Multiple sequence alignment - TraesCS6A01G234500

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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 TraesCS6A01G234500 chr6A 100.000 4621 0 0 1 4621 442400846 442396226 0.000000e+00 8534.0
1 TraesCS6A01G234500 chr6B 92.965 3895 174 57 793 4621 474180221 474176361 0.000000e+00 5583.0
2 TraesCS6A01G234500 chr6B 95.665 346 14 1 1 346 474187633 474187289 5.220000e-154 555.0
3 TraesCS6A01G234500 chr6B 88.430 121 9 4 374 493 160912490 160912374 1.730000e-29 141.0
4 TraesCS6A01G234500 chr6D 93.177 1920 97 17 2725 4621 306710537 306708629 0.000000e+00 2789.0
5 TraesCS6A01G234500 chr6D 88.348 1931 145 51 775 2643 306712466 306710554 0.000000e+00 2246.0
6 TraesCS6A01G234500 chr6D 96.221 344 12 1 2 345 306713057 306712715 3.120000e-156 562.0
7 TraesCS6A01G234500 chr2A 92.593 108 6 2 381 487 101847024 101846918 2.230000e-33 154.0
8 TraesCS6A01G234500 chr2A 97.561 41 0 1 343 382 701366214 701366174 8.300000e-08 69.4
9 TraesCS6A01G234500 chr2A 100.000 28 0 0 356 383 100597982 100597955 8.000000e-03 52.8
10 TraesCS6A01G234500 chr1D 93.269 104 7 0 375 478 483907685 483907582 2.230000e-33 154.0
11 TraesCS6A01G234500 chr2B 90.000 120 8 4 376 493 743693001 743692884 8.010000e-33 152.0
12 TraesCS6A01G234500 chrUn 93.878 98 6 0 381 478 331949583 331949680 1.040000e-31 148.0
13 TraesCS6A01G234500 chr7D 92.308 104 8 0 378 481 57100428 57100325 1.040000e-31 148.0
14 TraesCS6A01G234500 chr4D 93.878 98 6 0 382 479 494042372 494042469 1.040000e-31 148.0
15 TraesCS6A01G234500 chr4D 93.000 100 7 0 379 478 497510908 497511007 3.730000e-31 147.0
16 TraesCS6A01G234500 chr4D 100.000 28 0 0 355 382 150590764 150590737 8.000000e-03 52.8
17 TraesCS6A01G234500 chr3A 91.589 107 9 0 374 480 444462761 444462655 1.040000e-31 148.0
18 TraesCS6A01G234500 chr3A 98.276 58 0 1 693 750 610428290 610428234 2.940000e-17 100.0
19 TraesCS6A01G234500 chr3A 100.000 28 0 0 356 383 12334576 12334549 8.000000e-03 52.8
20 TraesCS6A01G234500 chr3D 97.619 42 0 1 342 382 501804249 501804208 2.310000e-08 71.3
21 TraesCS6A01G234500 chr7B 100.000 28 0 0 356 383 709495057 709495030 8.000000e-03 52.8
22 TraesCS6A01G234500 chr7A 100.000 28 0 0 356 383 548567182 548567155 8.000000e-03 52.8
23 TraesCS6A01G234500 chr5B 100.000 28 0 0 356 383 580683512 580683485 8.000000e-03 52.8


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 TraesCS6A01G234500 chr6A 442396226 442400846 4620 True 8534.000000 8534 100.000 1 4621 1 chr6A.!!$R1 4620
1 TraesCS6A01G234500 chr6B 474176361 474180221 3860 True 5583.000000 5583 92.965 793 4621 1 chr6B.!!$R2 3828
2 TraesCS6A01G234500 chr6D 306708629 306713057 4428 True 1865.666667 2789 92.582 2 4621 3 chr6D.!!$R1 4619

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
362 363 0.034283 ACTCCCTCCGTCCTAGTGTC 60.034 60.000 0.00 0.0 0.00 3.67 F
