.25 0.00 0.00 4.79
574 590 4.796231 GATGGCGAGCGTGACGGT 62.796 66.667 10.29 10.29 41.33 4.83
578 594 4.994201 GCGAGCGTGACGGTGACA 62.994 66.667 16.53 0.00 37.83 3.58
579 595 2.354188 CGAGCGTGACGGTGACAA 60.354 61.111 16.53 0.00 37.83 3.18
580 596 2.645510 CGAGCGTGACGGTGACAAC 61.646 63.158 16.53 0.00 37.83 3.32
589 605 0.038526 ACGGTGACAACGACATCCTC 60.039 55.000 21.82 0.00 34.93 3.71
590 606 0.736325 CGGTGACAACGACATCCTCC 60.736 60.000 7.21 0.00 0.00 4.30
593 609 1.546476 GTGACAACGACATCCTCCTCT 59.454 52.381 0.00 0.00 0.00 3.69
595 611 2.753452 TGACAACGACATCCTCCTCTAC 59.247 50.000 0.00 0.00 0.00 2.59
597 613 2.014857 CAACGACATCCTCCTCTACGA 58.985 52.381 0.00 0.00 0.00 3.43
608 624 3.127352 CTCTACGACGGCCTCCAGC 62.127 68.421 0.00 0.00 42.60 4.85
610 626 1.822613 CTACGACGGCCTCCAGCTA 60.823 63.158 0.00 0.00 43.05 3.32
613 629 1.144057 CGACGGCCTCCAGCTATTT 59.856 57.895 0.00 0.00 43.05 1.40
630 646 2.579207 TTTAGCTCGTTCCATCCTCG 57.421 50.000 0.00 0.00 0.00 4.63
631 647 0.102481 TTAGCTCGTTCCATCCTCGC 59.898 55.000 0.00 0.00 0.00 5.03
633 649 2.107141 CTCGTTCCATCCTCGCCC 59.893 66.667 0.00 0.00 0.00 6.13
637 653 4.161295 TTCCATCCTCGCCCGCTG 62.161 66.667 0.00 0.00 0.00 5.18
685 701 3.072476 CACCACCTCCTCCACCTG 58.928 66.667 0.00 0.00 0.00 4.00
694 710 2.104170 CTCCTCCACCTGTTCTACCTC 58.896 57.143 0.00 0.00 0.00 3.85
709 725 1.834822 CCTCTCCATCGACCTCCCC 60.835 68.421 0.00 0.00 0.00 4.81
711 727 3.227276 CTCCATCGACCTCCCCCG 61.227 72.222 0.00 0.00 0.00 5.73
714 730 3.917760 CATCGACCTCCCCCGCTC 61.918 72.222 0.00 0.00 0.00 5.03
737 753 2.425592 CTTGGCACCGTGACTCCA 59.574 61.111 5.82 0.00 0.00 3.86
740 756 4.699522 GGCACCGTGACTCCACCC 62.700 72.222 1.65 0.00 40.12 4.61
766 782 4.803908 GGGCCCCCGCAGAGAAAG 62.804 72.222 12.23 0.00 36.38 2.62
767 783 4.035102 GGCCCCCGCAGAGAAAGT 62.035 66.667 0.00 0.00 36.38 2.66
772 788 3.181967 CCGCAGAGAAAGTCCGCG 61.182 66.667 0.00 0.00 45.25 6.46
798 814 1.375523 CAGACCTAACGTGGTGGGC 60.376 63.158 1.67 0.67 41.00 5.36
820 836 1.522580 GAGCGCCAAGGATCTGGAC 60.523 63.158 2.29 0.00 38.96 4.02
822 838 2.892425 CGCCAAGGATCTGGACGC 60.892 66.667 5.19 0.00 38.96 5.19
826 842 3.077556 AAGGATCTGGACGCGGCT 61.078 61.111 13.91 0.00 0.00 5.52
851 867 3.630148 GGATCCGTGCACGCGATG 61.630 66.667 33.20 22.30 38.18 3.84
856 872 4.580044 CGTGCACGCGATGATGGC 62.580 66.667 28.16 6.90 0.00 4.40
857 873 3.498834 GTGCACGCGATGATGGCA 61.499 61.111 15.93 9.65 0.00 4.92
858 874 3.498834 TGCACGCGATGATGGCAC 61.499 61.111 15.93 0.00 0.00 5.01
878 894 2.948720 GCCACCAGCTTCCTCGACT 61.949 63.158 0.00 0.00 38.99 4.18
882 898 1.048601 ACCAGCTTCCTCGACTTGAA 58.951 50.000 0.00 0.00 0.00 2.69
896 918 1.291877 CTTGAAGTTCCACCGAGGCG 61.292 60.000 0.00 0.00 37.29 5.52
901 923 3.691342 TTCCACCGAGGCGTCCTG 61.691 66.667 2.98 0.00 37.29 3.86
916 939 3.531207 CTGGAGATCCGCCGCTGA 61.531 66.667 0.00 0.00 39.43 4.26
924 947 0.179045 ATCCGCCGCTGAAGCTATTT 60.179 50.000 0.10 0.00 39.32 1.40
936 959 4.424626 TGAAGCTATTTGACTACAGCGAG 58.575 43.478 0.00 0.00 39.04 5.03
937 960 3.444703 AGCTATTTGACTACAGCGAGG 57.555 47.619 0.00 0.00 39.04 4.63
963 986 1.740296 CCGGAACCTGATCGCGTTT 60.740 57.895 5.77 0.00 0.00 3.60
