Multiple sequence alignment - TraesCS3B01G358900

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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 TraesCS3B01G358900 chr3B 100.000 3887 0 0 1 3887 571305100 571301214 0.000000e+00 7179
1 TraesCS3B01G358900 chr3B 97.024 168 4 1 345 512 142684098 142684264 8.220000e-72 281
2 TraesCS3B01G358900 chr3D 94.690 3164 137 9 734 3887 435299691 435296549 0.000000e+00 4883
3 TraesCS3B01G358900 chr3D 95.977 174 6 1 338 510 591102584 591102411 8.220000e-72 281
4 TraesCS3B01G358900 chr3D 89.450 218 21 2 507 723 435299996 435299780 1.380000e-69 274
5 TraesCS3B01G358900 chr3D 85.306 245 14 5 1 245 435300404 435300182 2.340000e-57 233
6 TraesCS3B01G358900 chr3D 95.000 120 2 1 231 346 435300114 435299995 6.630000e-43 185
7 TraesCS3B01G358900 chr3A 96.371 1488 54 0 1265 2752 574017316 574015829 0.000000e+00 2449
8 TraesCS3B01G358900 chr3A 93.275 1145 46 13 2751 3887 574015477 574014356 0.000000e+00 1659
9 TraesCS3B01G358900 chr3A 95.046 323 12 2 1 323 574017639 574017321 4.480000e-139 505
10 TraesCS3B01G358900 chr2D 96.491 171 5 1 345 514 161906852 161907022 8.220000e-72 281
11 TraesCS3B01G358900 chr2D 94.972 179 7 2 337 513 426427793 426427971 2.960000e-71 279
12 TraesCS3B01G358900 chr2D 95.954 173 6 1 337 508 560959477 560959649 2.960000e-71 279
13 TraesCS3B01G358900 chr2A 96.512 172 3 2 340 510 310407931 310408100 8.220000e-72 281
14 TraesCS3B01G358900 chr7D 94.944 178 6 3 345 521 192936020 192936195 3.830000e-70 276
15 TraesCS3B01G358900 chr2B 95.402 174 6 2 345 517 28427337 28427165 3.830000e-70 276
16 TraesCS3B01G358900 chr4B 91.371 197 13 4 318 510 53588030 53587834 2.300000e-67 267


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 TraesCS3B01G358900 chr3B 571301214 571305100 3886 True 7179.000000 7179 100.000000 1 3887 1 chr3B.!!$R1 3886
1 TraesCS3B01G358900 chr3D 435296549 435300404 3855 True 1393.750000 4883 91.111500 1 3887 4 chr3D.!!$R2 3886
2 TraesCS3B01G358900 chr3A 574014356 574017639 3283 True 1537.666667 2449 94.897333 1 3887 3 chr3A.!!$R1 3886

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
950 1125 0.776451 GTGTGCGTGTCTGTCGTTAG 59.224 55.0 0.0 0.0 0.0 2.34 F
1597 1772 0.541764 TTGGTGGATTGGTGAAGGGC 60.542 55.0 0.0 0.0 0.0 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2861 3389 0.472471 TCTGGTTTCCTGGGTGTCAC 59.528 55.0 0.0 0.0 0.0 3.67 R
2987 3515 0.740737 CGTGCATCTCCATTTTCCCC 59.259 55.0 0.0 0.0 0.0 4.81 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
25 26 5.503520 CGCCTTCTGTATTTTCGGGTAATTC 60.504 44.000 0.00 0.00 0.00 2.17
112 113 3.314388 CTGTTGCCGCGGAAAGAGC 62.314 63.158 28.36 13.81 0.00 4.09
147 148 9.039870 CGCATCTAGAGTTCAAATTTCTATTCT 57.960 33.333 0.00 0.00 0.00 2.40
203 204 1.453235 GCTGGCTATGCTCCATGGA 59.547 57.895 15.27 15.27 32.37 3.41
216 217 3.065925 GCTCCATGGACTAGCATGTTTTC 59.934 47.826 11.44 0.00 36.26 2.29
330 417 6.345920 GCAATTAGCAAGTTAGTACATCGT 57.654 37.500 0.00 0.00 44.79 3.73
344 431 9.136952 GTTAGTACATCGTAAACTTTCACATCT 57.863 33.333 0.00 0.00 0.00 2.90
346 433 8.684973 AGTACATCGTAAACTTTCACATCTAC 57.315 34.615 0.00 0.00 0.00 2.59
347 434 8.521176 AGTACATCGTAAACTTTCACATCTACT 58.479 33.333 0.00 0.00 0.00 2.57
348 435 7.813852 ACATCGTAAACTTTCACATCTACTC 57.186 36.000 0.00 0.00 0.00 2.59
349 436 6.812160 ACATCGTAAACTTTCACATCTACTCC 59.188 38.462 0.00 0.00 0.00 3.85
350 437 5.717119 TCGTAAACTTTCACATCTACTCCC 58.283 41.667 0.00 0.00 0.00 4.30
351 438 5.479375 TCGTAAACTTTCACATCTACTCCCT 59.521 40.000 0.00 0.00 0.00 4.20
352 439 5.805994 CGTAAACTTTCACATCTACTCCCTC 59.194 44.000 0.00 0.00 0.00 4.30
353 440 4.828072 AACTTTCACATCTACTCCCTCC 57.172 45.455 0.00 0.00 0.00 4.30
354 441 2.761208 ACTTTCACATCTACTCCCTCCG 59.239 50.000 0.00 0.00 0.00 4.63
355 442 2.526888 TTCACATCTACTCCCTCCGT 57.473 50.000 0.00 0.00 0.00 4.69
356 443 2.526888 TCACATCTACTCCCTCCGTT 57.473 50.000 0.00 0.00 0.00 4.44
357 444 2.376109 TCACATCTACTCCCTCCGTTC 58.624 52.381 0.00 0.00 0.00 3.95
358 445 1.409427 CACATCTACTCCCTCCGTTCC 59.591 57.143 0.00 0.00 0.00 3.62
359 446 1.288335 ACATCTACTCCCTCCGTTCCT 59.712 52.381 0.00 0.00 0.00 3.36
360 447 2.512896 ACATCTACTCCCTCCGTTCCTA 59.487 50.000 0.00 0.00 0.00 2.94
361 448 3.053095 ACATCTACTCCCTCCGTTCCTAA 60.053 47.826 0.00 0.00 0.00 2.69
362 449 3.744940 TCTACTCCCTCCGTTCCTAAA 57.255 47.619 0.00 0.00 0.00 1.85
363 450 4.261411 TCTACTCCCTCCGTTCCTAAAT 57.739 45.455 0.00 0.00 0.00 1.40
364 451 5.393068 TCTACTCCCTCCGTTCCTAAATA 57.607 43.478 0.00 0.00 0.00 1.40
365 452 5.961897 TCTACTCCCTCCGTTCCTAAATAT 58.038 41.667 0.00 0.00 0.00 1.28