363 364 0.034380 CTCCCTCCGTCCTAGTGTCA 60.034 60.000 0.00 0.0 0.00 3.58 F
1479 1564 0.035317 TGCTGACAGCCTAACACCTG 59.965 55.000 24.33 0.0 41.51 4.00 F
1480 1565 0.321671 GCTGACAGCCTAACACCTGA 59.678 55.000 17.01 0.0 34.48 3.86 F
1852 1937 0.733729 CATGCTCCTCTGAAGCTTGC 59.266 55.000 2.10 0.0 0.00 4.01 F
2688 2812 1.668628 GGGTTACACGCTTTGCCAATG 60.669 52.381 0.00 0.0 0.00 2.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1816 1901 0.542702 ATGGGGCAAAGTGAAGGGTG 60.543 55.000 0.00 0.0 0.00 4.61 R
1937 2060 0.804989 CGCACCAAGGCCTAAAGAAG 59.195 55.000 5.16 0.0 0.00 2.85 R
2545 2669 1.134580 AGTCCAGTCCATGATTGAGCG 60.135 52.381 0.00 0.0 0.00 5.03 R
2648 2772 2.029649 CCAAAGCTTGCTTACTGTGCAT 60.030 45.455 8.36 0.0 40.34 3.96 R
3297 3429 2.708861 ACACCACACTAATGAGGGACAA 59.291 45.455 0.00 0.0 40.68 3.18 R
4102 4235 1.198867 TGAAGCGCACGCAAATAACAT 59.801 42.857 18.24 0.0 44.88 2.71 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
55 56 1.943116 TTGTTGCAGCTGCGGTTGTT 61.943 50.000 32.11 0.00 45.83 2.83
122 123 0.535335 TTACACGAGGGAGATGCCAC 59.465 55.000 0.00 0.00 38.95 5.01
187 188 2.690881 TGGGCCCGTATTCCAGCT 60.691 61.111 19.37 0.00 0.00 4.24
214 215 5.594725 TCCTGTACAGATGATCAGACCTAAC 59.405 44.000 24.68 1.90 0.00 2.34
226 227 5.122512 TCAGACCTAACGAAGACAAGAAG 57.877 43.478 0.00 0.00 0.00 2.85
232 233 6.159988 ACCTAACGAAGACAAGAAGAAGATG 58.840 40.000 0.00 0.00 0.00 2.90
263 264 2.417933 GCTCTGTGTCCATTGCAACTAG 59.582 50.000 0.00 0.00 0.00 2.57
285 286 3.118992 GGAGCTCACAATTTTCCCCAATC 60.119 47.826 17.19 0.00 0.00 2.67
286 287 3.766051 GAGCTCACAATTTTCCCCAATCT 59.234 43.478 9.40 0.00 0.00 2.40
292 293 4.098501 CACAATTTTCCCCAATCTCCTAGC 59.901 45.833 0.00 0.00 0.00 3.42
310 311 4.039730 CCTAGCCAGCTAACATGTACAGAT 59.960 45.833 0.00 0.00 0.00 2.90
319 320 6.327626 AGCTAACATGTACAGATTATCACCCT 59.672 38.462 0.00 0.00 0.00 4.34
331 332 5.911178 AGATTATCACCCTTGATTACCCTGA 59.089 40.000 0.00 0.00 39.66 3.86
345 346 6.380274 TGATTACCCTGAGAATCGTTTCTACT 59.620 38.462 8.69 0.00 42.34 2.57
346 347 4.722361 ACCCTGAGAATCGTTTCTACTC 57.278 45.455 8.69 0.00 42.34 2.59
347 348 3.447944 ACCCTGAGAATCGTTTCTACTCC 59.552 47.826 8.69 0.00 42.34 3.85
348 349 3.181474 CCCTGAGAATCGTTTCTACTCCC 60.181 52.174 8.69 0.00 42.34 4.30
349 350 3.702045 CCTGAGAATCGTTTCTACTCCCT 59.298 47.826 8.69 0.00 42.34 4.20
350 351 4.202070 CCTGAGAATCGTTTCTACTCCCTC 60.202 50.000 8.69 0.00 42.34 4.30
351 352 3.700038 TGAGAATCGTTTCTACTCCCTCC 59.300 47.826 8.69 0.00 42.34 4.30
352 353 2.688958 AGAATCGTTTCTACTCCCTCCG 59.311 50.000 6.96 0.00 40.47 4.63
353 354 2.140839 ATCGTTTCTACTCCCTCCGT 57.859 50.000 0.00 0.00 0.00 4.69
354 355 1.457346 TCGTTTCTACTCCCTCCGTC 58.543 55.000 0.00 0.00 0.00 4.79
355 356 0.455005 CGTTTCTACTCCCTCCGTCC 59.545 60.000 0.00 0.00 0.00 4.79
356 357 1.849977 GTTTCTACTCCCTCCGTCCT 58.150 55.000 0.00 0.00 0.00 3.85