967 990 1.429463 GAACCTGATCGCGTTTGAGT 58.571 50.000 5.77 0.00 0.00 3.41
980 1003 2.229784 CGTTTGAGTAGACCTACCCGTT 59.770 50.000 3.74 0.00 36.75 4.44
1012 1035 1.229428 CATCACCATGTACGCCATCC 58.771 55.000 0.00 0.00 0.00 3.51
1034 1057 1.489649 CATGGACTGCCTCCTCAAGAT 59.510 52.381 0.00 0.00 40.26 2.40
1036 1059 0.179936 GGACTGCCTCCTCAAGATGG 59.820 60.000 0.00 0.00 35.89 3.51
1037 1060 1.198713 GACTGCCTCCTCAAGATGGA 58.801 55.000 0.00 0.00 0.00 3.41
1091 1114 1.006825 CTCGTGAACCGCATGAACGA 61.007 55.000 0.00 0.67 41.77 3.85
1099 1122 1.136774 CGCATGAACGACGAGAGGA 59.863 57.895 0.00 0.00 34.06 3.71
1100 1123 0.456142 CGCATGAACGACGAGAGGAA 60.456 55.000 0.00 0.00 34.06 3.36
1101 1124 1.710013 GCATGAACGACGAGAGGAAA 58.290 50.000 0.00 0.00 0.00 3.13
1102 1125 2.271800 GCATGAACGACGAGAGGAAAT 58.728 47.619 0.00 0.00 0.00 2.17
1112 1135 1.152383 GAGAGGAAATACGCCGCCAC 61.152 60.000 0.00 0.00 0.00 5.01
1165 1188 3.365265 CCTCAGCCAACCGCAACC 61.365 66.667 0.00 0.00 41.38 3.77
1170 1193 3.977244 GCCAACCGCAACCACCTG 61.977 66.667 0.00 0.00 37.47 4.00
1192 1215 1.313091 CGACGTGATGGAGGAGGTCA 61.313 60.000 0.00 0.00 0.00 4.02
1194 1217 0.826715 ACGTGATGGAGGAGGTCATG 59.173 55.000 0.00 0.00 35.53 3.07
1203 1226 1.757699 GAGGAGGTCATGAGGTACCAC 59.242 57.143 15.94 8.81 38.30 4.16
1209 1232 1.482593 GTCATGAGGTACCACAGAGGG 59.517 57.143 17.33 7.32 43.89 4.30
1211 1234 1.759445 CATGAGGTACCACAGAGGGAG 59.241 57.143 17.33 0.34 43.89 4.30
1212 1235 1.081481 TGAGGTACCACAGAGGGAGA 58.919 55.000 15.94 0.00 43.89 3.71
1287 1322 4.143333 GCCTCCGCGGTCTTGCTA 62.143 66.667 27.15 1.93 34.25 3.49
1289 1324 2.105128 CTCCGCGGTCTTGCTAGG 59.895 66.667 27.15 0.00 0.00 3.02
1291 1326 4.148825 CCGCGGTCTTGCTAGGCT 62.149 66.667 19.50 0.00 0.00 4.58
1296 1331 0.741221 CGGTCTTGCTAGGCTTGACC 60.741 60.000 17.31 17.31 42.82 4.02
1310 1345 1.468506 TTGACCGTGCTGCAGACCTA 61.469 55.000 20.43 0.00 0.00 3.08
1325 1360 0.037605 ACCTACTACACTGCCGTTGC 60.038 55.000 0.00 0.00 38.26 4.17
1326 1361 0.739813 CCTACTACACTGCCGTTGCC 60.740 60.000 0.00 0.00 36.33 4.52
1339 1374 1.609580 CCGTTGCCTACTACAAGCCAA 60.610 52.381 0.00 0.00 0.00 4.52
1351 1386 7.773690 CCTACTACAAGCCAACCAAGTAATTAT 59.226 37.037 0.00 0.00 0.00 1.28
1352 1387 9.174166 CTACTACAAGCCAACCAAGTAATTATT 57.826 33.333 0.00 0.00 0.00 1.40
1354 1389 9.695155 ACTACAAGCCAACCAAGTAATTATTAT 57.305 29.630 0.00 0.00 0.00 1.28
1435 1480 4.466827 ACCCGGTCTTTTGTTTCATTACT 58.533 39.130 0.00 0.00 0.00 2.24
1479 1524 1.512230 GATGCCATTTCCAGCGCAA 59.488 52.632 11.47 0.00 34.38 4.85
1513 1564 4.895224 TCGCTCACCAGTACTAGTTATG 57.105 45.455 0.00 0.00 0.00 1.90
1518 1569 6.395629 GCTCACCAGTACTAGTTATGAACAA 58.604 40.000 0.00 0.00 0.00 2.83
1536 1587 4.370364 ACAAGACAAAATTGCTGACGTT 57.630 36.364 0.00 0.00 0.00 3.99
1560 1611 5.516984 AGCCAAGATTCCTCTGAAATTCAT 58.483 37.500 0.00 0.00 33.32 2.57
1808 1863 9.745880 GTTTCAATGACTTCTATAGGTCGAATA 57.254 33.333 0.00 0.00 35.45 1.75
2080 2135 9.453830 AATTCTTCCTAAACCTAGAGATATGGT 57.546 33.333 0.00 0.00 35.29 3.55
2081 2136 8.480133 TTCTTCCTAAACCTAGAGATATGGTC 57.520 38.462 0.00 0.00 32.98 4.02
