Multiple sequence alignment - TraesCS3D01G123400

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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 TraesCS3D01G123400 chr3D 100.000 3222 0 0 1 3222 81205416 81208637 0.000000e+00 5951.0
1 TraesCS3D01G123400 chr3A 89.758 2763 131 65 534 3222 95476395 95479079 0.000000e+00 3395.0
2 TraesCS3D01G123400 chr3A 79.087 263 31 10 2 264 95475735 95475973 3.330000e-35 159.0
3 TraesCS3D01G123400 chr3B 91.944 1651 87 25 1586 3222 126920831 126922449 0.000000e+00 2270.0
4 TraesCS3D01G123400 chr3B 88.305 1009 55 24 539 1512 126919552 126920532 0.000000e+00 1151.0
5 TraesCS3D01G123400 chrUn 92.683 246 11 3 2702 2943 275342139 275342381 6.620000e-92 348.0
6 TraesCS3D01G123400 chrUn 92.276 246 12 3 2702 2943 275341219 275341461 3.080000e-90 342.0
7 TraesCS3D01G123400 chrUn 91.020 245 14 5 2703 2943 379041228 379040988 1.110000e-84 324.0
8 TraesCS3D01G123400 chrUn 90.726 248 14 5 2702 2943 309341283 309341527 4.010000e-84 322.0
9 TraesCS3D01G123400 chrUn 90.726 248 14 5 2702 2943 412286057 412285813 4.010000e-84 322.0
10 TraesCS3D01G123400 chrUn 78.014 282 41 11 2311 2581 275341866 275342137 1.200000e-34 158.0
11 TraesCS3D01G123400 chrUn 77.660 282 42 11 2311 2581 275340946 275341217 5.570000e-33 152.0
12 TraesCS3D01G123400 chrUn 88.776 98 11 0 2311 2408 374008512 374008609 1.570000e-23 121.0
13 TraesCS3D01G123400 chr7B 92.683 246 11 3 2702 2943 77863580 77863822 6.620000e-92 348.0
14 TraesCS3D01G123400 chr7B 80.471 297 25 10 2311 2581 77863289 77863578 2.540000e-46 196.0
15 TraesCS3D01G123400 chr2B 91.020 245 14 5 2703 2943 758941108 758940868 1.110000e-84 324.0
16 TraesCS3D01G123400 chr1A 76.294 367 52 20 1745 2087 127077178 127076823 2.570000e-36 163.0
17 TraesCS3D01G123400 chr1A 81.068 206 24 8 1317 1519 127077526 127077333 2.000000e-32 150.0
18 TraesCS3D01G123400 chr1D 76.152 369 50 20 1745 2087 116004954 116004598 3.330000e-35 159.0
19 TraesCS3D01G123400 chr1D 80.583 206 25 8 1317 1519 116005301 116005108 9.320000e-31 145.0
20 TraesCS3D01G123400 chr1B 81.553 206 23 8 1317 1519 177838252 177838059 4.300000e-34 156.0
21 TraesCS3D01G123400 chr1B 75.198 379 58 21 1745 2099 177837905 177837539 2.590000e-31 147.0
22 TraesCS3D01G123400 chr5D 88.235 102 12 0 1984 2085 457777219 457777320 4.370000e-24 122.0
23 TraesCS3D01G123400 chr5B 88.235 102 12 0 1984 2085 559992272 559992373 4.370000e-24 122.0
24 TraesCS3D01G123400 chr5B 91.429 70 6 0 2019 2088 64265122 64265053 2.650000e-16 97.1
25 TraesCS3D01G123400 chr5A 87.255 102 13 0 1984 2085 575658613 575658714 2.030000e-22 117.0
26 TraesCS3D01G123400 chr4A 89.655 87 7 1 2419 2503 607906713 607906799 3.400000e-20 110.0


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 TraesCS3D01G123400 chr3D 81205416 81208637 3221 False 5951.0 5951 100.00000 1 3222 1 chr3D.!!$F1 3221
1 TraesCS3D01G123400 chr3A 95475735 95479079 3344 False 1777.0 3395 84.42250 2 3222 2 chr3A.!!$F1 3220
2 TraesCS3D01G123400 chr3B 126919552 126922449 2897 False 1710.5 2270 90.12450 539 3222 2 chr3B.!!$F1 2683
3 TraesCS3D01G123400 chrUn 275340946 275342381 1435 False 250.0 348 85.15825 2311 2943 4 chrUn.!!$F3 632
4 TraesCS3D01G123400 chr7B 77863289 77863822 533 False 272.0 348 86.57700 2311 2943 2 chr7B.!!$F1 632

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
331 520 0.175531 CAATCCCAAAATCCGCCACC 59.824 55.0 0.00 0.0 0.0 4.61 F
638 840 0.515564 CGTGTCATCCGGGAACAAAC 59.484 55.0 0.00 0.0 0.0 2.93 F
1577 1868 0.040425 GCTTTCTTTCTTGCGGCGAA 60.040 50.0 12.98 0.0 0.0 4.70 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1228 1486 0.510359 GTCGTCTTCTTGTGCTGCTG 59.490 55.000 0.00 0.0 0.0 4.41 R
1584 2089 1.057851 TCCCAACCCAACGAACTCCT 61.058 55.000 0.00 0.0 0.0 3.69 R
3139 3726 1.376037 GAACTTGACGAGGGCCAGG 60.376 63.158 6.18 0.0 0.0 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
24 25 1.433534 CTCTCTTTTGACACGCCTCC 58.566 55.000 0.00 0.00 0.00 4.30
25 26 0.319555 TCTCTTTTGACACGCCTCCG 60.320 55.000 0.00 0.00 41.14 4.63
27 28 2.203084 TTTTGACACGCCTCCGCA 60.203 55.556 0.00 0.00 38.22 5.69
28 29 2.443957 CTTTTGACACGCCTCCGCAC 62.444 60.000 0.00 0.00 38.22 5.34
31 32 4.664677 GACACGCCTCCGCACACT 62.665 66.667 0.00 0.00 38.22 3.55