357 358 2.681976 CGTTTCTACTCCCTCCGTCCTA 60.682 54.545 0.00 0.00 0.00 2.94
358 359 2.950975 GTTTCTACTCCCTCCGTCCTAG 59.049 54.545 0.00 0.00 0.00 3.02
359 360 1.890552 TCTACTCCCTCCGTCCTAGT 58.109 55.000 0.00 0.00 0.00 2.57
360 361 1.489649 TCTACTCCCTCCGTCCTAGTG 59.510 57.143 0.00 0.00 0.00 2.74
361 362 1.212441 CTACTCCCTCCGTCCTAGTGT 59.788 57.143 0.00 0.00 0.00 3.55
362 363 0.034283 ACTCCCTCCGTCCTAGTGTC 60.034 60.000 0.00 0.00 0.00 3.67
363 364 0.034380 CTCCCTCCGTCCTAGTGTCA 60.034 60.000 0.00 0.00 0.00 3.58
364 365 0.406750 TCCCTCCGTCCTAGTGTCAA 59.593 55.000 0.00 0.00 0.00 3.18
365 366 1.203087 TCCCTCCGTCCTAGTGTCAAA 60.203 52.381 0.00 0.00 0.00 2.69
366 367 1.621814 CCCTCCGTCCTAGTGTCAAAA 59.378 52.381 0.00 0.00 0.00 2.44
367 368 2.038033 CCCTCCGTCCTAGTGTCAAAAA 59.962 50.000 0.00 0.00 0.00 1.94
390 391 9.628500 AAAAACATCTTACATTATACTCCCTCC 57.372 33.333 0.00 0.00 0.00 4.30
391 392 6.591750 ACATCTTACATTATACTCCCTCCG 57.408 41.667 0.00 0.00 0.00 4.63
392 393 6.075984 ACATCTTACATTATACTCCCTCCGT 58.924 40.000 0.00 0.00 0.00 4.69
393 394 6.208994 ACATCTTACATTATACTCCCTCCGTC 59.791 42.308 0.00 0.00 0.00 4.79
394 395 5.075493 TCTTACATTATACTCCCTCCGTCC 58.925 45.833 0.00 0.00 0.00 4.79
395 396 2.606378 ACATTATACTCCCTCCGTCCC 58.394 52.381 0.00 0.00 0.00 4.46
396 397 2.090943 ACATTATACTCCCTCCGTCCCA 60.091 50.000 0.00 0.00 0.00 4.37
397 398 2.852714 TTATACTCCCTCCGTCCCAA 57.147 50.000 0.00 0.00 0.00 4.12
398 399 2.852714 TATACTCCCTCCGTCCCAAA 57.147 50.000 0.00 0.00 0.00 3.28
399 400 1.961133 ATACTCCCTCCGTCCCAAAA 58.039 50.000 0.00 0.00 0.00 2.44
400 401 1.961133 TACTCCCTCCGTCCCAAAAT 58.039 50.000 0.00 0.00 0.00 1.82
401 402 1.961133 ACTCCCTCCGTCCCAAAATA 58.039 50.000 0.00 0.00 0.00 1.40
402 403 2.271777 ACTCCCTCCGTCCCAAAATAA 58.728 47.619 0.00 0.00 0.00 1.40
403 404 2.645797 ACTCCCTCCGTCCCAAAATAAA 59.354 45.455 0.00 0.00 0.00 1.40
404 405 3.268595 ACTCCCTCCGTCCCAAAATAAAT 59.731 43.478 0.00 0.00 0.00 1.40
405 406 3.626930 TCCCTCCGTCCCAAAATAAATG 58.373 45.455 0.00 0.00 0.00 2.32
406 407 3.010808 TCCCTCCGTCCCAAAATAAATGT 59.989 43.478 0.00 0.00 0.00 2.71
407 408 3.380320 CCCTCCGTCCCAAAATAAATGTC 59.620 47.826 0.00 0.00 0.00 3.06
408 409 4.270008 CCTCCGTCCCAAAATAAATGTCT 58.730 43.478 0.00 0.00 0.00 3.41
409 410 4.335594 CCTCCGTCCCAAAATAAATGTCTC 59.664 45.833 0.00 0.00 0.00 3.36
410 411 4.912586 TCCGTCCCAAAATAAATGTCTCA 58.087 39.130 0.00 0.00 0.00 3.27
411 412 5.317808 TCCGTCCCAAAATAAATGTCTCAA 58.682 37.500 0.00 0.00 0.00 3.02
412 413 5.414454 TCCGTCCCAAAATAAATGTCTCAAG 59.586 40.000 0.00 0.00 0.00 3.02
413 414 5.095490 CGTCCCAAAATAAATGTCTCAAGC 58.905 41.667 0.00 0.00 0.00 4.01
414 415 5.106157 CGTCCCAAAATAAATGTCTCAAGCT 60.106 40.000 0.00 0.00 0.00 3.74
415 416 6.570378 CGTCCCAAAATAAATGTCTCAAGCTT 60.570 38.462 0.00 0.00 0.00 3.74
416 417 7.361713 CGTCCCAAAATAAATGTCTCAAGCTTA 60.362 37.037 0.00 0.00 0.00 3.09