2082 2137 6.715718 TCTTCCTAAACCTAGAGATATGGTCG 59.284 42.308 0.00 0.00 32.98 4.79
2083 2138 4.765856 TCCTAAACCTAGAGATATGGTCGC 59.234 45.833 0.00 0.00 32.98 5.19
2084 2139 4.082136 CCTAAACCTAGAGATATGGTCGCC 60.082 50.000 0.00 0.00 32.98 5.54
2085 2140 1.926108 ACCTAGAGATATGGTCGCCC 58.074 55.000 0.00 0.00 0.00 6.13
2094 2149 4.089105 TGGTCGCCCATTTTGTCC 57.911 55.556 0.00 0.00 35.17 4.02
2095 2150 1.605165 TGGTCGCCCATTTTGTCCC 60.605 57.895 0.00 0.00 35.17 4.46
2096 2151 1.304134 GGTCGCCCATTTTGTCCCT 60.304 57.895 0.00 0.00 0.00 4.20
2097 2152 0.898326 GGTCGCCCATTTTGTCCCTT 60.898 55.000 0.00 0.00 0.00 3.95
2098 2153 0.526211 GTCGCCCATTTTGTCCCTTC 59.474 55.000 0.00 0.00 0.00 3.46
2099 2154 0.111446 TCGCCCATTTTGTCCCTTCA 59.889 50.000 0.00 0.00 0.00 3.02
2100 2155 0.527565 CGCCCATTTTGTCCCTTCAG 59.472 55.000 0.00 0.00 0.00 3.02
2101 2156 0.897621 GCCCATTTTGTCCCTTCAGG 59.102 55.000 0.00 0.00 0.00 3.86
2112 2167 2.286826 CCTTCAGGGACATCCGACA 58.713 57.895 0.00 0.00 41.52 4.35
2113 2168 0.613260 CCTTCAGGGACATCCGACAA 59.387 55.000 0.00 0.00 41.52 3.18
2114 2169 1.003118 CCTTCAGGGACATCCGACAAA 59.997 52.381 0.00 0.00 41.52 2.83
2127 2182 5.011125 ACATCCGACAAACCTAGAGATATGG 59.989 44.000 0.00 0.00 0.00 2.74
2157 2212 3.243468 TGCATGTCACCACAAAATCACAG 60.243 43.478 0.00 0.00 35.64 3.66
2194 2249 9.784531 AAGCATGCTGACATACTATAAGTTATT 57.215 29.630 23.48 0.00 33.67 1.40
2223 2278 1.645034 CAGTGTGAGTTATGAGGCCG 58.355 55.000 0.00 0.00 0.00 6.13
2319 2376 6.771188 AAGAGAGTGTGAGTTAAACATTCG 57.229 37.500 0.00 0.00 38.79 3.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.704103 TGCCCTCCGTGAGCTCCT 62.704 66.667 12.15 0.00 0.00 3.69
4 5 3.984193 ATTGCTGCCCTCCGTGAGC 62.984 63.158 0.00 0.00 0.00 4.26
18 19 2.555547 GGGATGTAGGCGCCATTGC 61.556 63.158 31.54 13.51 0.00 3.56
21 22 2.343475 CTTGGGGATGTAGGCGCCAT 62.343 60.000 31.54 14.27 46.05 4.40
22 23 3.012119 TTGGGGATGTAGGCGCCA 61.012 61.111 31.54 12.31 45.28 5.69
33 34 1.899437 GATGCAGACGACCTTGGGGA 61.899 60.000 0.00 0.00 36.25 4.81
59 60 1.560004 TTGCGCTTGCTGTCGAAGAG 61.560 55.000 9.73 0.00 36.85 2.85
92 93 4.840005 GTAGTGCTCCAGCCGGGC 62.840 72.222 12.11 12.11 41.18 6.13
93 94 2.859273 CTTGTAGTGCTCCAGCCGGG 62.859 65.000 2.18 0.00 41.18 5.73
95 96 1.016130 CACTTGTAGTGCTCCAGCCG 61.016 60.000 0.00 0.00 39.62 5.52
106 107 1.291877 GGACGCAGCACCACTTGTAG 61.292 60.000 0.00 0.00 0.00 2.74
131 132 2.742116 GCAGGCCCCCTACGATGAA 61.742 63.158 0.00 0.00 29.64 2.57
156 157 4.790962 ATGTCCCGGCAGCAGCAG 62.791 66.667 2.65 0.00 44.61 4.24
157 158 4.783621 GATGTCCCGGCAGCAGCA 62.784 66.667 2.65 0.00 44.61 4.41
169 170 1.040339 AGGCCTCTGACTCCGATGTC 61.040 60.000 0.00 0.00 37.47 3.06
172 173 1.760086 CCAGGCCTCTGACTCCGAT 60.760 63.158 0.00 0.00 43.49 4.18
174 175 2.681778 ACCAGGCCTCTGACTCCG 60.682 66.667 0.00 0.00 43.49 4.63
217 218 2.451990 CGTGTCCATGCATTCGCGA 61.452 57.895 3.71 3.71 42.97 5.87
220 221 1.004610 GTCATCGTGTCCATGCATTCG 60.005 52.381 0.00 0.00 0.00 3.34
221 222 1.004610 CGTCATCGTGTCCATGCATTC 60.005 52.381 0.00 0.00 0.00 2.67
223 224 1.431488 GCGTCATCGTGTCCATGCAT 61.431 55.000 0.00 0.00 39.49 3.96
229 230 4.796231 AGCCGCGTCATCGTGTCC 62.796 66.667 4.92 0.00 44.70 4.02