366 453 6.379579 TCTACTCCCTCCGTTCCTAAATATT 58.620 40.000 0.00 0.00 0.00 1.28
367 454 5.970501 ACTCCCTCCGTTCCTAAATATTT 57.029 39.130 5.89 5.89 0.00 1.40
368 455 5.681639 ACTCCCTCCGTTCCTAAATATTTG 58.318 41.667 11.05 1.40 0.00 2.32
369 456 5.191124 ACTCCCTCCGTTCCTAAATATTTGT 59.809 40.000 11.05 0.00 0.00 2.83
370 457 5.677567 TCCCTCCGTTCCTAAATATTTGTC 58.322 41.667 11.05 0.00 0.00 3.18
371 458 5.427481 TCCCTCCGTTCCTAAATATTTGTCT 59.573 40.000 11.05 0.00 0.00 3.41
372 459 6.069847 TCCCTCCGTTCCTAAATATTTGTCTT 60.070 38.462 11.05 0.00 0.00 3.01
373 460 6.602009 CCCTCCGTTCCTAAATATTTGTCTTT 59.398 38.462 11.05 0.00 0.00 2.52
374 461 7.122204 CCCTCCGTTCCTAAATATTTGTCTTTT 59.878 37.037 11.05 0.00 0.00 2.27
375 462 8.520351 CCTCCGTTCCTAAATATTTGTCTTTTT 58.480 33.333 11.05 0.00 0.00 1.94
378 465 9.783256 CCGTTCCTAAATATTTGTCTTTTTAGG 57.217 33.333 11.05 12.11 46.30 2.69
391 478 9.541143 TTTGTCTTTTTAGGATTTCAAATGGAC 57.459 29.630 0.00 0.00 0.00 4.02
392 479 8.477419 TGTCTTTTTAGGATTTCAAATGGACT 57.523 30.769 0.00 0.00 0.00 3.85
393 480 9.581289 TGTCTTTTTAGGATTTCAAATGGACTA 57.419 29.630 0.00 0.00 0.00 2.59
394 481 9.841880 GTCTTTTTAGGATTTCAAATGGACTAC 57.158 33.333 0.00 0.00 0.00 2.73
395 482 9.020731 TCTTTTTAGGATTTCAAATGGACTACC 57.979 33.333 0.00 0.00 0.00 3.18
408 495 3.900971 TGGACTACCACATACGGATGTA 58.099 45.455 14.23 0.00 44.82 2.29
409 496 4.476297 TGGACTACCACATACGGATGTAT 58.524 43.478 14.23 7.46 44.82 2.29
410 497 5.633117 TGGACTACCACATACGGATGTATA 58.367 41.667 14.23 8.27 44.82 1.47
411 498 6.250711 TGGACTACCACATACGGATGTATAT 58.749 40.000 14.23 4.37 44.82 0.86
412 499 6.376299 TGGACTACCACATACGGATGTATATC 59.624 42.308 14.23 7.00 44.82 1.63
413 500 6.432607 ACTACCACATACGGATGTATATCG 57.567 41.667 14.23 0.00 44.82 2.92
414 501 6.175471 ACTACCACATACGGATGTATATCGA 58.825 40.000 14.23 0.00 44.82 3.59
415 502 5.306532 ACCACATACGGATGTATATCGAC 57.693 43.478 14.23 0.00 44.82 4.20
416 503 4.763279 ACCACATACGGATGTATATCGACA 59.237 41.667 14.23 0.00 44.82 4.35
417 504 5.093457 CCACATACGGATGTATATCGACAC 58.907 45.833 14.23 0.00 44.82 3.67
418 505 5.335348 CCACATACGGATGTATATCGACACA 60.335 44.000 14.23 0.00 44.82 3.72
419 506 6.322491 CACATACGGATGTATATCGACACAT 58.678 40.000 14.23 8.44 44.82 3.21
420 507 6.806739 CACATACGGATGTATATCGACACATT 59.193 38.462 14.23 0.00 44.82 2.71
421 508 7.328493 CACATACGGATGTATATCGACACATTT 59.672 37.037 14.23 2.77 44.82 2.32
422 509 7.870954 ACATACGGATGTATATCGACACATTTT 59.129 33.333 12.79 2.51 44.77 1.82
423 510 9.349145 CATACGGATGTATATCGACACATTTTA 57.651 33.333 0.00 4.12 39.28 1.52
424 511 7.869016 ACGGATGTATATCGACACATTTTAG 57.131 36.000 9.69 5.76 35.55 1.85
425 512 7.654568 ACGGATGTATATCGACACATTTTAGA 58.345 34.615 9.69 0.00 35.55 2.10
426 513 8.304596 ACGGATGTATATCGACACATTTTAGAT 58.695 33.333 9.69 0.00 35.55 1.98
427 514 9.140286 CGGATGTATATCGACACATTTTAGATT 57.860 33.333 9.69 0.00 35.55 2.40
436 523 8.996024 TCGACACATTTTAGATTGTAGATTCA 57.004 30.769 0.00 0.00 0.00 2.57
437 524 8.869897 TCGACACATTTTAGATTGTAGATTCAC 58.130 33.333 0.00 0.00 0.00 3.18
438 525 8.873830 CGACACATTTTAGATTGTAGATTCACT 58.126 33.333 0.00 0.00 0.00 3.41
440 527 9.725019 ACACATTTTAGATTGTAGATTCACTCA 57.275 29.630 0.00 0.00 0.00 3.41
447 534 7.934855 AGATTGTAGATTCACTCATTTTGCT 57.065 32.000 0.00 0.00 0.00 3.91
448 535 7.983307 AGATTGTAGATTCACTCATTTTGCTC 58.017 34.615 0.00 0.00 0.00 4.26
449 536 6.500684 TTGTAGATTCACTCATTTTGCTCC 57.499 37.500 0.00 0.00 0.00 4.70
450 537 4.631377 TGTAGATTCACTCATTTTGCTCCG 59.369 41.667 0.00 0.00 0.00 4.63
451 538 3.679389 AGATTCACTCATTTTGCTCCGT 58.321 40.909 0.00 0.00 0.00 4.69
452 539 4.832248 AGATTCACTCATTTTGCTCCGTA 58.168 39.130 0.00 0.00 0.00 4.02
453 540 5.431765 AGATTCACTCATTTTGCTCCGTAT 58.568 37.500 0.00 0.00 0.00 3.06
454 541 4.944962 TTCACTCATTTTGCTCCGTATG 57.055 40.909 0.00 0.00 0.00 2.39
455 542 3.937814 TCACTCATTTTGCTCCGTATGT 58.062 40.909 0.00 0.00 0.00 2.29
456 543 5.079689 TCACTCATTTTGCTCCGTATGTA 57.920 39.130 0.00 0.00 0.00 2.29
457 544 5.109210 TCACTCATTTTGCTCCGTATGTAG 58.891 41.667 0.00 0.00 0.00 2.74
458 545 4.870426 CACTCATTTTGCTCCGTATGTAGT 59.130 41.667 0.00 0.00 0.00 2.73
459 546 5.005779 CACTCATTTTGCTCCGTATGTAGTC 59.994 44.000 0.00 0.00 0.00 2.59
460 547 5.079689 TCATTTTGCTCCGTATGTAGTCA 57.920 39.130 0.00 0.00 0.00 3.41
461 548 5.670485 TCATTTTGCTCCGTATGTAGTCAT 58.330 37.500 0.00 0.00 38.00 3.06
462 549 6.112734 TCATTTTGCTCCGTATGTAGTCATT 58.887 36.000 0.00 0.00 35.70 2.57
463 550 6.597672 TCATTTTGCTCCGTATGTAGTCATTT 59.402 34.615 0.00 0.00 35.70 2.32