417 418 7.970614 GTCCCAAAATAAATGTCTCAAGCTTAG 59.029 37.037 0.00 0.00 0.00 2.18
418 419 7.669722 TCCCAAAATAAATGTCTCAAGCTTAGT 59.330 33.333 0.00 0.00 0.00 2.24
419 420 8.956426 CCCAAAATAAATGTCTCAAGCTTAGTA 58.044 33.333 0.00 0.00 0.00 1.82
468 469 7.639113 AAGTTGAGACACTTATTTTGGAACA 57.361 32.000 0.00 0.00 35.10 3.18
469 470 7.264373 AGTTGAGACACTTATTTTGGAACAG 57.736 36.000 0.00 0.00 42.39 3.16
470 471 7.054124 AGTTGAGACACTTATTTTGGAACAGA 58.946 34.615 0.00 0.00 42.39 3.41
471 472 7.227512 AGTTGAGACACTTATTTTGGAACAGAG 59.772 37.037 0.00 0.00 42.39 3.35
472 473 5.997746 TGAGACACTTATTTTGGAACAGAGG 59.002 40.000 0.00 0.00 42.39 3.69
473 474 5.316987 AGACACTTATTTTGGAACAGAGGG 58.683 41.667 0.00 0.00 42.39 4.30
491 492 5.127194 CAGAGGGAGTACATTTGTAGTGCTA 59.873 44.000 14.27 0.00 40.66 3.49
517 518 7.976135 ATGCTAATGATGTCTCCTGATTAAC 57.024 36.000 0.00 0.00 0.00 2.01
568 569 8.060931 TGTTATGGATGCATAAAAAGCTACAA 57.939 30.769 19.77 0.00 0.00 2.41
603 605 5.446143 AACAGTTGCGTTGAATTATTGGA 57.554 34.783 0.00 0.00 0.00 3.53
605 607 4.277174 ACAGTTGCGTTGAATTATTGGACA 59.723 37.500 0.00 0.00 0.00 4.02
606 608 4.853196 CAGTTGCGTTGAATTATTGGACAG 59.147 41.667 0.00 0.00 0.00 3.51
607 609 4.518970 AGTTGCGTTGAATTATTGGACAGT 59.481 37.500 0.00 0.00 0.00 3.55
609 611 3.124466 TGCGTTGAATTATTGGACAGTCG 59.876 43.478 0.00 0.00 0.00 4.18
610 612 3.670203 CGTTGAATTATTGGACAGTCGC 58.330 45.455 0.00 0.00 0.00 5.19
614 616 3.124466 TGAATTATTGGACAGTCGCGTTG 59.876 43.478 5.77 8.99 0.00 4.10
615 617 2.157834 TTATTGGACAGTCGCGTTGT 57.842 45.000 16.52 16.52 0.00 3.32
616 618 2.157834 TATTGGACAGTCGCGTTGTT 57.842 45.000 17.33 6.95 0.00 2.83
617 619 1.305201 ATTGGACAGTCGCGTTGTTT 58.695 45.000 17.33 0.00 0.00 2.83
618 620 0.375454 TTGGACAGTCGCGTTGTTTG 59.625 50.000 17.33 8.08 0.00 2.93
619 621 0.741574 TGGACAGTCGCGTTGTTTGT 60.742 50.000 17.33 10.76 0.00 2.83
620 622 0.375803 GGACAGTCGCGTTGTTTGTT 59.624 50.000 17.33 0.00 0.00 2.83
621 623 1.202098 GGACAGTCGCGTTGTTTGTTT 60.202 47.619 17.33 0.00 0.00 2.83
622 624 2.098870 GACAGTCGCGTTGTTTGTTTC 58.901 47.619 17.33 3.58 0.00 2.78
623 625 1.735571 ACAGTCGCGTTGTTTGTTTCT 59.264 42.857 5.77 0.00 0.00 2.52
625 627 2.776225 CAGTCGCGTTGTTTGTTTCTTC 59.224 45.455 5.77 0.00 0.00 2.87
627 629 1.064357 TCGCGTTGTTTGTTTCTTCCC 59.936 47.619 5.77 0.00 0.00 3.97
631 648 3.181490 GCGTTGTTTGTTTCTTCCCTCTT 60.181 43.478 0.00 0.00 0.00 2.85
634 651 5.288472 CGTTGTTTGTTTCTTCCCTCTTTTG 59.712 40.000 0.00 0.00 0.00 2.44
642 659 4.519906 TCTTCCCTCTTTTGTTGTTCCT 57.480 40.909 0.00 0.00 0.00 3.36
647 664 2.943033 CCTCTTTTGTTGTTCCTGACGT 59.057 45.455 0.00 0.00 0.00 4.34
648 665 3.242739 CCTCTTTTGTTGTTCCTGACGTG 60.243 47.826 0.00 0.00 0.00 4.49
649 666 3.340034 TCTTTTGTTGTTCCTGACGTGT 58.660 40.909 0.00 0.00 0.00 4.49
659 676 1.476891 TCCTGACGTGTCTATGAAGGC 59.523 52.381 0.00 0.00 0.00 4.35