230 231 3.248171 GAGCCGCGTCATCGTGTC 61.248 66.667 4.92 0.00 44.70 3.67
231 232 4.796231 GGAGCCGCGTCATCGTGT 62.796 66.667 4.92 0.00 44.70 4.49
244 245 3.929948 CGAATTCGCGGCAGGAGC 61.930 66.667 15.93 0.00 41.10 4.70
248 249 4.520846 GGCACGAATTCGCGGCAG 62.521 66.667 32.49 18.59 44.67 4.85
253 254 0.459585 TGTAGGAGGCACGAATTCGC 60.460 55.000 27.03 12.06 44.43 4.70
255 256 2.673368 CTGTTGTAGGAGGCACGAATTC 59.327 50.000 0.00 0.00 0.00 2.17
257 258 1.899814 TCTGTTGTAGGAGGCACGAAT 59.100 47.619 0.00 0.00 0.00 3.34
273 274 1.276421 CCTTGGAGGACGACATTCTGT 59.724 52.381 0.00 0.00 37.67 3.41
285 286 2.125912 CGCTCGTGTCCTTGGAGG 60.126 66.667 0.00 0.00 36.46 4.30
288 289 2.805353 CGTCGCTCGTGTCCTTGG 60.805 66.667 0.00 0.00 34.52 3.61
290 291 2.561885 CTCGTCGCTCGTGTCCTT 59.438 61.111 0.00 0.00 40.80 3.36
302 318 4.838486 CGTCGCCAGCTCCTCGTC 62.838 72.222 0.00 0.00 0.00 4.20
304 320 3.417275 ATTCGTCGCCAGCTCCTCG 62.417 63.158 0.00 0.00 0.00 4.63
307 323 2.125512 ACATTCGTCGCCAGCTCC 60.126 61.111 0.00 0.00 0.00 4.70
318 334 1.991430 CCGTCGAGAAGCACATTCG 59.009 57.895 0.00 0.00 43.16 3.34
319 335 0.737715 AGCCGTCGAGAAGCACATTC 60.738 55.000 0.00 0.00 38.28 2.67
322 338 2.049156 CAGCCGTCGAGAAGCACA 60.049 61.111 0.00 0.00 0.00 4.57
323 339 3.482783 GCAGCCGTCGAGAAGCAC 61.483 66.667 0.00 0.00 0.00 4.40
328 344 1.139734 GATGAAGCAGCCGTCGAGA 59.860 57.895 0.00 0.00 0.00 4.04
337 353 1.372087 GGCGTTGGAGGATGAAGCAG 61.372 60.000 0.00 0.00 0.00 4.24
344 360 1.841302 TTGAGCAGGCGTTGGAGGAT 61.841 55.000 0.00 0.00 0.00 3.24
352 368 2.432628 GCGTACTTGAGCAGGCGT 60.433 61.111 0.00 0.00 0.00 5.68
369 385 1.767759 AGATCTTTTGGCCATTCGGG 58.232 50.000 6.09 0.00 40.85 5.14
370 386 2.099756 GGAAGATCTTTTGGCCATTCGG 59.900 50.000 6.09 0.00 0.00 4.30
373 389 3.102204 CCTGGAAGATCTTTTGGCCATT 58.898 45.455 6.09 0.00 34.07 3.16
374 390 2.625087 CCCTGGAAGATCTTTTGGCCAT 60.625 50.000 6.09 0.00 34.07 4.40
375 391 1.272648 CCCTGGAAGATCTTTTGGCCA 60.273 52.381 9.87 0.00 34.07 5.36
376 392 1.005924 TCCCTGGAAGATCTTTTGGCC 59.994 52.381 9.87 6.69 34.07 5.36
387 403 1.809684 GTCGTTTCCTTCCCTGGAAG 58.190 55.000 17.35 17.35 45.58 3.46
388 404 0.034337 CGTCGTTTCCTTCCCTGGAA 59.966 55.000 0.00 0.00 43.63 3.53
389 405 0.828762 TCGTCGTTTCCTTCCCTGGA 60.829 55.000 0.00 0.00 0.00 3.86
390 406 0.389948 CTCGTCGTTTCCTTCCCTGG 60.390 60.000 0.00 0.00 0.00 4.45
391 407 0.389948 CCTCGTCGTTTCCTTCCCTG 60.390 60.000 0.00 0.00 0.00 4.45
392 408 0.541296 TCCTCGTCGTTTCCTTCCCT 60.541 55.000 0.00 0.00 0.00 4.20
393 409 0.389556 GTCCTCGTCGTTTCCTTCCC 60.390 60.000 0.00 0.00 0.00 3.97
394 410 0.731855 CGTCCTCGTCGTTTCCTTCC 60.732 60.000 0.00 0.00 0.00 3.46
395 411 0.239347 TCGTCCTCGTCGTTTCCTTC 59.761 55.000 0.00 0.00 38.33 3.46
396 412 0.886563 ATCGTCCTCGTCGTTTCCTT 59.113 50.000 0.00 0.00 38.33 3.36
397 413 0.170561 CATCGTCCTCGTCGTTTCCT 59.829 55.000 0.00 0.00 38.33 3.36
398 414 0.169672 TCATCGTCCTCGTCGTTTCC 59.830 55.000 0.00 0.00 38.33 3.13
399 415 1.135746 AGTCATCGTCCTCGTCGTTTC 60.136 52.381 0.00 0.00 38.33 2.78
400 416 0.879765 AGTCATCGTCCTCGTCGTTT 59.120 50.000 0.00 0.00 38.33 3.60