464 551 5.794687 TTTGCTCCGTATGTAGTCATTTG 57.205 39.130 0.00 0.00 35.70 2.32
465 552 4.465632 TGCTCCGTATGTAGTCATTTGT 57.534 40.909 0.00 0.00 35.70 2.83
466 553 4.827692 TGCTCCGTATGTAGTCATTTGTT 58.172 39.130 0.00 0.00 35.70 2.83
467 554 4.629634 TGCTCCGTATGTAGTCATTTGTTG 59.370 41.667 0.00 0.00 35.70 3.33
468 555 4.868171 GCTCCGTATGTAGTCATTTGTTGA 59.132 41.667 0.00 0.00 35.70 3.18
469 556 5.350365 GCTCCGTATGTAGTCATTTGTTGAA 59.650 40.000 0.00 0.00 35.70 2.69
470 557 6.128391 GCTCCGTATGTAGTCATTTGTTGAAA 60.128 38.462 0.00 0.00 35.70 2.69
471 558 7.414098 GCTCCGTATGTAGTCATTTGTTGAAAT 60.414 37.037 0.00 0.00 35.70 2.17
472 559 7.970384 TCCGTATGTAGTCATTTGTTGAAATC 58.030 34.615 0.00 0.00 35.70 2.17
473 560 7.822334 TCCGTATGTAGTCATTTGTTGAAATCT 59.178 33.333 0.00 0.00 35.70 2.40
474 561 8.116753 CCGTATGTAGTCATTTGTTGAAATCTC 58.883 37.037 0.00 0.00 35.70 2.75
475 562 8.873830 CGTATGTAGTCATTTGTTGAAATCTCT 58.126 33.333 0.00 0.00 35.70 3.10
479 566 9.996554 TGTAGTCATTTGTTGAAATCTCTAGAA 57.003 29.630 0.00 0.00 35.70 2.10
482 569 9.784531 AGTCATTTGTTGAAATCTCTAGAAAGA 57.215 29.630 0.00 0.00 35.70 2.52
483 570 9.818796 GTCATTTGTTGAAATCTCTAGAAAGAC 57.181 33.333 0.00 0.00 35.70 3.01
484 571 9.559732 TCATTTGTTGAAATCTCTAGAAAGACA 57.440 29.630 0.00 0.00 28.65 3.41
499 586 9.595823 TCTAGAAAGACAAATATTTAGGAACGG 57.404 33.333 0.00 0.00 0.00 4.44
500 587 9.595823 CTAGAAAGACAAATATTTAGGAACGGA 57.404 33.333 0.00 0.00 0.00 4.69
501 588 8.494016 AGAAAGACAAATATTTAGGAACGGAG 57.506 34.615 0.00 0.00 0.00 4.63
502 589 7.553044 AGAAAGACAAATATTTAGGAACGGAGG 59.447 37.037 0.00 0.00 0.00 4.30
503 590 5.681639 AGACAAATATTTAGGAACGGAGGG 58.318 41.667 0.00 0.00 0.00 4.30
504 591 5.427481 AGACAAATATTTAGGAACGGAGGGA 59.573 40.000 0.00 0.00 0.00 4.20
505 592 5.681639 ACAAATATTTAGGAACGGAGGGAG 58.318 41.667 0.00 0.00 0.00 4.30
521 608 5.358090 GGAGGGAGTAGTTTTCTTATTCCG 58.642 45.833 0.00 0.00 0.00 4.30
522 609 5.128335 GGAGGGAGTAGTTTTCTTATTCCGA 59.872 44.000 0.00 0.00 0.00 4.55
560 647 9.902684 ATCAAGTCACATCTAATTTGAAGATCT 57.097 29.630 0.00 0.00 31.22 2.75
599 686 5.703978 TTTTGATTCATTTCGCCTGAGAA 57.296 34.783 0.00 0.00 0.00 2.87
602 689 7.572523 TTTGATTCATTTCGCCTGAGAATAT 57.427 32.000 0.00 0.00 0.00 1.28
683 771 5.794687 GGAAAACTTCCTTGTGTTTTTGG 57.205 39.130 0.00 0.00 46.57 3.28
707 795 5.007921 GTCTTACCAAAGCACCGAAGTAAAA 59.992 40.000 0.00 0.00 32.36 1.52
708 796 5.589452 TCTTACCAAAGCACCGAAGTAAAAA 59.411 36.000 0.00 0.00 32.36 1.94
749 920 5.922053 AGAATGCTATGATGTACAAGCTGA 58.078 37.500 16.15 0.38 35.40 4.26
779 952 5.294552 GCACTTGTCTTAAGAACAGAGTGTT 59.705 40.000 24.43 0.00 44.37 3.32
801 974 9.274065 GTGTTAGTATAATTTTCTCCTTTTGCG 57.726 33.333 0.00 0.00 0.00 4.85
806 979 6.759497 ATAATTTTCTCCTTTTGCGCTACT 57.241 33.333 9.73 0.00 0.00 2.57
812 985 3.250040 TCTCCTTTTGCGCTACTGTTTTC 59.750 43.478 9.73 0.00 0.00 2.29
815 988 3.975035 CCTTTTGCGCTACTGTTTTCTTC 59.025 43.478 9.73 0.00 0.00 2.87
816 989 4.497340 CCTTTTGCGCTACTGTTTTCTTCA 60.497 41.667 9.73 0.00 0.00 3.02
817 990 4.829064 TTTGCGCTACTGTTTTCTTCAT 57.171 36.364 9.73 0.00 0.00 2.57
820 993 5.933187 TGCGCTACTGTTTTCTTCATTTA 57.067 34.783 9.73 0.00 0.00 1.40
821 994 6.307031 TGCGCTACTGTTTTCTTCATTTAA 57.693 33.333 9.73 0.00 0.00 1.52
822 995 6.908825 TGCGCTACTGTTTTCTTCATTTAAT 58.091 32.000 9.73 0.00 0.00 1.40
823 996 6.801377 TGCGCTACTGTTTTCTTCATTTAATG 59.199 34.615 9.73 0.00 0.00 1.90
824 997 7.021196 GCGCTACTGTTTTCTTCATTTAATGA 58.979 34.615 3.20 3.20 37.55 2.57
825 998 7.537306 GCGCTACTGTTTTCTTCATTTAATGAA 59.463 33.333 17.92 17.92 46.30 2.57
861 1036 5.276348 GCTGTCATTTGGTTTCAAAGAAACG 60.276 40.000 14.32 3.30 44.87 3.60
870 1045 4.319984 GGTTTCAAAGAAACGCCGTAGATT 60.320 41.667 14.32 0.00 0.00 2.40
873 1048 5.712217 TCAAAGAAACGCCGTAGATTATG 57.288 39.130 0.00 0.00 0.00 1.90
874 1049 5.172934 TCAAAGAAACGCCGTAGATTATGT 58.827 37.500 0.00 0.00 0.00 2.29
880 1055 0.949105 GCCGTAGATTATGTGCCGGG 60.949 60.000 2.18 0.00 36.05 5.73
893 1068 1.826487 GCCGGGGAACACAGTTTGT 60.826 57.895 2.18 0.00 41.74 2.83
950 1125 0.776451 GTGTGCGTGTCTGTCGTTAG 59.224 55.000 0.00 0.00 0.00 2.34
979 1154 8.964476 TTATGTCTGTTTCTCTTCAGAGTTTT 57.036 30.769 3.73 0.00 42.60 2.43
981 1156 7.772332 TGTCTGTTTCTCTTCAGAGTTTTAC 57.228 36.000 3.73 0.22 42.60 2.01
990 1165 8.824159 TCTCTTCAGAGTTTTACTTCATTGAG 57.176 34.615 3.73 0.00 42.60 3.02
991 1166 8.424918 TCTCTTCAGAGTTTTACTTCATTGAGT 58.575 33.333 3.73 0.00 42.60 3.41
1008 1183 6.875726 TCATTGAGTAAAGAAGGATGTCACAG 59.124 38.462 0.00 0.00 0.00 3.66
1016 1191 3.848975 AGAAGGATGTCACAGGAAAGGAT 59.151 43.478 0.00 0.00 0.00 3.24