663 680 0.608130 ACGTGTCTATGAAGGCTGCA 59.392 50.000 0.00 0.00 0.00 4.41
675 692 4.132336 TGAAGGCTGCATAGATCATGTTC 58.868 43.478 0.50 0.00 36.95 3.18
685 702 2.440409 AGATCATGTTCTTTTGCGGCT 58.560 42.857 0.00 0.00 0.00 5.52
686 703 3.609853 AGATCATGTTCTTTTGCGGCTA 58.390 40.909 0.00 0.00 0.00 3.93
687 704 4.202441 AGATCATGTTCTTTTGCGGCTAT 58.798 39.130 0.00 0.00 0.00 2.97
688 705 3.763097 TCATGTTCTTTTGCGGCTATG 57.237 42.857 0.00 0.00 0.00 2.23
689 706 2.159393 TCATGTTCTTTTGCGGCTATGC 60.159 45.455 0.00 0.00 0.00 3.14
690 707 1.242989 TGTTCTTTTGCGGCTATGCA 58.757 45.000 0.00 0.00 44.61 3.96
697 714 2.407268 TGCGGCTATGCAAGATTGG 58.593 52.632 0.00 0.00 43.02 3.16
698 715 0.394216 TGCGGCTATGCAAGATTGGT 60.394 50.000 0.00 0.00 43.02 3.67
699 716 0.308993 GCGGCTATGCAAGATTGGTC 59.691 55.000 0.00 0.00 34.15 4.02
700 717 1.667236 CGGCTATGCAAGATTGGTCA 58.333 50.000 0.00 0.00 0.00 4.02
701 718 1.331756 CGGCTATGCAAGATTGGTCAC 59.668 52.381 0.00 0.00 0.00 3.67
702 719 2.368439 GGCTATGCAAGATTGGTCACA 58.632 47.619 0.00 0.00 0.00 3.58
703 720 2.954318 GGCTATGCAAGATTGGTCACAT 59.046 45.455 0.00 0.00 0.00 3.21
704 721 4.136796 GGCTATGCAAGATTGGTCACATA 58.863 43.478 0.00 0.00 0.00 2.29
705 722 4.214971 GGCTATGCAAGATTGGTCACATAG 59.785 45.833 0.00 10.88 37.68 2.23
706 723 5.059161 GCTATGCAAGATTGGTCACATAGA 58.941 41.667 15.94 0.00 37.28 1.98
707 724 5.528690 GCTATGCAAGATTGGTCACATAGAA 59.471 40.000 15.94 0.00 37.28 2.10
708 725 6.038603 GCTATGCAAGATTGGTCACATAGAAA 59.961 38.462 15.94 0.00 37.28 2.52
709 726 5.885230 TGCAAGATTGGTCACATAGAAAG 57.115 39.130 0.00 0.00 0.00 2.62
710 727 4.701651 TGCAAGATTGGTCACATAGAAAGG 59.298 41.667 0.00 0.00 0.00 3.11
711 728 4.096984 GCAAGATTGGTCACATAGAAAGGG 59.903 45.833 0.00 0.00 0.00 3.95
712 729 5.500234 CAAGATTGGTCACATAGAAAGGGA 58.500 41.667 0.00 0.00 0.00 4.20
713 730 5.365021 AGATTGGTCACATAGAAAGGGAG 57.635 43.478 0.00 0.00 0.00 4.30
714 731 5.032846 AGATTGGTCACATAGAAAGGGAGA 58.967 41.667 0.00 0.00 0.00 3.71
715 732 5.488919 AGATTGGTCACATAGAAAGGGAGAA 59.511 40.000 0.00 0.00 0.00 2.87
716 733 5.779241 TTGGTCACATAGAAAGGGAGAAT 57.221 39.130 0.00 0.00 0.00 2.40
717 734 5.779241 TGGTCACATAGAAAGGGAGAATT 57.221 39.130 0.00 0.00 0.00 2.17
718 735 5.500234 TGGTCACATAGAAAGGGAGAATTG 58.500 41.667 0.00 0.00 0.00 2.32
719 736 4.336713 GGTCACATAGAAAGGGAGAATTGC 59.663 45.833 0.00 0.00 0.00 3.56
720 737 5.189180 GTCACATAGAAAGGGAGAATTGCT 58.811 41.667 0.00 0.00 0.00 3.91
721 738 5.065731 GTCACATAGAAAGGGAGAATTGCTG 59.934 44.000 0.00 0.00 0.00 4.41
722 739 3.950395 ACATAGAAAGGGAGAATTGCTGC 59.050 43.478 0.00 0.00 0.00 5.25
733 750 2.100252 AGAATTGCTGCCATCGAATTGG 59.900 45.455 0.37 0.37 39.94 3.16
747 764 2.733227 CGAATTGGCAATCTTCAGGTGC 60.733 50.000 14.04 0.00 37.55 5.01
748 765 1.927487 ATTGGCAATCTTCAGGTGCA 58.073 45.000 6.96 0.00 40.12 4.57
749 766 1.250328 TTGGCAATCTTCAGGTGCAG 58.750 50.000 0.00 0.00 40.12 4.41