401 417 0.168348 CAGTCATCGTCCTCGTCGTT 59.832 55.000 0.00 0.00 38.33 3.85
402 418 1.645704 CCAGTCATCGTCCTCGTCGT 61.646 60.000 0.00 0.00 38.33 4.34
403 419 1.062685 CCAGTCATCGTCCTCGTCG 59.937 63.158 0.00 0.00 38.33 5.12
404 420 1.433879 CCCAGTCATCGTCCTCGTC 59.566 63.158 0.00 0.00 38.33 4.20
405 421 2.711922 GCCCAGTCATCGTCCTCGT 61.712 63.158 0.00 0.00 38.33 4.18
406 422 2.105128 GCCCAGTCATCGTCCTCG 59.895 66.667 0.00 0.00 38.55 4.63
409 425 3.391665 CTGGGCCCAGTCATCGTCC 62.392 68.421 39.52 1.51 39.10 4.79
418 434 2.111878 CCGATTAGCTGGGCCCAG 59.888 66.667 42.66 42.66 46.15 4.45
429 445 0.179040 GACCCATTTCCGGCCGATTA 60.179 55.000 30.73 11.47 0.00 1.75
430 446 1.453197 GACCCATTTCCGGCCGATT 60.453 57.895 30.73 4.80 0.00 3.34
431 447 2.192175 GACCCATTTCCGGCCGAT 59.808 61.111 30.73 9.88 0.00 4.18
436 452 1.858739 TTCCCCAGACCCATTTCCGG 61.859 60.000 0.00 0.00 0.00 5.14
440 456 1.382629 CGGTTCCCCAGACCCATTT 59.617 57.895 0.00 0.00 33.49 2.32
441 457 1.850755 ACGGTTCCCCAGACCCATT 60.851 57.895 0.00 0.00 33.49 3.16
442 458 2.204090 ACGGTTCCCCAGACCCAT 60.204 61.111 0.00 0.00 33.49 4.00
453 469 2.807631 TAGGTCGCGCTTCACGGTTC 62.808 60.000 5.56 0.00 43.93 3.62
464 480 1.626654 CCAAGCACAAGTAGGTCGCG 61.627 60.000 0.00 0.00 0.00 5.87
466 482 2.163818 TTCCAAGCACAAGTAGGTCG 57.836 50.000 0.00 0.00 0.00 4.79
475 491 1.398692 GAACCTGGTTTCCAAGCACA 58.601 50.000 14.28 0.00 34.75 4.57
476 492 0.673985 GGAACCTGGTTTCCAAGCAC 59.326 55.000 14.28 0.00 44.14 4.40
496 512 3.993081 ACAGCTTCTGAATGACGAAGAAG 59.007 43.478 7.18 7.18 46.34 2.85
520 536 0.401738 TCTTTCTCCCCAGGTGCTTG 59.598 55.000 0.00 0.00 0.00 4.01
523 539 1.377856 GCTCTTTCTCCCCAGGTGC 60.378 63.158 0.00 0.00 0.00 5.01
525 541 0.695347 CTTGCTCTTTCTCCCCAGGT 59.305 55.000 0.00 0.00 0.00 4.00
530 546 1.809547 GTTGCTCTTGCTCTTTCTCCC 59.190 52.381 0.00 0.00 40.48 4.30
532 548 4.002316 AGATGTTGCTCTTGCTCTTTCTC 58.998 43.478 0.00 0.00 40.48 2.87
533 549 3.752222 CAGATGTTGCTCTTGCTCTTTCT 59.248 43.478 0.00 0.00 40.48 2.52
534 550 3.501445 ACAGATGTTGCTCTTGCTCTTTC 59.499 43.478 0.00 0.00 40.48 2.62
535 551 3.252701 CACAGATGTTGCTCTTGCTCTTT 59.747 43.478 0.00 0.00 40.48 2.52
536 552 2.812591 CACAGATGTTGCTCTTGCTCTT 59.187 45.455 0.00 0.00 40.48 2.85
537 553 2.038164 TCACAGATGTTGCTCTTGCTCT 59.962 45.455 0.00 0.00 40.48 4.09
538 554 2.420642 TCACAGATGTTGCTCTTGCTC 58.579 47.619 0.00 0.00 40.48 4.26
539 555 2.556144 TCACAGATGTTGCTCTTGCT 57.444 45.000 0.00 0.00 40.48 3.91
540 556 2.159421 CCATCACAGATGTTGCTCTTGC 60.159 50.000 6.29 0.00 40.20 4.01
541 557 2.159421 GCCATCACAGATGTTGCTCTTG 60.159 50.000 6.29 0.00 0.00 3.02
542 558 2.089980 GCCATCACAGATGTTGCTCTT 58.910 47.619 6.29 0.00 0.00 2.85
543 559 1.747709 GCCATCACAGATGTTGCTCT 58.252 50.000 6.29 0.00 0.00 4.09
553 569 2.125952 TCACGCTCGCCATCACAG 60.126 61.111 0.00 0.00 0.00 3.66
554 570 2.432456 GTCACGCTCGCCATCACA 60.432 61.111 0.00 0.00 0.00 3.58
555 571 3.545481 CGTCACGCTCGCCATCAC 61.545 66.667 0.00 0.00 0.00 3.06
556 572 4.794439 CCGTCACGCTCGCCATCA 62.794 66.667 0.00 0.00 0.00 3.07
565 581 2.656007 TCGTTGTCACCGTCACGC 60.656 61.111 0.00 0.00 0.00 5.34
566 582 0.937699 ATGTCGTTGTCACCGTCACG 60.938 55.000 0.00 0.00 0.00 4.35