45 46 3.502920 CGCACACTGAGAGTAGTTAAGG 58.497 50.000 0.00 0.00 0.00 2.69
58 59 7.416731 AGAGTAGTTAAGGGTTACTATGTGGA 58.583 38.462 0.00 0.00 0.00 4.02
61 62 8.339247 AGTAGTTAAGGGTTACTATGTGGAGTA 58.661 37.037 0.00 0.00 0.00 2.59
68 69 9.839185 AAGGGTTACTATGTGGAGTATATACAT 57.161 33.333 15.18 4.64 38.48 2.29
104 105 3.349488 TCGTAGGCGAGTGAATACATG 57.651 47.619 0.00 0.00 42.81 3.21
142 143 9.623000 AAGTTTATAACACATATACTTCACCCC 57.377 33.333 0.00 0.00 0.00 4.95
144 145 9.623000 GTTTATAACACATATACTTCACCCCTT 57.377 33.333 0.00 0.00 0.00 3.95
175 176 8.538409 ACAATATTTCACCAATTCAAAGCTTC 57.462 30.769 0.00 0.00 0.00 3.86
190 191 1.421268 AGCTTCCCTGTGAACATGACA 59.579 47.619 0.00 0.00 0.00 3.58
195 196 2.371510 TCCCTGTGAACATGACATGACA 59.628 45.455 22.19 16.79 0.00 3.58
198 199 4.563374 CCCTGTGAACATGACATGACACTA 60.563 45.833 29.83 21.83 39.57 2.74
208 209 7.766283 ACATGACATGACACTATATATCTCGG 58.234 38.462 22.19 0.00 0.00 4.63
210 211 7.379098 TGACATGACACTATATATCTCGGTC 57.621 40.000 0.00 0.00 0.00 4.79
212 213 7.665974 TGACATGACACTATATATCTCGGTCTT 59.334 37.037 0.00 0.00 0.00 3.01
213 214 8.046294 ACATGACACTATATATCTCGGTCTTC 57.954 38.462 0.00 0.00 0.00 2.87
215 216 8.515414 CATGACACTATATATCTCGGTCTTCAA 58.485 37.037 0.00 0.00 0.00 2.69
217 218 8.350722 TGACACTATATATCTCGGTCTTCAAAC 58.649 37.037 0.00 0.00 0.00 2.93
232 233 5.795441 GTCTTCAAACGAGAATGCCAATTAC 59.205 40.000 0.00 0.00 0.00 1.89
238 239 4.997565 ACGAGAATGCCAATTACCAATTG 58.002 39.130 0.00 0.00 46.09 2.32
256 257 5.327091 CAATTGCCGTCACTATTCTTTCAG 58.673 41.667 0.00 0.00 0.00 3.02
259 260 3.006430 TGCCGTCACTATTCTTTCAGTGA 59.994 43.478 0.44 0.44 46.75 3.41
270 271 9.539825 ACTATTCTTTCAGTGATATGACATGTC 57.460 33.333 19.27 19.27 0.00 3.06
274 275 7.267857 TCTTTCAGTGATATGACATGTCGATT 58.732 34.615 20.54 10.63 0.00 3.34
300 489 5.751586 TGATTTACTTGATTAGGTGTCCCC 58.248 41.667 0.00 0.00 0.00 4.81
301 490 5.251932 TGATTTACTTGATTAGGTGTCCCCA 59.748 40.000 0.00 0.00 34.66 4.96
303 492 5.789574 TTACTTGATTAGGTGTCCCCAAT 57.210 39.130 0.00 0.00 34.66 3.16
304 493 6.894735 TTACTTGATTAGGTGTCCCCAATA 57.105 37.500 0.00 0.00 34.66 1.90
305 494 5.789574 ACTTGATTAGGTGTCCCCAATAA 57.210 39.130 0.00 0.00 34.66 1.40
307 496 5.253096 ACTTGATTAGGTGTCCCCAATAACT 59.747 40.000 0.00 0.00 34.66 2.24
308 497 5.789574 TGATTAGGTGTCCCCAATAACTT 57.210 39.130 0.00 0.00 34.66 2.66
309 498 6.147437 TGATTAGGTGTCCCCAATAACTTT 57.853 37.500 0.00 0.00 34.66 2.66
311 500 3.895704 AGGTGTCCCCAATAACTTTGT 57.104 42.857 0.00 0.00 34.66 2.83
313 502 3.139397 AGGTGTCCCCAATAACTTTGTCA 59.861 43.478 0.00 0.00 34.66 3.58
315 504 4.526650 GGTGTCCCCAATAACTTTGTCAAT 59.473 41.667 0.00 0.00 0.00 2.57
316 505 5.336451 GGTGTCCCCAATAACTTTGTCAATC 60.336 44.000 0.00 0.00 0.00 2.67
317 506 4.770010 TGTCCCCAATAACTTTGTCAATCC 59.230 41.667 0.00 0.00 0.00 3.01
320 509 4.530161 CCCCAATAACTTTGTCAATCCCAA 59.470 41.667 0.00 0.00 0.00 4.12
322 511 6.465035 CCCCAATAACTTTGTCAATCCCAAAA 60.465 38.462 0.00 0.00 31.86 2.44
323 512 7.167535 CCCAATAACTTTGTCAATCCCAAAAT 58.832 34.615 0.00 0.00 31.86 1.82
325 514 7.334171 CCAATAACTTTGTCAATCCCAAAATCC 59.666 37.037 0.00 0.00 31.86 3.01
327 516 3.253230 CTTTGTCAATCCCAAAATCCGC 58.747 45.455 0.00 0.00 31.86 5.54
329 518 1.181786 GTCAATCCCAAAATCCGCCA 58.818 50.000 0.00 0.00 0.00 5.69
330 519 1.135112 GTCAATCCCAAAATCCGCCAC 60.135 52.381 0.00 0.00 0.00 5.01
331 520 0.175531 CAATCCCAAAATCCGCCACC 59.824 55.000 0.00 0.00 0.00 4.61
334 523 2.283532 CCAAAATCCGCCACCCCA 60.284 61.111 0.00 0.00 0.00 4.96
337 526 1.304134 AAAATCCGCCACCCCAGTC 60.304 57.895 0.00 0.00 0.00 3.51
338 527 1.789576 AAAATCCGCCACCCCAGTCT 61.790 55.000 0.00 0.00 0.00 3.24
341 530 1.789576 ATCCGCCACCCCAGTCTTTT 61.790 55.000 0.00 0.00 0.00 2.27
343 532 0.676782 CCGCCACCCCAGTCTTTTAG 60.677 60.000 0.00 0.00 0.00 1.85
345 534 1.271163 CGCCACCCCAGTCTTTTAGAA 60.271 52.381 0.00 0.00 0.00 2.10
349 538 3.328050 CCACCCCAGTCTTTTAGAAGTCT 59.672 47.826 0.00 0.00 32.57 3.24
350 539 4.202472 CCACCCCAGTCTTTTAGAAGTCTT 60.202 45.833 0.00 0.00 30.42 3.01
351 540 4.998033 CACCCCAGTCTTTTAGAAGTCTTC 59.002 45.833 4.26 4.26 30.42 2.87
353 542 4.998033 CCCCAGTCTTTTAGAAGTCTTCAC 59.002 45.833 14.97 3.20 30.42 3.18
355 544 5.467063 CCCAGTCTTTTAGAAGTCTTCACAC 59.533 44.000 14.97 2.32 30.42 3.82