750 767 0.609957 TGGCAATCTTCAGGTGCAGG 60.610 55.000 0.00 0.00 40.12 4.85
751 768 1.509923 GCAATCTTCAGGTGCAGGC 59.490 57.895 0.00 0.00 38.19 4.85
752 769 1.246056 GCAATCTTCAGGTGCAGGCA 61.246 55.000 0.00 0.00 38.19 4.75
753 770 0.524862 CAATCTTCAGGTGCAGGCAC 59.475 55.000 15.78 15.78 45.49 5.01
754 771 0.403271 AATCTTCAGGTGCAGGCACT 59.597 50.000 22.24 7.35 45.52 4.40
771 788 2.622064 ACTGTTCAAGTGGACTGGAC 57.378 50.000 2.17 0.00 37.88 4.02
772 789 1.837439 ACTGTTCAAGTGGACTGGACA 59.163 47.619 2.17 0.00 37.88 4.02
773 790 2.238646 ACTGTTCAAGTGGACTGGACAA 59.761 45.455 2.17 0.00 37.88 3.18
778 795 2.771943 TCAAGTGGACTGGACAAGTTCT 59.228 45.455 0.00 0.00 40.07 3.01
812 829 2.734673 CGCGCTCTTTCCTGACAGC 61.735 63.158 5.56 0.00 0.00 4.40
817 834 3.201290 CGCTCTTTCCTGACAGCAATAT 58.799 45.455 0.00 0.00 0.00 1.28
819 836 4.194640 GCTCTTTCCTGACAGCAATATGA 58.805 43.478 0.00 0.00 0.00 2.15
846 863 4.798387 CCAAGTTTCTTGTTACAGTGTTGC 59.202 41.667 0.00 0.00 0.00 4.17
878 897 0.175073 GAGCAACGGTGGTAGGTAGG 59.825 60.000 4.49 0.00 35.00 3.18
885 904 3.467226 TGGTAGGTAGGCGGCAGC 61.467 66.667 13.08 0.00 44.18 5.25
900 919 1.956629 GCAGCGGCACTCCTACCTAA 61.957 60.000 3.18 0.00 40.72 2.69
902 921 1.143401 GCGGCACTCCTACCTAACC 59.857 63.158 0.00 0.00 0.00 2.85
903 922 1.821258 CGGCACTCCTACCTAACCC 59.179 63.158 0.00 0.00 0.00 4.11
904 923 0.686769 CGGCACTCCTACCTAACCCT 60.687 60.000 0.00 0.00 0.00 4.34
935 956 3.119096 GCGGAACCAAGGAGCGAC 61.119 66.667 0.00 0.00 0.00 5.19
952 973 2.159827 GCGACGATTGTTTGACTTCTCC 60.160 50.000 0.00 0.00 0.00 3.71
963 984 1.909302 TGACTTCTCCCCACCAGAATC 59.091 52.381 0.00 0.00 0.00 2.52
964 985 2.192263 GACTTCTCCCCACCAGAATCT 58.808 52.381 0.00 0.00 0.00 2.40
967 988 0.547471 TCTCCCCACCAGAATCTGCA 60.547 55.000 4.40 0.00 0.00 4.41
971 992 0.679002 CCCACCAGAATCTGCACAGG 60.679 60.000 4.40 3.44 0.00 4.00
983 1004 2.492773 GCACAGGCAGCAAACCAGT 61.493 57.895 0.00 0.00 40.72 4.00
990 1011 0.039165 GCAGCAAACCAGTAGGCAAC 60.039 55.000 0.00 0.00 39.06 4.17
1064 1085 2.989824 CCGAGGTGACCACTCCGT 60.990 66.667 3.63 0.00 35.16 4.69
1066 1087 2.971452 GAGGTGACCACTCCGTCC 59.029 66.667 3.63 0.00 35.16 4.79
1067 1088 2.603776 AGGTGACCACTCCGTCCC 60.604 66.667 3.63 0.00 35.16 4.46
1068 1089 4.065281 GGTGACCACTCCGTCCCG 62.065 72.222 0.00 0.00 31.35 5.14
1069 1090 4.736896 GTGACCACTCCGTCCCGC 62.737 72.222 0.00 0.00 31.35 6.13
1106 1127 3.121030 GCGTGAATGCGTGCTCCT 61.121 61.111 0.00 0.00 0.00 3.69
1108 1129 1.737735 CGTGAATGCGTGCTCCTGA 60.738 57.895 0.00 0.00 0.00 3.86
1109 1130 1.790387 GTGAATGCGTGCTCCTGAC 59.210 57.895 0.00 0.00 0.00 3.51
1110 1131 1.375908 TGAATGCGTGCTCCTGACC 60.376 57.895 0.00 0.00 0.00 4.02
1111 1132 2.045926 AATGCGTGCTCCTGACCC 60.046 61.111 0.00 0.00 0.00 4.46
1112 1133 3.958147 AATGCGTGCTCCTGACCCG 62.958 63.158 0.00 0.00 0.00 5.28