567 583 0.782384 GATGTCGTTGTCACCGTCAC 59.218 55.000 0.00 0.00 0.00 3.67
568 584 0.319211 GGATGTCGTTGTCACCGTCA 60.319 55.000 0.00 0.00 0.00 4.35
569 585 0.038526 AGGATGTCGTTGTCACCGTC 60.039 55.000 0.00 0.00 0.00 4.79
570 586 0.038526 GAGGATGTCGTTGTCACCGT 60.039 55.000 0.00 0.00 0.00 4.83
571 587 0.736325 GGAGGATGTCGTTGTCACCG 60.736 60.000 0.00 0.00 0.00 4.94
572 588 0.608640 AGGAGGATGTCGTTGTCACC 59.391 55.000 0.00 0.00 0.00 4.02
573 589 1.546476 AGAGGAGGATGTCGTTGTCAC 59.454 52.381 0.00 0.00 0.00 3.67
574 590 1.924731 AGAGGAGGATGTCGTTGTCA 58.075 50.000 0.00 0.00 0.00 3.58
575 591 2.223294 CGTAGAGGAGGATGTCGTTGTC 60.223 54.545 0.00 0.00 0.00 3.18
576 592 1.743958 CGTAGAGGAGGATGTCGTTGT 59.256 52.381 0.00 0.00 0.00 3.32
577 593 2.014857 TCGTAGAGGAGGATGTCGTTG 58.985 52.381 0.00 0.00 0.00 4.10
578 594 2.015587 GTCGTAGAGGAGGATGTCGTT 58.984 52.381 0.00 0.00 36.95 3.85
579 595 1.666054 GTCGTAGAGGAGGATGTCGT 58.334 55.000 0.00 0.00 36.95 4.34
580 596 0.582482 CGTCGTAGAGGAGGATGTCG 59.418 60.000 0.00 0.00 46.48 4.35
589 605 2.439701 TGGAGGCCGTCGTAGAGG 60.440 66.667 0.00 0.00 42.73 3.69
590 606 3.111939 CTGGAGGCCGTCGTAGAG 58.888 66.667 0.00 0.00 36.95 2.43
593 609 0.754217 AATAGCTGGAGGCCGTCGTA 60.754 55.000 0.00 0.00 43.05 3.43
595 611 0.387929 TAAATAGCTGGAGGCCGTCG 59.612 55.000 0.00 0.00 43.05 5.12
597 613 0.106894 GCTAAATAGCTGGAGGCCGT 59.893 55.000 5.19 0.00 45.62 5.68
608 624 4.230657 CGAGGATGGAACGAGCTAAATAG 58.769 47.826 0.00 0.00 0.00 1.73
610 626 2.803492 GCGAGGATGGAACGAGCTAAAT 60.803 50.000 0.00 0.00 0.00 1.40
613 629 1.734137 GCGAGGATGGAACGAGCTA 59.266 57.895 0.00 0.00 0.00 3.32
619 635 4.162690 AGCGGGCGAGGATGGAAC 62.163 66.667 0.00 0.00 0.00 3.62
620 636 4.161295 CAGCGGGCGAGGATGGAA 62.161 66.667 0.00 0.00 0.00 3.53
670 686 0.838122 AGAACAGGTGGAGGAGGTGG 60.838 60.000 0.00 0.00 0.00 4.61
685 701 2.619646 GAGGTCGATGGAGAGGTAGAAC 59.380 54.545 0.00 0.00 0.00 3.01
694 710 3.227276 CGGGGGAGGTCGATGGAG 61.227 72.222 0.00 0.00 0.00 3.86
715 731 4.680237 TCACGGTGCCAAGGCGAG 62.680 66.667 6.60 2.84 45.51 5.03
719 735 2.358737 GGAGTCACGGTGCCAAGG 60.359 66.667 2.51 0.00 0.00 3.61
720 736 1.961277 GTGGAGTCACGGTGCCAAG 60.961 63.158 2.51 0.00 33.87 3.61
723 739 4.699522 GGGTGGAGTCACGGTGCC 62.700 72.222 2.51 0.00 44.50 5.01
750 766 3.978571 GACTTTCTCTGCGGGGGCC 62.979 68.421 0.00 0.00 0.00 5.80
751 767 2.436824 GACTTTCTCTGCGGGGGC 60.437 66.667 0.00 0.00 0.00 5.80
752 768 2.269241 GGACTTTCTCTGCGGGGG 59.731 66.667 0.00 0.00 0.00 5.40
753 769 2.125512 CGGACTTTCTCTGCGGGG 60.126 66.667 0.00 0.00 0.00 5.73
754 770 2.815647 GCGGACTTTCTCTGCGGG 60.816 66.667 0.00 0.00 41.56 6.13
757 773 2.433318 AGCGCGGACTTTCTCTGC 60.433 61.111 8.83 0.00 46.69 4.26
758 774 2.734673 GCAGCGCGGACTTTCTCTG 61.735 63.158 13.03 4.87 0.00 3.35
759 775 2.433318 GCAGCGCGGACTTTCTCT 60.433 61.111 13.03 0.00 0.00 3.10
760 776 3.491652 GGCAGCGCGGACTTTCTC 61.492 66.667 13.03 0.00 0.00 2.87
772 788 2.820037 GTTAGGTCTGGCGGCAGC 60.820 66.667 32.43 25.44 44.18 5.25
778 794 1.375523 CCACCACGTTAGGTCTGGC 60.376 63.158 0.00 0.00 40.77 4.85
779 795 1.295423 CCCACCACGTTAGGTCTGG 59.705 63.158 0.00 0.00 40.77 3.86