1017 1192 3.641434 AGGATGTCACAGGAAAGGATG 57.359 47.619 0.00 0.00 0.00 3.51
1044 1219 2.424379 GGAAGTTGTGTCCCCCTTTCTT 60.424 50.000 0.00 0.00 0.00 2.52
1063 1238 6.735678 TTCTTATGCAGTTATCGAAAGCAA 57.264 33.333 0.00 0.00 38.85 3.91
1086 1261 3.131396 AGTTCATTCGTTGACACTGGAC 58.869 45.455 0.00 0.00 32.84 4.02
1155 1330 1.067283 AGAGAAGCACGTGACATGGAG 60.067 52.381 22.23 0.00 0.00 3.86
1206 1381 7.554118 TGGGAAAGTGAGATTATCAATGACTTC 59.446 37.037 0.00 0.00 40.43 3.01
1215 1390 7.512992 AGATTATCAATGACTTCGGAGGAATT 58.487 34.615 0.00 0.00 0.00 2.17
1272 1447 3.514645 CCAGCAGCAATTTGTACATTCC 58.485 45.455 0.00 0.00 0.00 3.01
1293 1468 3.304928 CCAAGCTTCAGATTGTGAACACC 60.305 47.826 0.00 0.00 40.45 4.16
1386 1561 5.006261 TGCGTTGTTATCATCATCTTTACCG 59.994 40.000 0.00 0.00 0.00 4.02
1389 1564 6.292168 CGTTGTTATCATCATCTTTACCGTCC 60.292 42.308 0.00 0.00 0.00 4.79
1401 1576 2.851263 TACCGTCCAAATTGCTGTCT 57.149 45.000 0.00 0.00 0.00 3.41
1463 1638 4.858965 AGAAAATCCTTGAGAGCTCCAT 57.141 40.909 10.93 0.00 0.00 3.41
1472 1647 6.318112 TCCTTGAGAGCTCCATGATATCTAA 58.682 40.000 10.93 0.00 0.00 2.10
1473 1648 6.958778 TCCTTGAGAGCTCCATGATATCTAAT 59.041 38.462 10.93 0.00 0.00 1.73
1501 1676 8.534496 TGCAGCTCAGCTATTATAATCTTGATA 58.466 33.333 0.00 0.00 36.40 2.15
1550 1725 8.455903 TGCTTCTCTATATTCCCAGAAAATTG 57.544 34.615 0.00 0.00 0.00 2.32
1597 1772 0.541764 TTGGTGGATTGGTGAAGGGC 60.542 55.000 0.00 0.00 0.00 5.19
1605 1780 3.070302 GGATTGGTGAAGGGCTAGTAGAG 59.930 52.174 0.00 0.00 0.00 2.43
1655 1830 1.349026 TGGGAAGGAGTGCTTTGAGAG 59.651 52.381 0.00 0.00 0.00 3.20
1659 1834 3.008049 GGAAGGAGTGCTTTGAGAGGTTA 59.992 47.826 0.00 0.00 0.00 2.85
1719 1894 4.748102 CGTAACTGTACTGTGAACCAATGT 59.252 41.667 6.13 0.00 0.00 2.71
1734 1909 4.406456 ACCAATGTAAGTTGCATCCTTGA 58.594 39.130 6.93 0.00 0.00 3.02
1842 2017 0.798771 CTCGCCGTGCTTGTCTAGTC 60.799 60.000 0.00 0.00 0.00 2.59
1859 2034 5.299782 GTCTAGTCGGAGAACATATTCAGGT 59.700 44.000 0.00 0.00 39.69 4.00
1866 2041 5.980116 CGGAGAACATATTCAGGTAACAGAG 59.020 44.000 0.00 0.00 37.29 3.35
1870 2045 6.377429 AGAACATATTCAGGTAACAGAGACGA 59.623 38.462 0.00 0.00 37.29 4.20
2521 2696 3.009723 GGAGCGGATGAACAAGATTCAA 58.990 45.455 0.00 0.00 31.55 2.69
2607 2782 2.642171 TCCCTGGTGAGAACATACCT 57.358 50.000 0.00 0.00 37.84 3.08
2781 3309 2.679837 CCAGGTGAATGAGATGTTTCCG 59.320 50.000 0.00 0.00 0.00 4.30
2811 3339 3.495806 CCTTCCTGGAGGTATTCAGATGC 60.496 52.174 5.02 0.00 38.35 3.91
2861 3389 2.238144 AGGATGGAGTGTGGATGAACTG 59.762 50.000 0.00 0.00 0.00 3.16
2862 3390 2.026822 GGATGGAGTGTGGATGAACTGT 60.027 50.000 0.00 0.00 0.00 3.55
2951 3479 7.500892 ACATATGTAATAAGTCAATTTCCGCCA 59.499 33.333 6.56 0.00 29.06 5.69
3130 3659 4.269183 TGTGGCCTATGGTTATGAACTTG 58.731 43.478 3.32 0.00 0.00 3.16
3186 3715 5.414789 TTCACTGATTTCCCGAGTCATTA 57.585 39.130 0.00 0.00 0.00 1.90
3188 3717 5.601662 TCACTGATTTCCCGAGTCATTATC 58.398 41.667 0.00 0.00 0.00 1.75
3235 3764 4.367450 GCATTGTCAGGAGAGAGTGATAC 58.633 47.826 0.00 0.00 27.74 2.24
3271 3800 5.517054 GCAAGTTTGATTAGAGTCTCTACCG 59.483 44.000 9.20 0.00 0.00 4.02
3298 3827 3.003480 GTGCAAGTTATGGTCAGTCTCC 58.997 50.000 0.00 0.00 0.00 3.71
3309 3838 0.610174 TCAGTCTCCCTCACACATGC 59.390 55.000 0.00 0.00 0.00 4.06
3317 3846 4.019411 TCTCCCTCACACATGCTATTTCAA 60.019 41.667 0.00 0.00 0.00 2.69
3318 3847 4.661222 TCCCTCACACATGCTATTTCAAA 58.339 39.130 0.00 0.00 0.00 2.69
3445 3975 3.915437 AAGCCATAAAGGTTTGACACG 57.085 42.857 0.00 0.00 39.62 4.49
3447 3977 2.812011 AGCCATAAAGGTTTGACACGTC 59.188 45.455 0.00 0.00 40.61 4.34
3481 4011 1.578206 GAGGAAACCGGAAGCACTGC 61.578 60.000 9.46 0.00 0.00 4.40
3495 4025 5.163581 GGAAGCACTGCACATTCAATTCTAT 60.164 40.000 3.30 0.00 0.00 1.98
3514 4044 5.991861 TCTATGCGGGGTTCAAACTTATTA 58.008 37.500 0.00 0.00 0.00 0.98
3530 4060 6.266131 ACTTATTATGCAGGGAGAAATGGA 57.734 37.500 0.00 0.00 0.00 3.41
3531 4061 6.856757 ACTTATTATGCAGGGAGAAATGGAT 58.143 36.000 0.00 0.00 0.00 3.41
3532 4062 7.988937 ACTTATTATGCAGGGAGAAATGGATA 58.011 34.615 0.00 0.00 0.00 2.59
3570 4105 7.092137 TCTCACAGCCATTCATAAGAATTTG 57.908 36.000 0.00 0.00 42.46 2.32
3589 4124 4.517952 TTGTGCCATAACTTTCATGTGG 57.482 40.909 0.00 0.00 0.00 4.17
3638 4173 3.821033 GCTATGTGGTGTCTTTTTGGTCT 59.179 43.478 0.00 0.00 0.00 3.85
3643 4178 5.630121 TGTGGTGTCTTTTTGGTCTATGAT 58.370 37.500 0.00 0.00 0.00 2.45
3655 4190 6.378661 TTGGTCTATGATAGGCATATTGCT 57.621 37.500 6.39 0.00 44.28 3.91
3659 4194 7.180946 TGGTCTATGATAGGCATATTGCTTACT 59.819 37.037 6.39 0.00 44.28 2.24
3660 4195 7.708752 GGTCTATGATAGGCATATTGCTTACTC 59.291 40.741 6.39 0.00 44.28 2.59