1115 1136 4.742201 CGTGCTCCTGACCCGGTG 62.742 72.222 0.00 0.00 0.00 4.94
1116 1137 3.311110 GTGCTCCTGACCCGGTGA 61.311 66.667 0.00 0.00 0.00 4.02
1124 1169 0.105964 CTGACCCGGTGAGTGTTTGA 59.894 55.000 0.00 0.00 0.00 2.69
1126 1171 1.142060 TGACCCGGTGAGTGTTTGATT 59.858 47.619 0.00 0.00 0.00 2.57
1300 1345 1.109323 GGCACCACCAACAGCTTCTT 61.109 55.000 0.00 0.00 38.86 2.52
1320 1378 2.492773 CCCCCGAGCATTTGCATCC 61.493 63.158 5.20 0.00 45.16 3.51
1321 1379 2.492773 CCCCGAGCATTTGCATCCC 61.493 63.158 5.20 0.00 45.16 3.85
1330 1388 2.026641 CATTTGCATCCCATTCCGAGT 58.973 47.619 0.00 0.00 0.00 4.18
1438 1523 5.472820 CACAATCTCTCTCTCCTTTTGCTTT 59.527 40.000 0.00 0.00 0.00 3.51
1442 1527 3.744660 TCTCTCTCCTTTTGCTTTCACC 58.255 45.455 0.00 0.00 0.00 4.02
1453 1538 0.593128 GCTTTCACCGCTCACACAAT 59.407 50.000 0.00 0.00 0.00 2.71
1479 1564 0.035317 TGCTGACAGCCTAACACCTG 59.965 55.000 24.33 0.00 41.51 4.00
1480 1565 0.321671 GCTGACAGCCTAACACCTGA 59.678 55.000 17.01 0.00 34.48 3.86
1481 1566 1.270839 GCTGACAGCCTAACACCTGAA 60.271 52.381 17.01 0.00 34.48 3.02
1485 1570 1.348036 ACAGCCTAACACCTGAAGTCC 59.652 52.381 0.00 0.00 33.40 3.85
1622 1707 3.695606 ATGTGCCAGACGCTCGGT 61.696 61.111 0.00 0.00 38.78 4.69
1838 1923 0.901580 CCTTCACTTTGCCCCATGCT 60.902 55.000 0.00 0.00 42.00 3.79
1844 1929 1.000521 TTTGCCCCATGCTCCTCTG 60.001 57.895 0.00 0.00 42.00 3.35
1845 1930 1.499913 TTTGCCCCATGCTCCTCTGA 61.500 55.000 0.00 0.00 42.00 3.27
1852 1937 0.733729 CATGCTCCTCTGAAGCTTGC 59.266 55.000 2.10 0.00 0.00 4.01
1871 1982 5.793026 TTGCAAAGAATTGTTTTGGTGTC 57.207 34.783 0.00 0.00 38.85 3.67
1902 2025 9.695526 TTATTCATTCATCTTGTTTTGAAGGTG 57.304 29.630 0.00 0.00 35.68 4.00
1920 2043 3.055530 AGGTGTCTGATCATCCACTGTTC 60.056 47.826 18.81 7.42 0.00 3.18
1926 2049 3.018856 TGATCATCCACTGTTCATTGCC 58.981 45.455 0.00 0.00 30.36 4.52
1937 2060 4.702131 ACTGTTCATTGCCCTGTTAATCTC 59.298 41.667 0.00 0.00 0.00 2.75
1986 2109 2.301346 GTTGCTGATGTATCCAAGGGG 58.699 52.381 0.00 0.00 0.00 4.79
2042 2165 5.202004 AGGACTTTCGGTGAGTATCTACAT 58.798 41.667 0.00 0.00 34.92 2.29
2090 2213 8.752766 AAGAAAACACATATCAAGAAATGCAG 57.247 30.769 0.00 0.00 0.00 4.41
2120 2243 4.019321 GGCCCATATCTGCTGATTTAGGTA 60.019 45.833 11.65 0.00 34.32 3.08
2179 2302 4.689612 TTGGAGTAGATACCAATCCTGC 57.310 45.455 0.00 0.00 40.59 4.85
2207 2330 5.050159 GCAAGAAAAGGGTATTTTTGCAGTG 60.050 40.000 8.94 0.00 36.89 3.66
2392 2516 4.273480 CGTTATCTGATGATTGTGGAACCC 59.727 45.833 0.00 0.00 32.65 4.11
2461 2585 6.454795 TCAAATTGGCTGATAAACTTGAACC 58.545 36.000 0.00 0.00 0.00 3.62
2469 2593 5.645497 GCTGATAAACTTGAACCACTGATCT 59.355 40.000 0.00 0.00 0.00 2.75
2514 2638 6.544197 TCTTAACTGCATCTTTGGTGTACAAA 59.456 34.615 0.00 0.00 46.34 2.83
2535 2659 6.479660 ACAAATGGCATTCTGTTTACACAAAG 59.520 34.615 14.04 0.00 30.36 2.77
2545 2669 6.494842 TCTGTTTACACAAAGAAACTGATGC 58.505 36.000 0.00 0.00 38.09 3.91