802 818 1.522580 GTCCAGATCCTTGGCGCTC 60.523 63.158 7.64 0.00 38.16 5.03
803 819 2.586792 GTCCAGATCCTTGGCGCT 59.413 61.111 7.64 0.00 38.16 5.92
865 881 2.447244 ACTTCAAGTCGAGGAAGCTG 57.553 50.000 16.93 1.31 43.32 4.24
878 894 1.301401 CGCCTCGGTGGAACTTCAA 60.301 57.895 0.00 0.00 38.35 2.69
882 898 3.692406 GGACGCCTCGGTGGAACT 61.692 66.667 0.00 0.00 38.35 3.01
896 918 4.593864 GCGGCGGATCTCCAGGAC 62.594 72.222 9.78 0.00 35.14 3.85
901 923 2.279784 CTTCAGCGGCGGATCTCC 60.280 66.667 9.78 0.00 0.00 3.71
916 939 3.786635 CCTCGCTGTAGTCAAATAGCTT 58.213 45.455 0.00 0.00 34.13 3.74
924 947 1.185618 ACAAGGCCTCGCTGTAGTCA 61.186 55.000 5.23 0.00 0.00 3.41
936 959 1.971695 CAGGTTCCGGAACAAGGCC 60.972 63.158 40.12 26.75 42.85 5.19
937 960 0.322546 ATCAGGTTCCGGAACAAGGC 60.323 55.000 40.12 26.35 42.85 4.35
963 986 2.440409 GTGAACGGGTAGGTCTACTCA 58.560 52.381 8.53 2.25 36.34 3.41
967 990 1.315257 GGCGTGAACGGGTAGGTCTA 61.315 60.000 4.84 0.00 37.49 2.59
1082 1105 1.710013 TTTCCTCTCGTCGTTCATGC 58.290 50.000 0.00 0.00 0.00 4.06
1091 1114 1.226888 GCGGCGTATTTCCTCTCGT 60.227 57.895 9.37 0.00 0.00 4.18
1143 1166 4.988598 CGGTTGGCTGAGGTGCGT 62.989 66.667 0.00 0.00 0.00 5.24
1152 1175 4.204028 AGGTGGTTGCGGTTGGCT 62.204 61.111 0.00 0.00 44.05 4.75
1165 1188 2.815211 CATCACGTCGGCCAGGTG 60.815 66.667 16.89 16.89 41.50 4.00
1170 1193 3.432051 CTCCTCCATCACGTCGGCC 62.432 68.421 0.00 0.00 0.00 6.13
1175 1198 0.826715 CATGACCTCCTCCATCACGT 59.173 55.000 0.00 0.00 0.00 4.49
1192 1215 1.646447 TCTCCCTCTGTGGTACCTCAT 59.354 52.381 16.68 0.00 0.00 2.90
1194 1217 2.035632 CATCTCCCTCTGTGGTACCTC 58.964 57.143 14.36 10.53 0.00 3.85
1203 1226 2.450320 CCTGGGCCATCTCCCTCTG 61.450 68.421 6.72 0.00 46.67 3.35
1273 1308 4.143333 GCCTAGCAAGACCGCGGA 62.143 66.667 35.90 6.13 36.85 5.54
1275 1310 2.125512 AAGCCTAGCAAGACCGCG 60.126 61.111 0.00 0.00 36.85 6.46
1279 1314 0.037232 ACGGTCAAGCCTAGCAAGAC 60.037 55.000 3.67 3.67 35.15 3.01
1287 1322 4.254709 TGCAGCACGGTCAAGCCT 62.255 61.111 0.00 0.00 34.25 4.58
1289 1324 2.666190 TCTGCAGCACGGTCAAGC 60.666 61.111 9.47 0.00 0.00 4.01
1291 1326 1.468506 TAGGTCTGCAGCACGGTCAA 61.469 55.000 9.47 0.00 0.00 3.18
1296 1331 0.526211 TGTAGTAGGTCTGCAGCACG 59.474 55.000 9.47 0.00 34.04 5.34
1310 1345 0.037605 GTAGGCAACGGCAGTGTAGT 60.038 55.000 0.00 0.00 43.71 2.73
1319 1354 0.036765 TGGCTTGTAGTAGGCAACGG 60.037 55.000 0.00 0.00 46.29 4.44
1325 1360 3.418684 ACTTGGTTGGCTTGTAGTAGG 57.581 47.619 0.00 0.00 0.00 3.18
1326 1361 8.732746 ATAATTACTTGGTTGGCTTGTAGTAG 57.267 34.615 0.00 0.00 0.00 2.57
1339 1374 6.018507 GTCGCGTCCAATAATAATTACTTGGT 60.019 38.462 5.77 0.00 39.33 3.67
1351 1386 4.056740 TGTTTGTTAGTCGCGTCCAATAA 58.943 39.130 5.77 0.00 0.00 1.40
1352 1387 3.651206 TGTTTGTTAGTCGCGTCCAATA 58.349 40.909 5.77 0.00 0.00 1.90
1353 1388 2.478894 CTGTTTGTTAGTCGCGTCCAAT 59.521 45.455 5.77 0.00 0.00 3.16
1354 1389 1.862201 CTGTTTGTTAGTCGCGTCCAA 59.138 47.619 5.77 0.00 0.00 3.53
1355 1390 1.202440 ACTGTTTGTTAGTCGCGTCCA 60.202 47.619 5.77 0.00 0.00 4.02
1381 1416 5.230942 GTGTGGATCTAATGCTTAGCGTAT 58.769 41.667 0.00 0.00 33.23 3.06