356 545 5.175856 CCAGTCTTTTAGAAGTCTTCACACG 59.824 44.000 14.97 0.00 30.42 4.49
357 546 5.175856 CAGTCTTTTAGAAGTCTTCACACGG 59.824 44.000 14.97 2.65 30.42 4.94
360 549 2.433868 TAGAAGTCTTCACACGGTGC 57.566 50.000 14.97 0.00 32.98 5.01
361 550 0.597637 AGAAGTCTTCACACGGTGCG 60.598 55.000 14.97 0.00 32.98 5.34
363 552 2.644555 AAGTCTTCACACGGTGCGCT 62.645 55.000 9.73 0.00 32.98 5.92
364 553 2.661537 TCTTCACACGGTGCGCTG 60.662 61.111 9.73 4.06 32.98 5.18
365 554 4.374702 CTTCACACGGTGCGCTGC 62.375 66.667 9.73 0.69 32.98 5.25
366 555 4.908687 TTCACACGGTGCGCTGCT 62.909 61.111 9.73 0.00 32.98 4.24
375 564 3.365265 TGCGCTGCTCTGACGAGA 61.365 61.111 9.73 0.00 39.74 4.04
386 575 2.637947 TCTGACGAGAGAGAGGTGATG 58.362 52.381 0.00 0.00 0.00 3.07
387 576 2.237392 TCTGACGAGAGAGAGGTGATGA 59.763 50.000 0.00 0.00 0.00 2.92
390 579 2.354510 GACGAGAGAGAGGTGATGACAG 59.645 54.545 0.00 0.00 0.00 3.51
391 580 1.065401 CGAGAGAGAGGTGATGACAGC 59.935 57.143 0.00 0.00 43.79 4.40
398 587 2.805353 GTGATGACAGCGACGCGT 60.805 61.111 13.85 13.85 0.00 6.01
399 588 2.504026 TGATGACAGCGACGCGTC 60.504 61.111 28.96 28.96 34.56 5.19
401 590 1.801913 GATGACAGCGACGCGTCTT 60.802 57.895 33.94 26.50 34.86 3.01
402 591 1.734359 GATGACAGCGACGCGTCTTC 61.734 60.000 33.94 28.54 34.86 2.87
408 597 3.827784 CGACGCGTCTTCGGCTTG 61.828 66.667 33.94 14.30 34.80 4.01
410 599 4.664677 ACGCGTCTTCGGCTTGCT 62.665 61.111 5.58 0.00 37.56 3.91
411 600 3.414700 CGCGTCTTCGGCTTGCTT 61.415 61.111 0.00 0.00 37.56 3.91
414 603 2.022129 CGTCTTCGGCTTGCTTCGT 61.022 57.895 0.00 0.00 0.00 3.85
415 604 1.557443 CGTCTTCGGCTTGCTTCGTT 61.557 55.000 0.00 0.00 0.00 3.85
417 606 0.865769 TCTTCGGCTTGCTTCGTTTC 59.134 50.000 0.00 0.00 0.00 2.78
420 609 1.438710 CGGCTTGCTTCGTTTCGTG 60.439 57.895 0.00 0.00 0.00 4.35
421 610 1.647084 GGCTTGCTTCGTTTCGTGT 59.353 52.632 0.00 0.00 0.00 4.49
422 611 0.863144 GGCTTGCTTCGTTTCGTGTA 59.137 50.000 0.00 0.00 0.00 2.90
423 612 1.136336 GGCTTGCTTCGTTTCGTGTAG 60.136 52.381 0.00 0.00 0.00 2.74
424 613 1.525619 GCTTGCTTCGTTTCGTGTAGT 59.474 47.619 0.00 0.00 0.00 2.73
426 615 1.401530 TGCTTCGTTTCGTGTAGTCG 58.598 50.000 0.00 0.00 0.00 4.18
428 617 1.381429 GCTTCGTTTCGTGTAGTCGTC 59.619 52.381 0.00 0.00 0.00 4.20
429 618 1.636135 CTTCGTTTCGTGTAGTCGTCG 59.364 52.381 0.00 0.00 0.00 5.12
430 619 0.722469 TCGTTTCGTGTAGTCGTCGC 60.722 55.000 0.00 0.00 0.00 5.19
432 621 1.462378 CGTTTCGTGTAGTCGTCGCTA 60.462 52.381 0.00 0.00 0.00 4.26
433 622 2.164427 GTTTCGTGTAGTCGTCGCTAG 58.836 52.381 0.00 0.00 0.00 3.42
436 625 1.591619 TCGTGTAGTCGTCGCTAGATG 59.408 52.381 0.00 6.68 34.75 2.90
439 628 1.938577 TGTAGTCGTCGCTAGATGGTC 59.061 52.381 0.00 0.00 34.23 4.02
444 633 1.535896 TCGTCGCTAGATGGTCTATGC 59.464 52.381 0.00 0.00 34.23 3.14
446 635 2.095008 CGTCGCTAGATGGTCTATGCAT 60.095 50.000 3.79 3.79 0.00 3.96
447 636 3.612717 CGTCGCTAGATGGTCTATGCATT 60.613 47.826 3.54 0.00 0.00 3.56
453 642 5.123502 GCTAGATGGTCTATGCATTTGGATG 59.876 44.000 3.54 0.00 36.32 3.51
454 643 5.057843 AGATGGTCTATGCATTTGGATGT 57.942 39.130 3.54 0.00 35.63 3.06
455 644 6.191657 AGATGGTCTATGCATTTGGATGTA 57.808 37.500 3.54 0.00 35.63 2.29
456 645 6.236409 AGATGGTCTATGCATTTGGATGTAG 58.764 40.000 3.54 0.00 35.63 2.74
457 646 5.372343 TGGTCTATGCATTTGGATGTAGT 57.628 39.130 3.54 0.00 35.63 2.73
458 647 5.754782 TGGTCTATGCATTTGGATGTAGTT 58.245 37.500 3.54 0.00 35.63 2.24
460 649 6.663093 TGGTCTATGCATTTGGATGTAGTTTT 59.337 34.615 3.54 0.00 35.63 2.43
462 651 8.682710 GGTCTATGCATTTGGATGTAGTTTTTA 58.317 33.333 3.54 0.00 35.63 1.52
482 671 9.620660 GTTTTTATTATTTCTTGTGGTCGATGT 57.379 29.630 0.00 0.00 0.00 3.06
487 676 4.330944 TTTCTTGTGGTCGATGTACTGT 57.669 40.909 0.00 0.00 0.00 3.55
488 677 4.330944 TTCTTGTGGTCGATGTACTGTT 57.669 40.909 0.00 0.00 0.00 3.16
489 678 3.649073 TCTTGTGGTCGATGTACTGTTG 58.351 45.455 0.00 0.00 0.00 3.33
490 679 3.069016 TCTTGTGGTCGATGTACTGTTGT 59.931 43.478 0.00 0.00 0.00 3.32
495 684 3.993736 TGGTCGATGTACTGTTGTGATTG 59.006 43.478 0.00 0.00 0.00 2.67
496 685 4.242475 GGTCGATGTACTGTTGTGATTGA 58.758 43.478 0.00 0.00 0.00 2.57
497 686 4.688879 GGTCGATGTACTGTTGTGATTGAA 59.311 41.667 0.00 0.00 0.00 2.69
499 688 5.633601 GTCGATGTACTGTTGTGATTGAAGA 59.366 40.000 0.00 0.00 0.00 2.87