3661 4196 8.474025 GTCTATGATAGGCATATTGCTTACTCT 58.526 37.037 0.00 0.00 44.28 3.24
3662 4197 9.700831 TCTATGATAGGCATATTGCTTACTCTA 57.299 33.333 0.00 0.00 44.28 2.43
3663 4198 9.743057 CTATGATAGGCATATTGCTTACTCTAC 57.257 37.037 0.00 0.00 44.28 2.59
3826 4361 4.476862 TGTTAATAGCTGCGAGATCGATC 58.523 43.478 17.91 17.91 43.02 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 3.440415 GCCGGCGAAGAAAAGGGG 61.440 66.667 12.58 0.00 0.00 4.79
63 64 4.585879 GCATACAGAACAAGGTAAAGGGA 58.414 43.478 0.00 0.00 0.00 4.20
112 113 3.791973 ACTCTAGATGCGGAACTCTTG 57.208 47.619 0.00 0.00 0.00 3.02
147 148 2.227865 GGCAACCGTGAAGCAGAAATAA 59.772 45.455 0.00 0.00 0.00 1.40
156 157 1.429463 GTCACTAGGCAACCGTGAAG 58.571 55.000 0.00 0.00 45.44 3.02
188 189 1.338579 GCTAGTCCATGGAGCATAGCC 60.339 57.143 28.03 17.36 36.20 3.93
203 204 3.498397 CCAGTTCGTGAAAACATGCTAGT 59.502 43.478 0.00 0.00 0.00 2.57
216 217 2.205074 GGCACATCTATCCAGTTCGTG 58.795 52.381 0.00 0.00 0.00 4.35
327 414 5.479375 AGGGAGTAGATGTGAAAGTTTACGA 59.521 40.000 0.00 0.00 0.00 3.43
330 417 5.105473 CGGAGGGAGTAGATGTGAAAGTTTA 60.105 44.000 0.00 0.00 0.00 2.01
344 431 6.384886 ACAAATATTTAGGAACGGAGGGAGTA 59.615 38.462 0.00 0.00 0.00 2.59
345 432 5.191124 ACAAATATTTAGGAACGGAGGGAGT 59.809 40.000 0.00 0.00 0.00 3.85
346 433 5.681639 ACAAATATTTAGGAACGGAGGGAG 58.318 41.667 0.00 0.00 0.00 4.30
347 434 5.427481 AGACAAATATTTAGGAACGGAGGGA 59.573 40.000 0.00 0.00 0.00 4.20
348 435 5.681639 AGACAAATATTTAGGAACGGAGGG 58.318 41.667 0.00 0.00 0.00 4.30
349 436 7.625828 AAAGACAAATATTTAGGAACGGAGG 57.374 36.000 0.00 0.00 0.00 4.30
365 452 9.541143 GTCCATTTGAAATCCTAAAAAGACAAA 57.459 29.630 0.00 0.00 0.00 2.83
366 453 8.923270 AGTCCATTTGAAATCCTAAAAAGACAA 58.077 29.630 0.00 0.00 30.54 3.18
367 454 8.477419 AGTCCATTTGAAATCCTAAAAAGACA 57.523 30.769 0.00 0.00 30.54 3.41
368 455 9.841880 GTAGTCCATTTGAAATCCTAAAAAGAC 57.158 33.333 0.00 0.00 0.00 3.01
369 456 9.020731 GGTAGTCCATTTGAAATCCTAAAAAGA 57.979 33.333 0.00 0.00 0.00 2.52
370 457 8.802267 TGGTAGTCCATTTGAAATCCTAAAAAG 58.198 33.333 0.00 0.00 39.03 2.27
371 458 8.581578 GTGGTAGTCCATTTGAAATCCTAAAAA 58.418 33.333 0.00 0.00 46.20 1.94
372 459 7.726291 TGTGGTAGTCCATTTGAAATCCTAAAA 59.274 33.333 0.00 0.00 46.20 1.52
373 460 7.235079 TGTGGTAGTCCATTTGAAATCCTAAA 58.765 34.615 0.00 0.00 46.20 1.85
374 461 6.785076 TGTGGTAGTCCATTTGAAATCCTAA 58.215 36.000 0.00 0.00 46.20 2.69
375 462 6.381498 TGTGGTAGTCCATTTGAAATCCTA 57.619 37.500 0.00 0.00 46.20 2.94
376 463 5.255397 TGTGGTAGTCCATTTGAAATCCT 57.745 39.130 0.00 0.00 46.20 3.24
377 464 6.238374 CGTATGTGGTAGTCCATTTGAAATCC 60.238 42.308 0.00 0.00 46.20 3.01
378 465 6.238374 CCGTATGTGGTAGTCCATTTGAAATC 60.238 42.308 0.00 0.00 46.20 2.17
379 466 5.588648 CCGTATGTGGTAGTCCATTTGAAAT 59.411 40.000 0.00 0.00 46.20 2.17
380 467 4.938832 CCGTATGTGGTAGTCCATTTGAAA 59.061 41.667 0.00 0.00 46.20 2.69
381 468 4.223255 TCCGTATGTGGTAGTCCATTTGAA 59.777 41.667 0.00 0.00 46.20 2.69
382 469 3.770388 TCCGTATGTGGTAGTCCATTTGA 59.230 43.478 0.00 0.00 46.20 2.69
383 470 4.131649 TCCGTATGTGGTAGTCCATTTG 57.868 45.455 0.00 0.00 46.20 2.32
384 471 4.163458 ACATCCGTATGTGGTAGTCCATTT 59.837 41.667 0.00 0.00 44.79 2.32
385 472 3.709653 ACATCCGTATGTGGTAGTCCATT 59.290 43.478 0.00 0.00 44.79 3.16
386 473 3.305720 ACATCCGTATGTGGTAGTCCAT 58.694 45.455 0.00 0.00 44.79 3.41
387 474 2.742348 ACATCCGTATGTGGTAGTCCA 58.258 47.619 0.00 0.00 44.79 4.02
388 475 6.457934 CGATATACATCCGTATGTGGTAGTCC 60.458 46.154 3.56 0.00 45.99 3.85
389 476 6.314648 TCGATATACATCCGTATGTGGTAGTC 59.685 42.308 3.56 0.00 45.99 2.59
390 477 6.093219 GTCGATATACATCCGTATGTGGTAGT 59.907 42.308 3.56 0.00 45.99 2.73
391 478 6.093082 TGTCGATATACATCCGTATGTGGTAG 59.907 42.308 3.56 0.00 45.99 3.18
392 479 5.939296 TGTCGATATACATCCGTATGTGGTA 59.061 40.000 3.56 0.00 45.99 3.25
393 480 4.763279 TGTCGATATACATCCGTATGTGGT 59.237 41.667 3.56 0.00 45.99 4.16
394 481 5.093457 GTGTCGATATACATCCGTATGTGG 58.907 45.833 3.56 0.00 45.99 4.17
395 482 5.695818 TGTGTCGATATACATCCGTATGTG 58.304 41.667 3.56 0.00 45.99 3.21
397 484 7.812309 AAATGTGTCGATATACATCCGTATG 57.188 36.000 11.62 0.00 36.52 2.39
398 485 9.569167 CTAAAATGTGTCGATATACATCCGTAT 57.431 33.333 11.62 0.00 36.52 3.06
399 486 8.785946 TCTAAAATGTGTCGATATACATCCGTA 58.214 33.333 11.62 5.86 36.52 4.02
400 487 7.654568 TCTAAAATGTGTCGATATACATCCGT 58.345 34.615 11.62 5.24 36.52 4.69
401 488 8.689251 ATCTAAAATGTGTCGATATACATCCG 57.311 34.615 11.62 0.00 36.52 4.18
410 497 9.599866 TGAATCTACAATCTAAAATGTGTCGAT 57.400 29.630 0.00 0.00 0.00 3.59