1435 1480 2.361104 GCAGGGGGCAATCGTTCA 60.361 61.111 0.00 0.00 43.97 3.18
1479 1524 0.883153 TGAGCGAATGCATGCAAACT 59.117 45.000 26.68 18.62 46.23 2.66
1513 1564 4.351192 ACGTCAGCAATTTTGTCTTGTTC 58.649 39.130 0.00 0.00 0.00 3.18
1518 1569 3.058224 GGCTAACGTCAGCAATTTTGTCT 60.058 43.478 13.86 0.00 43.67 3.41
1536 1587 6.065976 TGAATTTCAGAGGAATCTTGGCTA 57.934 37.500 0.00 0.00 31.93 3.93
1565 1616 5.761234 ACGGTTTGAGCTACAGAACATTTTA 59.239 36.000 0.00 0.00 0.00 1.52
1574 1625 2.673368 GGATCAACGGTTTGAGCTACAG 59.327 50.000 4.34 0.00 45.73 2.74
1728 1782 4.501571 CCTGATAAGTCCGGTGTGAATAGG 60.502 50.000 0.00 0.00 0.00 2.57
1781 1836 7.165460 TCGACCTATAGAAGTCATTGAAACA 57.835 36.000 0.00 0.00 33.08 2.83
1937 1992 1.761784 TGTAGTTACGTGGGTGGTTGT 59.238 47.619 0.00 0.00 0.00 3.32
2079 2134 0.526211 GAAGGGACAAAATGGGCGAC 59.474 55.000 0.00 0.00 0.00 5.19
2080 2135 0.111446 TGAAGGGACAAAATGGGCGA 59.889 50.000 0.00 0.00 0.00 5.54
2081 2136 0.527565 CTGAAGGGACAAAATGGGCG 59.472 55.000 0.00 0.00 0.00 6.13
2082 2137 0.897621 CCTGAAGGGACAAAATGGGC 59.102 55.000 0.00 0.00 37.23 5.36
2094 2149 0.613260 TTGTCGGATGTCCCTGAAGG 59.387 55.000 0.00 0.00 0.00 3.46
2095 2150 2.076863 GTTTGTCGGATGTCCCTGAAG 58.923 52.381 0.00 0.00 0.00 3.02
2096 2151 1.271163 GGTTTGTCGGATGTCCCTGAA 60.271 52.381 0.00 0.00 0.00 3.02
2097 2152 0.323629 GGTTTGTCGGATGTCCCTGA 59.676 55.000 0.00 0.00 0.00 3.86
2098 2153 0.324943 AGGTTTGTCGGATGTCCCTG 59.675 55.000 0.00 0.00 0.00 4.45
2099 2154 1.831736 CTAGGTTTGTCGGATGTCCCT 59.168 52.381 0.00 0.00 0.00 4.20
2100 2155 1.829222 TCTAGGTTTGTCGGATGTCCC 59.171 52.381 0.00 0.00 0.00 4.46
2101 2156 2.758979 TCTCTAGGTTTGTCGGATGTCC 59.241 50.000 0.00 0.00 0.00 4.02
2102 2157 4.657436 ATCTCTAGGTTTGTCGGATGTC 57.343 45.455 0.00 0.00 0.00 3.06
2103 2158 5.011125 CCATATCTCTAGGTTTGTCGGATGT 59.989 44.000 0.00 0.00 0.00 3.06
2104 2159 5.011125 ACCATATCTCTAGGTTTGTCGGATG 59.989 44.000 0.00 0.00 29.58 3.51
2105 2160 5.148502 ACCATATCTCTAGGTTTGTCGGAT 58.851 41.667 0.00 0.00 29.58 4.18
2106 2161 4.543689 ACCATATCTCTAGGTTTGTCGGA 58.456 43.478 0.00 0.00 29.58 4.55
2107 2162 4.341235 TGACCATATCTCTAGGTTTGTCGG 59.659 45.833 0.00 0.00 35.36 4.79
2108 2163 5.163550 TGTGACCATATCTCTAGGTTTGTCG 60.164 44.000 0.00 0.00 35.36 4.35
2109 2164 6.222038 TGTGACCATATCTCTAGGTTTGTC 57.778 41.667 0.00 0.00 35.36 3.18
2110 2165 6.814954 ATGTGACCATATCTCTAGGTTTGT 57.185 37.500 0.00 0.00 35.36 2.83
2111 2166 7.332926 GCATATGTGACCATATCTCTAGGTTTG 59.667 40.741 4.29 0.00 41.35 2.93
2112 2167 7.016563 TGCATATGTGACCATATCTCTAGGTTT 59.983 37.037 4.29 0.00 41.35 3.27
2113 2168 6.498303 TGCATATGTGACCATATCTCTAGGTT 59.502 38.462 4.29 0.00 41.35 3.50
2114 2169 6.019108 TGCATATGTGACCATATCTCTAGGT 58.981 40.000 4.29 0.00 41.35 3.08
2157 2212 2.170607 TCAGCATGCTTAACTCTACCCC 59.829 50.000 19.98 0.00 34.76 4.95
2194 2249 1.342074 ACTCACACTGCTTCAGCCTA 58.658 50.000 0.00 0.00 41.18 3.93
2223 2278 8.983724 GTTCTACCTGATAATTCATACTGCTTC 58.016 37.037 0.00 0.00 0.00 3.86
2319 2376 7.444183 TGCAACTTGATAACTTATATAGTGCCC 59.556 37.037 0.00 0.00 37.12 5.36


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

AutoCloner maintained by Alex Coulton.