500 689 5.633601 TCGATGTACTGTTGTGATTGAAGAC 59.366 40.000 0.00 0.00 0.00 3.01
501 690 5.443301 CGATGTACTGTTGTGATTGAAGACG 60.443 44.000 0.00 0.00 0.00 4.18
502 691 4.939271 TGTACTGTTGTGATTGAAGACGA 58.061 39.130 0.00 0.00 0.00 4.20
503 692 5.353111 TGTACTGTTGTGATTGAAGACGAA 58.647 37.500 0.00 0.00 0.00 3.85
504 693 5.462068 TGTACTGTTGTGATTGAAGACGAAG 59.538 40.000 0.00 0.00 0.00 3.79
524 713 8.897872 ACGAAGTAGATAGGAAGTTTTTCAAA 57.102 30.769 0.00 0.00 41.94 2.69
525 714 9.333724 ACGAAGTAGATAGGAAGTTTTTCAAAA 57.666 29.630 0.00 0.00 41.94 2.44
570 759 9.463443 AGCATGTTGTGTTTCTAGAAATAAAAC 57.537 29.630 28.22 28.22 38.97 2.43
582 771 8.950007 TCTAGAAATAAAACCTTGGAACCATT 57.050 30.769 0.00 0.00 0.00 3.16
590 779 3.708451 ACCTTGGAACCATTTATCACCC 58.292 45.455 0.00 0.00 0.00 4.61
591 780 3.031013 CCTTGGAACCATTTATCACCCC 58.969 50.000 0.00 0.00 0.00 4.95
594 783 2.024464 TGGAACCATTTATCACCCCTGG 60.024 50.000 0.00 0.00 0.00 4.45
610 812 1.067635 CCTGGCCAAAACCAATCGAAG 60.068 52.381 7.01 0.00 39.86 3.79
638 840 0.515564 CGTGTCATCCGGGAACAAAC 59.484 55.000 0.00 0.00 0.00 2.93
659 861 1.444212 CCCGCGCAAGATTTGGTTG 60.444 57.895 8.75 0.00 43.02 3.77
660 862 2.088178 CCGCGCAAGATTTGGTTGC 61.088 57.895 8.75 0.00 45.68 4.17
788 1000 4.544689 CTCGAGCGACGCCTCCTG 62.545 72.222 17.79 2.01 42.26 3.86
985 1226 4.426313 CGACCCCCTGCCCCTTTC 62.426 72.222 0.00 0.00 0.00 2.62
1022 1263 1.258982 GCTTCTGCGTTATCGTGGATG 59.741 52.381 0.00 0.00 39.49 3.51
1227 1485 4.531912 CAGCATTCGCAGCAGCCG 62.532 66.667 0.00 0.00 42.27 5.52
1230 1488 4.531912 CATTCGCAGCAGCCGCAG 62.532 66.667 0.58 0.00 42.27 5.18
1257 1515 3.891586 GAAGACGACGACGCAGCCA 62.892 63.158 7.30 0.00 43.96 4.75
1277 1557 3.447634 CTCCGACGCAGAGCTCGAG 62.448 68.421 8.45 8.45 33.54 4.04
1302 1582 2.752238 AGAGGCTGACGACGAGGG 60.752 66.667 0.00 0.00 0.00 4.30
1355 1635 3.827898 CGGAGCTCCACGGAGTCC 61.828 72.222 31.67 16.51 41.61 3.85
1358 1638 2.752238 AGCTCCACGGAGTCCTCG 60.752 66.667 14.48 0.00 41.61 4.63
1522 1802 4.388499 CCCCAAGTACGCGCCACT 62.388 66.667 5.73 7.16 0.00 4.00
1527 1815 3.338126 AAGTACGCGCCACTCTCCG 62.338 63.158 13.65 0.00 0.00 4.63
1536 1824 2.360980 CACTCTCCGTCCCCCTCT 59.639 66.667 0.00 0.00 0.00 3.69
1538 1826 2.360980 CTCTCCGTCCCCCTCTGT 59.639 66.667 0.00 0.00 0.00 3.41
1539 1827 1.755008 CTCTCCGTCCCCCTCTGTC 60.755 68.421 0.00 0.00 0.00 3.51
1540 1828 2.760385 CTCCGTCCCCCTCTGTCC 60.760 72.222 0.00 0.00 0.00 4.02
1541 1829 4.753662 TCCGTCCCCCTCTGTCCG 62.754 72.222 0.00 0.00 0.00 4.79
1577 1868 0.040425 GCTTTCTTTCTTGCGGCGAA 60.040 50.000 12.98 0.00 0.00 4.70
2090 2608 1.599576 GTCCCCTGGAAGTGAGCTC 59.400 63.158 6.82 6.82 31.38 4.09
2148 2680 8.555166 TTCGTTTCTTTACTTATGCAAAGTTG 57.445 30.769 16.02 9.50 34.17 3.16
2161 2693 1.476085 CAAAGTTGGTGTCCTGTTGCA 59.524 47.619 0.00 0.00 0.00 4.08
2253 2785 8.405418 ACTGATCAAATTGGATATCCTTGATG 57.595 34.615 29.03 21.46 38.06 3.07
2265 2797 2.806434 TCCTTGATGTGGGTGAATTGG 58.194 47.619 0.00 0.00 0.00 3.16
2269 2801 1.273154 TGATGTGGGTGAATTGGCCAT 60.273 47.619 6.09 0.00 0.00 4.40
2274 2806 1.133199 TGGGTGAATTGGCCATATCCC 60.133 52.381 6.09 14.98 34.77 3.85
2293 2825 5.138125 TCCCGTAGTACTTTTACAAGTGG 57.862 43.478 0.00 0.00 43.54 4.00
2303 2835 9.844790 AGTACTTTTACAAGTGGTTTTTGTTAC 57.155 29.630 4.49 0.00 43.54 2.50
2306 2838 8.081025 ACTTTTACAAGTGGTTTTTGTTACGAA 58.919 29.630 0.00 0.00 42.05 3.85
2308 2840 8.983307 TTTACAAGTGGTTTTTGTTACGAATT 57.017 26.923 0.00 0.00 39.36 2.17
2315 2858 8.079809 AGTGGTTTTTGTTACGAATTAGATTGG 58.920 33.333 0.00 0.00 0.00 3.16
2323 2866 4.096732 ACGAATTAGATTGGTTGCTTGC 57.903 40.909 0.00 0.00 0.00 4.01
2369 2912 3.684305 TGTCATGAACTGATGCTTTACGG 59.316 43.478 0.00 0.00 35.97 4.02
2379 2922 3.189702 TGATGCTTTACGGTTTGGTTAGC 59.810 43.478 0.00 0.00 0.00 3.09
2408 2951 1.215014 GGTTGCTTTGCTTGCGGTTC 61.215 55.000 0.00 0.00 0.00 3.62
2410 2953 0.388659 TTGCTTTGCTTGCGGTTCAT 59.611 45.000 0.00 0.00 0.00 2.57
2497 3070 2.203337 ACAGTGCATTGCGTGGGT 60.203 55.556 9.42 3.23 0.00 4.51
2498 3071 2.260869 ACAGTGCATTGCGTGGGTC 61.261 57.895 9.42 0.00 0.00 4.46
2499 3072 1.968017 CAGTGCATTGCGTGGGTCT 60.968 57.895 3.84 0.00 0.00 3.85
2500 3073 1.968017 AGTGCATTGCGTGGGTCTG 60.968 57.895 3.84 0.00 0.00 3.51