411 498 8.869897 GTGAATCTACAATCTAAAATGTGTCGA 58.130 33.333 0.00 0.00 0.00 4.20
412 499 8.873830 AGTGAATCTACAATCTAAAATGTGTCG 58.126 33.333 0.00 0.00 0.00 4.35
414 501 9.725019 TGAGTGAATCTACAATCTAAAATGTGT 57.275 29.630 0.00 0.00 36.14 3.72
421 508 9.453572 AGCAAAATGAGTGAATCTACAATCTAA 57.546 29.630 0.00 0.00 36.14 2.10
422 509 9.102757 GAGCAAAATGAGTGAATCTACAATCTA 57.897 33.333 0.00 0.00 36.14 1.98
423 510 7.066766 GGAGCAAAATGAGTGAATCTACAATCT 59.933 37.037 0.00 0.00 36.14 2.40
424 511 7.192232 GGAGCAAAATGAGTGAATCTACAATC 58.808 38.462 0.00 0.00 35.78 2.67
425 512 6.183360 CGGAGCAAAATGAGTGAATCTACAAT 60.183 38.462 0.00 0.00 0.00 2.71
426 513 5.122239 CGGAGCAAAATGAGTGAATCTACAA 59.878 40.000 0.00 0.00 0.00 2.41
427 514 4.631377 CGGAGCAAAATGAGTGAATCTACA 59.369 41.667 0.00 0.00 0.00 2.74
428 515 4.631813 ACGGAGCAAAATGAGTGAATCTAC 59.368 41.667 0.00 0.00 0.00 2.59
429 516 4.832248 ACGGAGCAAAATGAGTGAATCTA 58.168 39.130 0.00 0.00 0.00 1.98
430 517 3.679389 ACGGAGCAAAATGAGTGAATCT 58.321 40.909 0.00 0.00 0.00 2.40
431 518 5.065218 ACATACGGAGCAAAATGAGTGAATC 59.935 40.000 0.00 0.00 0.00 2.52
432 519 4.943705 ACATACGGAGCAAAATGAGTGAAT 59.056 37.500 0.00 0.00 0.00 2.57
433 520 4.323417 ACATACGGAGCAAAATGAGTGAA 58.677 39.130 0.00 0.00 0.00 3.18
434 521 3.937814 ACATACGGAGCAAAATGAGTGA 58.062 40.909 0.00 0.00 0.00 3.41
435 522 4.870426 ACTACATACGGAGCAAAATGAGTG 59.130 41.667 0.00 0.00 0.00 3.51
436 523 5.086104 ACTACATACGGAGCAAAATGAGT 57.914 39.130 0.00 0.00 0.00 3.41
437 524 5.109210 TGACTACATACGGAGCAAAATGAG 58.891 41.667 0.00 0.00 0.00 2.90
438 525 5.079689 TGACTACATACGGAGCAAAATGA 57.920 39.130 0.00 0.00 0.00 2.57
439 526 5.991328 ATGACTACATACGGAGCAAAATG 57.009 39.130 0.00 0.00 34.71 2.32
440 527 6.374333 ACAAATGACTACATACGGAGCAAAAT 59.626 34.615 0.00 0.00 35.50 1.82
441 528 5.703592 ACAAATGACTACATACGGAGCAAAA 59.296 36.000 0.00 0.00 35.50 2.44
442 529 5.242434 ACAAATGACTACATACGGAGCAAA 58.758 37.500 0.00 0.00 35.50 3.68
443 530 4.827692 ACAAATGACTACATACGGAGCAA 58.172 39.130 0.00 0.00 35.50 3.91
444 531 4.465632 ACAAATGACTACATACGGAGCA 57.534 40.909 0.00 0.00 35.50 4.26
445 532 4.868171 TCAACAAATGACTACATACGGAGC 59.132 41.667 0.00 0.00 35.50 4.70
446 533 6.961359 TTCAACAAATGACTACATACGGAG 57.039 37.500 0.00 0.00 37.92 4.63
447 534 7.822334 AGATTTCAACAAATGACTACATACGGA 59.178 33.333 0.00 0.00 37.92 4.69
448 535 7.974675 AGATTTCAACAAATGACTACATACGG 58.025 34.615 0.00 0.00 37.92 4.02
449 536 8.873830 AGAGATTTCAACAAATGACTACATACG 58.126 33.333 0.00 0.00 37.92 3.06
453 540 9.996554 TTCTAGAGATTTCAACAAATGACTACA 57.003 29.630 0.00 0.00 37.92 2.74
456 543 9.784531 TCTTTCTAGAGATTTCAACAAATGACT 57.215 29.630 0.00 0.00 37.92 3.41
457 544 9.818796 GTCTTTCTAGAGATTTCAACAAATGAC 57.181 33.333 0.00 0.00 37.92 3.06
458 545 9.559732 TGTCTTTCTAGAGATTTCAACAAATGA 57.440 29.630 0.00 0.00 31.94 2.57
473 560 9.595823 CCGTTCCTAAATATTTGTCTTTCTAGA 57.404 33.333 11.05 0.00 0.00 2.43
474 561 9.595823 TCCGTTCCTAAATATTTGTCTTTCTAG 57.404 33.333 11.05 0.00 0.00 2.43
475 562 9.595823 CTCCGTTCCTAAATATTTGTCTTTCTA 57.404 33.333 11.05 0.00 0.00 2.10
476 563 7.553044 CCTCCGTTCCTAAATATTTGTCTTTCT 59.447 37.037 11.05 0.00 0.00 2.52
477 564 7.201705 CCCTCCGTTCCTAAATATTTGTCTTTC 60.202 40.741 11.05 0.00 0.00 2.62
478 565 6.602009 CCCTCCGTTCCTAAATATTTGTCTTT 59.398 38.462 11.05 0.00 0.00 2.52
479 566 6.069847 TCCCTCCGTTCCTAAATATTTGTCTT 60.070 38.462 11.05 0.00 0.00 3.01
480 567 5.427481 TCCCTCCGTTCCTAAATATTTGTCT 59.573 40.000 11.05 0.00 0.00 3.41
481 568 5.677567 TCCCTCCGTTCCTAAATATTTGTC 58.322 41.667 11.05 0.00 0.00 3.18
482 569 5.191124 ACTCCCTCCGTTCCTAAATATTTGT 59.809 40.000 11.05 0.00 0.00 2.83
483 570 5.681639 ACTCCCTCCGTTCCTAAATATTTG 58.318 41.667 11.05 1.40 0.00 2.32
484 571 5.970501 ACTCCCTCCGTTCCTAAATATTT 57.029 39.130 5.89 5.89 0.00 1.40
485 572 6.141790 ACTACTCCCTCCGTTCCTAAATATT 58.858 40.000 0.00 0.00 0.00 1.28
486 573 5.713807 ACTACTCCCTCCGTTCCTAAATAT 58.286 41.667 0.00 0.00 0.00 1.28
487 574 5.134725 ACTACTCCCTCCGTTCCTAAATA 57.865 43.478 0.00 0.00 0.00 1.40
488 575 3.991683 ACTACTCCCTCCGTTCCTAAAT 58.008 45.455 0.00 0.00 0.00 1.40
489 576 3.463048 ACTACTCCCTCCGTTCCTAAA 57.537 47.619 0.00 0.00 0.00 1.85
490 577 3.463048 AACTACTCCCTCCGTTCCTAA 57.537 47.619 0.00 0.00 0.00 2.69
491 578 3.463048 AAACTACTCCCTCCGTTCCTA 57.537 47.619 0.00 0.00 0.00 2.94
492 579 2.322339 AAACTACTCCCTCCGTTCCT 57.678 50.000 0.00 0.00 0.00 3.36
493 580 2.566279 AGAAAACTACTCCCTCCGTTCC 59.434 50.000 0.00 0.00 0.00 3.62
494 581 3.957591 AGAAAACTACTCCCTCCGTTC 57.042 47.619 0.00 0.00 0.00 3.95
495 582 6.370186 AATAAGAAAACTACTCCCTCCGTT 57.630 37.500 0.00 0.00 0.00 4.44
496 583 5.105023 GGAATAAGAAAACTACTCCCTCCGT 60.105 44.000 0.00 0.00 0.00 4.69
497 584 5.358090 GGAATAAGAAAACTACTCCCTCCG 58.642 45.833 0.00 0.00 0.00 4.63
498 585 5.128335 TCGGAATAAGAAAACTACTCCCTCC 59.872 44.000 0.00 0.00 0.00 4.30
499 586 6.218108 TCGGAATAAGAAAACTACTCCCTC 57.782 41.667 0.00 0.00 0.00 4.30
500 587 6.616237 TTCGGAATAAGAAAACTACTCCCT 57.384 37.500 0.00 0.00 0.00 4.20
501 588 7.677454 TTTTCGGAATAAGAAAACTACTCCC 57.323 36.000 0.00 0.00 41.10 4.30
539 626 7.516470 CGCTCAGATCTTCAAATTAGATGTGAC 60.516 40.741 10.84 8.34 43.42 3.67
548 635 4.573900 AGTGTCGCTCAGATCTTCAAATT 58.426 39.130 0.00 0.00 0.00 1.82
560 647 0.537143 AAATGCCCAAGTGTCGCTCA 60.537 50.000 0.00 0.00 0.00 4.26
616 703 0.444260 GCTAACTTGGTTCAGCGAGC 59.556 55.000 0.00 0.00 0.00 5.03
620 707 1.502190 GCCGCTAACTTGGTTCAGC 59.498 57.895 0.00 0.00 0.00 4.26
621 708 1.787847 CGCCGCTAACTTGGTTCAG 59.212 57.895 0.00 0.00 0.00 3.02
643 730 7.145323 AGTTTTCCAGGAATTAATTTGACACG 58.855 34.615 1.58 0.00 0.00 4.49
644 731 8.887036 AAGTTTTCCAGGAATTAATTTGACAC 57.113 30.769 1.58 0.00 0.00 3.67
683 771 2.490991 ACTTCGGTGCTTTGGTAAGAC 58.509 47.619 0.00 0.00 32.92 3.01
707 795 0.395686 TCTGCTCTGCTCTGCTGTTT 59.604 50.000 0.00 0.00 0.00 2.83
708 796 0.037139 CTCTGCTCTGCTCTGCTGTT 60.037 55.000 0.00 0.00 0.00 3.16
709 797 0.899253 TCTCTGCTCTGCTCTGCTGT 60.899 55.000 0.00 0.00 0.00 4.40
710 798 0.246910 TTCTCTGCTCTGCTCTGCTG 59.753 55.000 0.00 0.00 0.00 4.41
711 799 1.134640 CATTCTCTGCTCTGCTCTGCT 60.135 52.381 0.00 0.00 0.00 4.24
712 800 1.292061 CATTCTCTGCTCTGCTCTGC 58.708 55.000 0.00 0.00 0.00 4.26
739 910 3.904136 AGTGCATTGTTCAGCTTGTAC 57.096 42.857 0.00 0.00 0.00 2.90
779 952 7.859325 AGCGCAAAAGGAGAAAATTATACTA 57.141 32.000 11.47 0.00 0.00 1.82
815 988 5.352569 AGCTCTCCTGTCGTTTCATTAAATG 59.647 40.000 0.00 0.00 33.61 2.32
816 989 5.352569 CAGCTCTCCTGTCGTTTCATTAAAT 59.647 40.000 0.00 0.00 36.79 1.40
817 990 4.690748 CAGCTCTCCTGTCGTTTCATTAAA 59.309 41.667 0.00 0.00 36.79 1.52
820 993 2.693069 CAGCTCTCCTGTCGTTTCATT 58.307 47.619 0.00 0.00 36.79 2.57
821 994 2.376808 CAGCTCTCCTGTCGTTTCAT 57.623 50.000 0.00 0.00 36.79 2.57
822 995 3.894257 CAGCTCTCCTGTCGTTTCA 57.106 52.632 0.00 0.00 36.79 2.69
834 1009 4.889409 TCTTTGAAACCAAATGACAGCTCT 59.111 37.500 0.00 0.00 33.55 4.09
861 1036 0.949105 CCCGGCACATAATCTACGGC 60.949 60.000 0.00 0.00 39.96 5.68
870 1045 1.298340 CTGTGTTCCCCGGCACATA 59.702 57.895 12.24 4.84 43.52 2.29
873 1048 1.826487 AAACTGTGTTCCCCGGCAC 60.826 57.895 0.00 0.00 36.26 5.01
874 1049 1.826054 CAAACTGTGTTCCCCGGCA 60.826 57.895 0.00 0.00 0.00 5.69
931 1106 0.776451 CTAACGACAGACACGCACAC 59.224 55.000 0.00 0.00 0.00 3.82
950 1125 7.870445 ACTCTGAAGAGAAACAGACATAAGAAC 59.130 37.037 14.20 0.00 44.74 3.01
979 1154 8.593679 TGACATCCTTCTTTACTCAATGAAGTA 58.406 33.333 10.36 0.00 41.22 2.24
981 1156 7.388776 TGTGACATCCTTCTTTACTCAATGAAG 59.611 37.037 6.20 6.20 41.90 3.02
990 1165 5.412904 CCTTTCCTGTGACATCCTTCTTTAC 59.587 44.000 0.00 0.00 0.00 2.01
991 1166 5.309543 TCCTTTCCTGTGACATCCTTCTTTA 59.690 40.000 0.00 0.00 0.00 1.85
995 1170 3.703001 TCCTTTCCTGTGACATCCTTC 57.297 47.619 0.00 0.00 0.00 3.46
998 1173 3.356529 ACATCCTTTCCTGTGACATCC 57.643 47.619 0.00 0.00 0.00 3.51
1008 1183 3.441500 ACTTCCTCCAACATCCTTTCC 57.558 47.619 0.00 0.00 0.00 3.13
1016 1191 1.133915 GGGACACAACTTCCTCCAACA 60.134 52.381 0.00 0.00 33.17 3.33
1017 1192 1.605753 GGGACACAACTTCCTCCAAC 58.394 55.000 0.00 0.00 33.17 3.77
1044 1219 5.419542 ACTCTTGCTTTCGATAACTGCATA 58.580 37.500 0.00 0.00 33.50 3.14
1063 1238 3.069586 TCCAGTGTCAACGAATGAACTCT 59.930 43.478 0.00 0.00 40.50 3.24
1086 1261 3.958798 TCTCTGAAGGTAAACTATCCCCG 59.041 47.826 0.00 0.00 0.00 5.73
1155 1330 2.167900 AGACACCCGCTTTAGTACATCC 59.832 50.000 0.00 0.00 0.00 3.51
1206 1381 1.097547 AATGCCGAGCAATTCCTCCG 61.098 55.000 2.68 0.00 43.62 4.63
1215 1390 2.689553 TGTCATCTAAATGCCGAGCA 57.310 45.000 1.01 1.01 44.86 4.26
1250 1425 2.660189 ATGTACAAATTGCTGCTGGC 57.340 45.000 0.00 0.00 42.22 4.85
1272 1447 3.607775 CGGTGTTCACAATCTGAAGCTTG 60.608 47.826 2.10 0.00 39.69 4.01
1293 1468 5.144359 CGGTCTTTTAAGTTGGACATTTCG 58.856 41.667 0.00 0.00 0.00 3.46
1429 1604 6.883217 TCAAGGATTTTCTTCTCAATCTCCAG 59.117 38.462 0.00 0.00 31.16 3.86
1442 1617 4.226846 TCATGGAGCTCTCAAGGATTTTCT 59.773 41.667 14.64 0.00 0.00 2.52
1463 1638 5.618236 AGCTGAGCTGCAAATTAGATATCA 58.382 37.500 5.97 0.00 37.57 2.15
1472 1647 8.512956 CAAGATTATAATAGCTGAGCTGCAAAT 58.487 33.333 18.79 9.33 40.10 2.32
1473 1648 7.716560 TCAAGATTATAATAGCTGAGCTGCAAA 59.283 33.333 18.79 4.70 40.10 3.68