2501 3074 2.112928 TGCATTGCGTGGGTCTGT 59.887 55.556 3.84 0.00 0.00 3.41
2502 3075 0.953471 GTGCATTGCGTGGGTCTGTA 60.953 55.000 3.84 0.00 0.00 2.74
2503 3076 0.953471 TGCATTGCGTGGGTCTGTAC 60.953 55.000 3.84 0.00 0.00 2.90
2514 3087 3.195825 GTGGGTCTGTACTCTGTAGCATT 59.804 47.826 0.00 0.00 0.00 3.56
2551 3124 1.019278 TTGCTTCGCTGATTCCGTCC 61.019 55.000 0.00 0.00 0.00 4.79
2603 3177 4.884164 GCTTGTAAGAATATGGCAGACCTT 59.116 41.667 0.00 0.00 36.63 3.50
2614 3188 1.597742 GCAGACCTTGAGCAAAGTGA 58.402 50.000 0.00 0.00 33.66 3.41
2673 3252 3.653835 AAGCTGTCCTTTTATCCCCTC 57.346 47.619 0.00 0.00 0.00 4.30
2795 3378 1.352352 CCAGAGGAATTGACCCTGTGT 59.648 52.381 7.71 0.00 41.85 3.72
2796 3379 2.430465 CAGAGGAATTGACCCTGTGTG 58.570 52.381 0.00 0.00 39.45 3.82
2969 3556 4.899352 ATCCATCAGCCTATGTCTAACC 57.101 45.455 0.00 0.00 0.00 2.85
3086 3673 4.518970 TGCACCCTTCAATAGTTTCTTGAC 59.481 41.667 0.00 0.00 32.57 3.18
3139 3726 0.733150 GTTCCAGATAGTTTGGCGGC 59.267 55.000 0.00 0.00 35.62 6.53
3182 3769 5.969423 TCGTTATCTTTTATCTCGGTTGGT 58.031 37.500 0.00 0.00 0.00 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.581934 CGTGTCAAAAGAGAGCACCA 58.418 50.000 0.00 0.00 0.00 4.17
12 13 4.228567 TGTGCGGAGGCGTGTCAA 62.229 61.111 0.00 0.00 44.10 3.18
13 14 4.961511 GTGTGCGGAGGCGTGTCA 62.962 66.667 0.00 0.00 44.10 3.58
15 16 4.969196 CAGTGTGCGGAGGCGTGT 62.969 66.667 0.00 0.00 44.10 4.49
24 25 3.502920 CCTTAACTACTCTCAGTGTGCG 58.497 50.000 0.00 0.00 0.00 5.34
25 26 3.258622 ACCCTTAACTACTCTCAGTGTGC 59.741 47.826 0.00 0.00 0.00 4.57
27 28 6.313324 AGTAACCCTTAACTACTCTCAGTGT 58.687 40.000 0.00 0.00 0.00 3.55
28 29 6.837471 AGTAACCCTTAACTACTCTCAGTG 57.163 41.667 0.00 0.00 0.00 3.66
31 32 7.341256 CCACATAGTAACCCTTAACTACTCTCA 59.659 40.741 0.00 0.00 31.30 3.27
58 59 6.768861 GCATCCCTACTCGAGATGTATATACT 59.231 42.308 21.68 0.00 39.66 2.12
61 62 5.761205 AGCATCCCTACTCGAGATGTATAT 58.239 41.667 21.68 2.35 39.66 0.86
118 119 9.623000 AAGGGGTGAAGTATATGTGTTATAAAC 57.377 33.333 0.00 0.00 0.00 2.01
124 125 8.943594 TTTAAAAGGGGTGAAGTATATGTGTT 57.056 30.769 0.00 0.00 0.00 3.32
147 148 9.341078 AGCTTTGAATTGGTGAAATATTGTTTT 57.659 25.926 0.00 0.00 0.00 2.43
175 176 2.485426 GTGTCATGTCATGTTCACAGGG 59.515 50.000 24.43 0.00 36.77 4.45
190 191 8.637196 TTGAAGACCGAGATATATAGTGTCAT 57.363 34.615 0.00 0.00 0.00 3.06
195 196 7.741027 TCGTTTGAAGACCGAGATATATAGT 57.259 36.000 0.00 0.00 0.00 2.12
206 207 1.128692 GGCATTCTCGTTTGAAGACCG 59.871 52.381 0.00 0.00 0.00 4.79
208 209 3.896648 TTGGCATTCTCGTTTGAAGAC 57.103 42.857 0.00 0.00 0.00 3.01
210 211 5.095490 GGTAATTGGCATTCTCGTTTGAAG 58.905 41.667 0.00 0.00 0.00 3.02
212 213 4.075682 TGGTAATTGGCATTCTCGTTTGA 58.924 39.130 0.00 0.00 0.00 2.69
213 214 4.433186 TGGTAATTGGCATTCTCGTTTG 57.567 40.909 0.00 0.00 0.00 2.93
215 216 5.410067 CAATTGGTAATTGGCATTCTCGTT 58.590 37.500 0.00 0.00 43.50 3.85
217 218 3.798337 GCAATTGGTAATTGGCATTCTCG 59.202 43.478 7.72 0.00 46.47 4.04
232 233 4.155826 TGAAAGAATAGTGACGGCAATTGG 59.844 41.667 0.00 0.00 0.00 3.16
238 239 3.585862 TCACTGAAAGAATAGTGACGGC 58.414 45.455 3.18 0.00 45.97 5.68
274 275 7.996644 GGGGACACCTAATCAAGTAAATCATTA 59.003 37.037 0.00 0.00 36.80 1.90
295 484 4.159693 GGGATTGACAAAGTTATTGGGGAC 59.840 45.833 0.00 0.00 0.00 4.46
296 485 4.202727 TGGGATTGACAAAGTTATTGGGGA 60.203 41.667 0.00 0.00 0.00 4.81
297 486 4.093011 TGGGATTGACAAAGTTATTGGGG 58.907 43.478 0.00 0.00 0.00 4.96
300 489 7.063308 CGGATTTTGGGATTGACAAAGTTATTG 59.937 37.037 0.00 0.00 38.84 1.90
301 490 7.096551 CGGATTTTGGGATTGACAAAGTTATT 58.903 34.615 0.00 0.00 38.84 1.40
303 492 5.565834 GCGGATTTTGGGATTGACAAAGTTA 60.566 40.000 0.00 0.00 38.84 2.24
304 493 4.799255 GCGGATTTTGGGATTGACAAAGTT 60.799 41.667 0.00 0.00 38.84 2.66
305 494 3.306019 GCGGATTTTGGGATTGACAAAGT 60.306 43.478 0.00 0.00 38.84 2.66
307 496 2.028567 GGCGGATTTTGGGATTGACAAA 60.029 45.455 0.00 0.00 36.15 2.83
308 497 1.548269 GGCGGATTTTGGGATTGACAA 59.452 47.619 0.00 0.00 0.00 3.18
309 498 1.181786 GGCGGATTTTGGGATTGACA 58.818 50.000 0.00 0.00 0.00 3.58
311 500 1.181786 GTGGCGGATTTTGGGATTGA 58.818 50.000 0.00 0.00 0.00 2.57
313 502 0.975556 GGGTGGCGGATTTTGGGATT 60.976 55.000 0.00 0.00 0.00 3.01
315 504 2.036572 GGGTGGCGGATTTTGGGA 59.963 61.111 0.00 0.00 0.00 4.37