1550 1725 5.248640 TCATAGCCCTCTTGCTAATAATGC 58.751 41.667 0.00 0.00 46.23 3.56
1597 1772 3.764434 TGACTTCTTGTGGCCTCTACTAG 59.236 47.826 3.32 0.00 0.00 2.57
1605 1780 1.517242 CTGTCTGACTTCTTGTGGCC 58.483 55.000 9.51 0.00 0.00 5.36
1655 1830 5.819379 TCAATCATCTCTGCAGTGATTAACC 59.181 40.000 24.89 0.00 39.76 2.85
1659 1834 4.639310 GGTTCAATCATCTCTGCAGTGATT 59.361 41.667 24.89 22.19 41.78 2.57
1706 1881 4.566545 TGCAACTTACATTGGTTCACAG 57.433 40.909 0.00 0.00 0.00 3.66
1719 1894 3.128589 GCCGAATTCAAGGATGCAACTTA 59.871 43.478 6.22 0.00 0.00 2.24
1734 1909 3.246699 CGGTAATCAACATACGCCGAATT 59.753 43.478 0.00 0.00 40.04 2.17
1842 2017 5.902681 TCTGTTACCTGAATATGTTCTCCG 58.097 41.667 3.72 0.00 35.33 4.63
1859 2034 2.552743 CTGAGTGGTGTCGTCTCTGTTA 59.447 50.000 0.00 0.00 0.00 2.41
1866 2041 2.989840 CTGATTTCTGAGTGGTGTCGTC 59.010 50.000 0.00 0.00 0.00 4.20
1870 2045 2.705658 TGGACTGATTTCTGAGTGGTGT 59.294 45.455 0.00 0.00 0.00 4.16
2127 2302 0.579156 GATTTGAGAGTGCGCCGATC 59.421 55.000 4.18 0.00 0.00 3.69
2495 2670 1.394917 CTTGTTCATCCGCTCCTTTCG 59.605 52.381 0.00 0.00 0.00 3.46
2521 2696 4.681025 CGAATTTAACAATGCTGTTGCTGT 59.319 37.500 1.78 0.00 45.53 4.40
2607 2782 2.036733 CCTACTCGGACTCAACCAAACA 59.963 50.000 0.00 0.00 33.16 2.83
2719 2894 5.009010 AGTCATTCAAGAACTTCAAACGCAT 59.991 36.000 0.00 0.00 0.00 4.73
2781 3309 0.615850 CCTCCAGGAAGGTCAGGTTC 59.384 60.000 0.00 0.00 39.02 3.62
2811 3339 5.416952 ACAAGGGAAAGATTCTATGTTGCTG 59.583 40.000 0.00 0.00 0.00 4.41
2861 3389 0.472471 TCTGGTTTCCTGGGTGTCAC 59.528 55.000 0.00 0.00 0.00 3.67
2862 3390 0.764890 CTCTGGTTTCCTGGGTGTCA 59.235 55.000 0.00 0.00 0.00 3.58
2924 3452 8.995220 GGCGGAAATTGACTTATTACATATGTA 58.005 33.333 11.62 11.62 0.00 2.29
2925 3453 7.500892 TGGCGGAAATTGACTTATTACATATGT 59.499 33.333 13.93 13.93 0.00 2.29
2987 3515 0.740737 CGTGCATCTCCATTTTCCCC 59.259 55.000 0.00 0.00 0.00 4.81
2995 3524 1.078918 CTGGCTTCGTGCATCTCCA 60.079 57.895 0.00 0.00 45.15 3.86
3186 3715 5.305128 TCACATGAAAAAGCCTGAAAAGGAT 59.695 36.000 0.00 0.00 0.00 3.24
3188 3717 4.947645 TCACATGAAAAAGCCTGAAAAGG 58.052 39.130 0.00 0.00 0.00 3.11
3235 3764 9.859427 TCTAATCAAACTTGCTTTCCATTAATG 57.141 29.630 8.58 8.58 0.00 1.90
3258 3787 3.439476 GCACAACTTCGGTAGAGACTCTA 59.561 47.826 8.17 8.17 0.00 2.43
3271 3800 4.275936 ACTGACCATAACTTGCACAACTTC 59.724 41.667 0.00 0.00 0.00 3.01
3298 3827 4.082625 TGCTTTGAAATAGCATGTGTGAGG 60.083 41.667 0.00 0.00 43.30 3.86
3309 3838 6.561614 ACTTCTGCATGATGCTTTGAAATAG 58.438 36.000 19.19 4.92 45.31 1.73
3317 3846 4.595762 AACAAACTTCTGCATGATGCTT 57.404 36.364 19.19 0.68 45.31 3.91
3318 3847 4.378770 CGTAACAAACTTCTGCATGATGCT 60.379 41.667 19.19 0.00 45.31 3.79
3321 3850 3.119849 GCCGTAACAAACTTCTGCATGAT 60.120 43.478 0.00 0.00 0.00 2.45
3438 3968 4.506886 AAACAAAAAGTGGACGTGTCAA 57.493 36.364 0.00 0.00 0.00 3.18
3445 3975 6.700081 GGTTTCCTCATAAACAAAAAGTGGAC 59.300 38.462 0.00 0.00 40.42 4.02
3447 3977 5.689961 CGGTTTCCTCATAAACAAAAAGTGG 59.310 40.000 0.00 0.00 40.42 4.00
3481 4011 2.951642 ACCCCGCATAGAATTGAATGTG 59.048 45.455 4.04 4.04 34.19 3.21
3495 4025 3.129638 GCATAATAAGTTTGAACCCCGCA 59.870 43.478 0.00 0.00 0.00 5.69
3514 4044 4.404640 CATGTATCCATTTCTCCCTGCAT 58.595 43.478 0.00 0.00 0.00 3.96
3530 4060 5.363562 TGTGAGAAGAAGATGGCATGTAT 57.636 39.130 3.81 0.00 0.00 2.29
3531 4061 4.763073 CTGTGAGAAGAAGATGGCATGTA 58.237 43.478 3.81 0.00 0.00 2.29
3532 4062 3.607741 CTGTGAGAAGAAGATGGCATGT 58.392 45.455 3.81 0.00 0.00 3.21
3538 4068 4.259356 TGAATGGCTGTGAGAAGAAGATG 58.741 43.478 0.00 0.00 0.00 2.90
3613 4148 4.588528 ACCAAAAAGACACCACATAGCAAT 59.411 37.500 0.00 0.00 0.00 3.56
3623 4158 5.297029 GCCTATCATAGACCAAAAAGACACC 59.703 44.000 0.00 0.00 0.00 4.16
3638 4173 9.480861 AGTAGAGTAAGCAATATGCCTATCATA 57.519 33.333 0.00 0.00 46.52 2.15
3643 4178 8.920174 TGTAAAGTAGAGTAAGCAATATGCCTA 58.080 33.333 0.00 0.00 46.52 3.93
3659 4194 7.817962 GCTTGAGTAGTGGAAATGTAAAGTAGA 59.182 37.037 0.00 0.00 0.00 2.59
3660 4195 7.819900 AGCTTGAGTAGTGGAAATGTAAAGTAG 59.180 37.037 0.00 0.00 0.00 2.57
3661 4196 7.676947 AGCTTGAGTAGTGGAAATGTAAAGTA 58.323 34.615 0.00 0.00 0.00 2.24
3662 4197 6.534634 AGCTTGAGTAGTGGAAATGTAAAGT 58.465 36.000 0.00 0.00 0.00 2.66
3663 4198 7.440523 AAGCTTGAGTAGTGGAAATGTAAAG 57.559 36.000 0.00 0.00 0.00 1.85
3748 4283 3.814268 CCGTCAATGGCCAAGGCG 61.814 66.667 23.80 23.80 43.06 5.52
3826 4361 1.532868 CTGAACAAGGAAAGACAGCCG 59.467 52.381 0.00 0.00 0.00 5.52


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

AutoCloner maintained by Alex Coulton.