316 505 3.074369 GGGGTGGCGGATTTTGGG 61.074 66.667 0.00 0.00 0.00 4.12
317 506 2.283532 TGGGGTGGCGGATTTTGG 60.284 61.111 0.00 0.00 0.00 3.28
320 509 1.789576 AAGACTGGGGTGGCGGATTT 61.790 55.000 0.00 0.00 0.00 2.17
322 511 1.789576 AAAAGACTGGGGTGGCGGAT 61.790 55.000 0.00 0.00 0.00 4.18
323 512 1.128809 TAAAAGACTGGGGTGGCGGA 61.129 55.000 0.00 0.00 0.00 5.54
325 514 0.323629 TCTAAAAGACTGGGGTGGCG 59.676 55.000 0.00 0.00 0.00 5.69
327 516 3.328050 AGACTTCTAAAAGACTGGGGTGG 59.672 47.826 0.00 0.00 36.38 4.61
329 518 4.658901 TGAAGACTTCTAAAAGACTGGGGT 59.341 41.667 16.02 0.00 37.53 4.95
330 519 4.998033 GTGAAGACTTCTAAAAGACTGGGG 59.002 45.833 16.02 0.00 37.53 4.96
331 520 5.467063 GTGTGAAGACTTCTAAAAGACTGGG 59.533 44.000 16.02 0.00 37.53 4.45
334 523 5.163437 ACCGTGTGAAGACTTCTAAAAGACT 60.163 40.000 16.02 0.00 38.83 3.24
337 526 4.318831 GCACCGTGTGAAGACTTCTAAAAG 60.319 45.833 16.02 5.40 35.23 2.27
338 527 3.558418 GCACCGTGTGAAGACTTCTAAAA 59.442 43.478 16.02 0.00 35.23 1.52
341 530 1.335597 CGCACCGTGTGAAGACTTCTA 60.336 52.381 16.02 3.03 35.23 2.10
343 532 1.853319 CGCACCGTGTGAAGACTTC 59.147 57.895 6.18 8.34 35.23 3.01
345 534 2.661866 GCGCACCGTGTGAAGACT 60.662 61.111 16.31 0.00 35.23 3.24
349 538 4.908687 AGCAGCGCACCGTGTGAA 62.909 61.111 16.31 0.00 35.23 3.18
356 545 4.724602 TCGTCAGAGCAGCGCACC 62.725 66.667 11.47 0.00 0.00 5.01
357 546 3.177920 CTCGTCAGAGCAGCGCAC 61.178 66.667 11.47 0.00 37.73 5.34
360 549 1.062365 CTCTCTCGTCAGAGCAGCG 59.938 63.158 0.00 0.00 45.46 5.18
361 550 0.378257 CTCTCTCTCGTCAGAGCAGC 59.622 60.000 8.11 0.00 45.46 5.25
363 552 0.326595 ACCTCTCTCTCGTCAGAGCA 59.673 55.000 8.11 0.00 45.46 4.26
364 553 0.732571 CACCTCTCTCTCGTCAGAGC 59.267 60.000 8.11 0.00 45.46 4.09
366 555 2.237392 TCATCACCTCTCTCTCGTCAGA 59.763 50.000 0.00 0.00 0.00 3.27
368 557 2.290323 TGTCATCACCTCTCTCTCGTCA 60.290 50.000 0.00 0.00 0.00 4.35
370 559 2.364632 CTGTCATCACCTCTCTCTCGT 58.635 52.381 0.00 0.00 0.00 4.18
371 560 1.065401 GCTGTCATCACCTCTCTCTCG 59.935 57.143 0.00 0.00 0.00 4.04
375 564 0.814457 GTCGCTGTCATCACCTCTCT 59.186 55.000 0.00 0.00 0.00 3.10
376 565 0.524392 CGTCGCTGTCATCACCTCTC 60.524 60.000 0.00 0.00 0.00 3.20
378 567 2.161486 GCGTCGCTGTCATCACCTC 61.161 63.158 10.68 0.00 0.00 3.85
380 569 3.545481 CGCGTCGCTGTCATCACC 61.545 66.667 16.36 0.00 0.00 4.02
382 571 2.472232 AAGACGCGTCGCTGTCATCA 62.472 55.000 31.56 0.00 35.68 3.07
385 574 2.428569 GAAGACGCGTCGCTGTCA 60.429 61.111 31.56 0.00 35.68 3.58
386 575 3.524759 CGAAGACGCGTCGCTGTC 61.525 66.667 31.56 24.19 34.33 3.51
391 580 3.827784 CAAGCCGAAGACGCGTCG 61.828 66.667 31.56 21.45 38.29 5.12
393 582 4.664677 AGCAAGCCGAAGACGCGT 62.665 61.111 13.85 13.85 38.29 6.01
395 584 2.476499 GAAGCAAGCCGAAGACGC 59.524 61.111 0.00 0.00 38.29 5.19
396 585 1.557443 AACGAAGCAAGCCGAAGACG 61.557 55.000 0.00 0.00 39.43 4.18
398 587 0.865769 GAAACGAAGCAAGCCGAAGA 59.134 50.000 0.00 0.00 0.00 2.87
399 588 0.451135 CGAAACGAAGCAAGCCGAAG 60.451 55.000 0.00 0.00 0.00 3.79
401 590 1.593209 ACGAAACGAAGCAAGCCGA 60.593 52.632 0.00 0.00 0.00 5.54
402 591 1.438710 CACGAAACGAAGCAAGCCG 60.439 57.895 0.00 0.00 0.00 5.52
404 593 1.525619 ACTACACGAAACGAAGCAAGC 59.474 47.619 0.00 0.00 0.00 4.01
405 594 2.160143 CGACTACACGAAACGAAGCAAG 60.160 50.000 0.00 0.00 35.09 4.01
406 595 1.782569 CGACTACACGAAACGAAGCAA 59.217 47.619 0.00 0.00 35.09 3.91
407 596 1.268692 ACGACTACACGAAACGAAGCA 60.269 47.619 0.00 0.00 37.03 3.91
408 597 1.381429 GACGACTACACGAAACGAAGC 59.619 52.381 0.00 0.00 37.03 3.86
410 599 1.662360 CGACGACTACACGAAACGAA 58.338 50.000 0.00 0.00 37.03 3.85
411 600 0.722469 GCGACGACTACACGAAACGA 60.722 55.000 0.00 0.00 37.03 3.85
414 603 2.068519 TCTAGCGACGACTACACGAAA 58.931 47.619 0.00 0.00 37.03 3.46
415 604 1.713597 TCTAGCGACGACTACACGAA 58.286 50.000 0.00 0.00 37.03 3.85
417 606 1.332993 CCATCTAGCGACGACTACACG 60.333 57.143 0.00 0.00 39.31 4.49
420 609 2.211806 AGACCATCTAGCGACGACTAC 58.788 52.381 0.00 0.00 0.00 2.73
421 610 2.616634 AGACCATCTAGCGACGACTA 57.383 50.000 0.00 0.00 0.00 2.59
422 611 2.616634 TAGACCATCTAGCGACGACT 57.383 50.000 0.00 0.00 0.00 4.18
423 612 2.666069 GCATAGACCATCTAGCGACGAC 60.666 54.545 0.00 0.00 31.67 4.34
424 613 1.535896 GCATAGACCATCTAGCGACGA 59.464 52.381 0.00 0.00 31.67 4.20
426 615 3.584406 ATGCATAGACCATCTAGCGAC 57.416 47.619 0.00 0.00 31.67 5.19
428 617 3.434641 CCAAATGCATAGACCATCTAGCG 59.565 47.826 0.00 0.00 31.67 4.26
429 618 4.645535 TCCAAATGCATAGACCATCTAGC 58.354 43.478 0.00 0.00 31.67 3.42
430 619 6.236409 ACATCCAAATGCATAGACCATCTAG 58.764 40.000 0.00 0.00 36.26 2.43
432 621 5.057843 ACATCCAAATGCATAGACCATCT 57.942 39.130 0.00 0.00 36.26 2.90
433 622 6.000219 ACTACATCCAAATGCATAGACCATC 59.000 40.000 0.00 0.00 36.26 3.51
436 625 6.699575 AAACTACATCCAAATGCATAGACC 57.300 37.500 0.00 0.00 36.26 3.85
455 644 9.840427 CATCGACCACAAGAAATAATAAAAACT 57.160 29.630 0.00 0.00 0.00 2.66
456 645 9.620660 ACATCGACCACAAGAAATAATAAAAAC 57.379 29.630 0.00 0.00 0.00 2.43
460 649 9.093970 CAGTACATCGACCACAAGAAATAATAA 57.906 33.333 0.00 0.00 0.00 1.40
462 651 7.103641 ACAGTACATCGACCACAAGAAATAAT 58.896 34.615 0.00 0.00 0.00 1.28
463 652 6.460781 ACAGTACATCGACCACAAGAAATAA 58.539 36.000 0.00 0.00 0.00 1.40
464 653 6.032956 ACAGTACATCGACCACAAGAAATA 57.967 37.500 0.00 0.00 0.00 1.40
465 654 4.894784 ACAGTACATCGACCACAAGAAAT 58.105 39.130 0.00 0.00 0.00 2.17
466 655 4.330944 ACAGTACATCGACCACAAGAAA 57.669 40.909 0.00 0.00 0.00 2.52
468 657 3.069016 ACAACAGTACATCGACCACAAGA 59.931 43.478 0.00 0.00 0.00 3.02
469 658 3.184379 CACAACAGTACATCGACCACAAG 59.816 47.826 0.00 0.00 0.00 3.16
470 659 3.127589 CACAACAGTACATCGACCACAA 58.872 45.455 0.00 0.00 0.00 3.33
471 660 2.362717 TCACAACAGTACATCGACCACA 59.637 45.455 0.00 0.00 0.00 4.17
473 662 3.953712 ATCACAACAGTACATCGACCA 57.046 42.857 0.00 0.00 0.00 4.02
475 664 5.633601 TCTTCAATCACAACAGTACATCGAC 59.366 40.000 0.00 0.00 0.00 4.20
478 667 5.633601 TCGTCTTCAATCACAACAGTACATC 59.366 40.000 0.00 0.00 0.00 3.06
479 668 5.538118 TCGTCTTCAATCACAACAGTACAT 58.462 37.500 0.00 0.00 0.00 2.29
482 671 5.597806 ACTTCGTCTTCAATCACAACAGTA 58.402 37.500 0.00 0.00 0.00 2.74
483 672 4.442706 ACTTCGTCTTCAATCACAACAGT 58.557 39.130 0.00 0.00 0.00 3.55
484 673 5.920840 TCTACTTCGTCTTCAATCACAACAG 59.079 40.000 0.00 0.00 0.00 3.16
487 676 7.122204 TCCTATCTACTTCGTCTTCAATCACAA 59.878 37.037 0.00 0.00 0.00 3.33
488 677 6.602009 TCCTATCTACTTCGTCTTCAATCACA 59.398 38.462 0.00 0.00 0.00 3.58
489 678 7.028926 TCCTATCTACTTCGTCTTCAATCAC 57.971 40.000 0.00 0.00 0.00 3.06
490 679 7.339721 ACTTCCTATCTACTTCGTCTTCAATCA 59.660 37.037 0.00 0.00 0.00 2.57
495 684 8.760103 AAAAACTTCCTATCTACTTCGTCTTC 57.240 34.615 0.00 0.00 0.00 2.87
496 685 8.365647 TGAAAAACTTCCTATCTACTTCGTCTT 58.634 33.333 0.00 0.00 0.00 3.01
497 686 7.893658 TGAAAAACTTCCTATCTACTTCGTCT 58.106 34.615 0.00 0.00 0.00 4.18
499 688 8.897872 TTTGAAAAACTTCCTATCTACTTCGT 57.102 30.769 0.00 0.00 0.00 3.85
524 713 9.243105 ACATGCTTTGTAGACTATTACCATTTT 57.757 29.630 0.00 0.00 36.57 1.82
525 714 8.807948 ACATGCTTTGTAGACTATTACCATTT 57.192 30.769 0.00 0.00 36.57 2.32
526 715 8.677300 CAACATGCTTTGTAGACTATTACCATT 58.323 33.333 0.00 0.00 37.68 3.16
528 717 7.119116 CACAACATGCTTTGTAGACTATTACCA 59.881 37.037 1.72 0.00 37.62 3.25
529 718 7.119262 ACACAACATGCTTTGTAGACTATTACC 59.881 37.037 1.72 0.00 37.62 2.85
530 719 8.029642 ACACAACATGCTTTGTAGACTATTAC 57.970 34.615 1.72 0.00 37.62 1.89
532 721 7.510549 AACACAACATGCTTTGTAGACTATT 57.489 32.000 1.72 0.00 37.62 1.73
535 724 5.590259 AGAAACACAACATGCTTTGTAGACT 59.410 36.000 1.72 0.00 37.62 3.24
541 730 7.935338 ATTTCTAGAAACACAACATGCTTTG 57.065 32.000 19.94 0.00 32.51 2.77
544 733 9.463443 GTTTTATTTCTAGAAACACAACATGCT 57.537 29.630 19.94 3.24 34.34 3.79
570 759 3.031013 GGGGTGATAAATGGTTCCAAGG 58.969 50.000 0.00 0.00 0.00 3.61
582 771 1.551329 GGTTTTGGCCAGGGGTGATAA 60.551 52.381 5.11 0.00 0.00 1.75
590 779 0.965439 TTCGATTGGTTTTGGCCAGG 59.035 50.000 5.11 0.00 40.01 4.45
591 780 1.669795 GCTTCGATTGGTTTTGGCCAG 60.670 52.381 5.11 0.00 40.01 4.85
594 783 2.061028 CTTGCTTCGATTGGTTTTGGC 58.939 47.619 0.00 0.00 0.00 4.52
610 812 2.690778 GGATGACACGCCACCTTGC 61.691 63.158 0.00 0.00 0.00 4.01
638 840 2.764314 CCAAATCTTGCGCGGGAGG 61.764 63.158 8.83 0.00 0.00 4.30
659 861 4.299316 GTCGCGCCGATGGATTGC 62.299 66.667 0.00 0.00 38.42 3.56
660 862 3.640000 GGTCGCGCCGATGGATTG 61.640 66.667 0.00 0.00 38.42 2.67
661 863 4.910585 GGGTCGCGCCGATGGATT 62.911 66.667 0.00 0.00 38.42 3.01
1045 1286 1.677820 CGTATTTCCACTCACACCCCC 60.678 57.143 0.00 0.00 0.00 5.40
1226 1484 1.206072 GTCTTCTTGTGCTGCTGCG 59.794 57.895 11.21 0.00 43.34 5.18
1227 1485 1.206072 CGTCTTCTTGTGCTGCTGC 59.794 57.895 8.89 8.89 40.20 5.25
1228 1486 0.510359 GTCGTCTTCTTGTGCTGCTG 59.490 55.000 0.00 0.00 0.00 4.41
1229 1487 0.941463 CGTCGTCTTCTTGTGCTGCT 60.941 55.000 0.00 0.00 0.00 4.24
1230 1488 0.939577 TCGTCGTCTTCTTGTGCTGC 60.940 55.000 0.00 0.00 0.00 5.25
1231 1489 0.778815 GTCGTCGTCTTCTTGTGCTG 59.221 55.000 0.00 0.00 0.00 4.41
1232 1490 0.660595 CGTCGTCGTCTTCTTGTGCT 60.661 55.000 0.00 0.00 0.00 4.40
1233 1491 1.767388 CGTCGTCGTCTTCTTGTGC 59.233 57.895 0.00 0.00 0.00 4.57
1234 1492 0.933047 TGCGTCGTCGTCTTCTTGTG 60.933 55.000 3.66 0.00 39.49 3.33
1235 1493 0.660595 CTGCGTCGTCGTCTTCTTGT 60.661 55.000 3.66 0.00 39.49 3.16
1236 1494 1.935065 GCTGCGTCGTCGTCTTCTTG 61.935 60.000 3.66 0.00 39.49 3.02
1237 1495 1.729838 GCTGCGTCGTCGTCTTCTT 60.730 57.895 3.66 0.00 39.49 2.52
1260 1518 3.500642 CTCGAGCTCTGCGTCGGA 61.501 66.667 12.85 0.00 36.81 4.55
1264 1522 2.745785 CGAGTCTCGAGCTCTGCGT 61.746 63.158 24.55 0.00 43.74 5.24
1277 1557 0.741574 TCGTCAGCCTCTCTCGAGTC 60.742 60.000 13.13 0.00 35.43 3.36
1522 1802 2.359404 GACAGAGGGGGACGGAGA 59.641 66.667 0.00 0.00 0.00 3.71
1527 1815 2.657066 GGAACGGACAGAGGGGGAC 61.657 68.421 0.00 0.00 0.00 4.46
1577 1868 1.956170 CAACGAACTCCTGCGCAGT 60.956 57.895 33.75 17.38 0.00 4.40
1584 2089 1.057851 TCCCAACCCAACGAACTCCT 61.058 55.000 0.00 0.00 0.00 3.69
1876 2381 2.506472 GGAGGGGTCGATTGAGGC 59.494 66.667 0.00 0.00 0.00 4.70
1880 2385 4.547367 GCGGGGAGGGGTCGATTG 62.547 72.222 0.00 0.00 0.00 2.67
2090 2608 2.203126 GAGGAGGATGGCGCAAGG 60.203 66.667 10.83 0.00 38.28 3.61
2148 2680 3.383761 CAGAAATTTGCAACAGGACACC 58.616 45.455 0.00 0.00 0.00 4.16
2253 2785 1.963515 GGATATGGCCAATTCACCCAC 59.036 52.381 10.96 0.00 0.00 4.61
2265 2797 5.846203 TGTAAAAGTACTACGGGATATGGC 58.154 41.667 0.00 0.00 0.00 4.40
2269 2801 6.437162 ACCACTTGTAAAAGTACTACGGGATA 59.563 38.462 0.00 0.00 0.00 2.59
2274 2806 8.177013 ACAAAAACCACTTGTAAAAGTACTACG 58.823 33.333 0.00 0.00 35.26 3.51
2293 2825 8.211838 GCAACCAATCTAATTCGTAACAAAAAC 58.788 33.333 0.00 0.00 0.00 2.43
2303 2835 4.361451 AGCAAGCAACCAATCTAATTCG 57.639 40.909 0.00 0.00 0.00 3.34
2306 2838 5.012239 TCTCAAGCAAGCAACCAATCTAAT 58.988 37.500 0.00 0.00 0.00 1.73
2308 2840 4.019792 TCTCAAGCAAGCAACCAATCTA 57.980 40.909 0.00 0.00 0.00 1.98
2309 2841 2.867624 TCTCAAGCAAGCAACCAATCT 58.132 42.857 0.00 0.00 0.00 2.40
2315 2858 1.538512 TGCAGATCTCAAGCAAGCAAC 59.461 47.619 3.85 0.00 34.97 4.17
2323 2866 2.084610 TGTCCGTTGCAGATCTCAAG 57.915 50.000 0.00 0.00 0.00 3.02
2379 2922 1.665169 GCAAAGCAACCTTGGTGTTTG 59.335 47.619 13.69 13.69 39.13 2.93
2442 3011 2.122768 ACAACATCTCCTGGGGATCTC 58.877 52.381 5.96 0.00 0.00 2.75
2497 3070 8.293699 TCAAATCTAATGCTACAGAGTACAGA 57.706 34.615 0.00 0.00 0.00 3.41
2498 3071 8.812329 GTTCAAATCTAATGCTACAGAGTACAG 58.188 37.037 0.00 0.00 0.00 2.74
2499 3072 8.311109 TGTTCAAATCTAATGCTACAGAGTACA 58.689 33.333 0.00 0.00 0.00 2.90
2500 3073 8.703604 TGTTCAAATCTAATGCTACAGAGTAC 57.296 34.615 0.00 0.00 0.00 2.73
2501 3074 8.749354 TCTGTTCAAATCTAATGCTACAGAGTA 58.251 33.333 0.00 0.00 35.84 2.59
2502 3075 7.615403 TCTGTTCAAATCTAATGCTACAGAGT 58.385 34.615 0.00 0.00 35.84 3.24
2503 3076 8.659925 ATCTGTTCAAATCTAATGCTACAGAG 57.340 34.615 0.00 0.00 39.85 3.35
2603 3177 2.627699 GGTTCCCAAATCACTTTGCTCA 59.372 45.455 0.00 0.00 40.39 4.26
2614 3188 4.746466 TGGTATTCAGTTGGTTCCCAAAT 58.254 39.130 0.00 0.00 45.73 2.32
2673 3252 8.454106 CCACTAGGTGAATTTCAGATTAACTTG 58.546 37.037 0.00 0.00 35.23 3.16
2795 3378 6.969043 ACATCCAATTCTTATAACTGACCCA 58.031 36.000 0.00 0.00 0.00 4.51
2796 3379 7.881775 AACATCCAATTCTTATAACTGACCC 57.118 36.000 0.00 0.00 0.00 4.46
2888 3475 8.405531 GCTGGACATCAAAGTTTGCTTATAATA 58.594 33.333 10.90 0.00 33.95 0.98
3086 3673 3.838903 AGTAACCACACTTCCTAGAAGGG 59.161 47.826 5.06 5.06 35.59 3.95
3139 3726 1.376037 GAACTTGACGAGGGCCAGG 60.376 63.158 6.18 0.00 0.00 4.45
3148 3735 8.861101 AGATAAAAGATAACGAAGAACTTGACG 58.139 33.333 0.00 0.00 0.00 4.35
3182 3769 3.620286 CGAGTGGTTCGTTGCGAA 58.380 55.556 0.00 0.00 44.27 4.70


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

AutoCloner maintained by Alex Coulton.