2688 2812 1.668628 GGGTTACACGCTTTGCCAATG 60.669 52.381 0.00 0.00 0.00 2.82
2710 2834 6.985188 TGTGCTCTTATAACAACTCCATTC 57.015 37.500 0.00 0.00 0.00 2.67
2742 2866 5.240183 AGAGATGTCAAAAACTGATGTGGTG 59.760 40.000 0.00 0.00 36.14 4.17
3306 3438 5.570205 TGGTGTAATTAGTTTGTCCCTCA 57.430 39.130 0.00 0.00 0.00 3.86
3393 3525 2.704725 ATCAACGATTGCCACACAAC 57.295 45.000 0.00 0.00 42.27 3.32
3725 3857 2.143122 TGGCTCGAGTTTTCATGACAC 58.857 47.619 15.13 0.00 0.00 3.67
3742 3874 4.009675 TGACACCAACATATTGAAGCTCC 58.990 43.478 0.00 0.00 38.15 4.70
3748 3880 4.142534 CCAACATATTGAAGCTCCAGTGTG 60.143 45.833 0.00 0.00 38.15 3.82
4038 4171 9.793259 TTCTTCTTAATGGATGGGTTATACATC 57.207 33.333 0.00 0.00 39.51 3.06
4126 4259 1.795170 ATTTGCGTGCGCTTCAAGGT 61.795 50.000 17.49 0.66 42.51 3.50
4201 4337 7.981225 GGAAGCACCATGTTTCAAAATATGTAT 59.019 33.333 10.18 0.00 39.01 2.29
4203 4339 8.931385 AGCACCATGTTTCAAAATATGTATTC 57.069 30.769 10.18 0.12 36.23 1.75
4386 4527 3.599343 TCACAGAATGGACTGAAATCCG 58.401 45.455 0.00 0.00 43.62 4.18
4544 4692 3.251484 TCTTCAGATCCTTGGACCTTGT 58.749 45.455 0.00 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.025396 CGACTATTTCAGTTGCCTGCATAG 60.025 45.833 0.00 0.00 37.72 2.23
55 56 1.350684 TGCTTAGGAGGCATCAACACA 59.649 47.619 0.00 0.00 34.56 3.72
122 123 3.995199 TCTCTGTGTGTTGCTTCCTTAG 58.005 45.455 0.00 0.00 0.00 2.18
187 188 3.382865 GTCTGATCATCTGTACAGGAGCA 59.617 47.826 22.48 18.77 0.00 4.26
214 215 5.226396 AGTCACATCTTCTTCTTGTCTTCG 58.774 41.667 0.00 0.00 0.00 3.79
226 227 5.042593 CACAGAGCTCATAGTCACATCTTC 58.957 45.833 17.77 0.00 0.00 2.87
232 233 2.493675 TGGACACAGAGCTCATAGTCAC 59.506 50.000 24.34 17.23 0.00 3.67
263 264 1.923356 TGGGGAAAATTGTGAGCTCC 58.077 50.000 12.15 3.09 0.00 4.70
285 286 3.384789 TGTACATGTTAGCTGGCTAGGAG 59.615 47.826 2.30 0.00 0.00 3.69
286 287 3.371034 TGTACATGTTAGCTGGCTAGGA 58.629 45.455 2.30 0.00 0.00 2.94
292 293 6.425114 GGTGATAATCTGTACATGTTAGCTGG 59.575 42.308 2.30 0.00 0.00 4.85
310 311 5.285401 TCTCAGGGTAATCAAGGGTGATAA 58.715 41.667 0.00 0.00 44.02 1.75
319 320 6.049955 AGAAACGATTCTCAGGGTAATCAA 57.950 37.500 1.52 0.00 42.26 2.57
345 346 0.406750 TTGACACTAGGACGGAGGGA 59.593 55.000 0.00 0.00 0.00 4.20
346 347 1.263356 TTTGACACTAGGACGGAGGG 58.737 55.000 0.00 0.00 0.00 4.30
347 348 3.396260 TTTTTGACACTAGGACGGAGG 57.604 47.619 0.00 0.00 0.00 4.30
364 365 9.628500 GGAGGGAGTATAATGTAAGATGTTTTT 57.372 33.333 0.00 0.00 0.00 1.94
365 366 7.931948 CGGAGGGAGTATAATGTAAGATGTTTT 59.068 37.037 0.00 0.00 0.00 2.43
366 367 7.070821 ACGGAGGGAGTATAATGTAAGATGTTT 59.929 37.037 0.00 0.00 0.00 2.83
367 368 6.553852 ACGGAGGGAGTATAATGTAAGATGTT 59.446 38.462 0.00 0.00 0.00 2.71
368 369 6.075984 ACGGAGGGAGTATAATGTAAGATGT 58.924 40.000 0.00 0.00 0.00 3.06
369 370 6.350277 GGACGGAGGGAGTATAATGTAAGATG 60.350 46.154 0.00 0.00 0.00 2.90
370 371 5.715753 GGACGGAGGGAGTATAATGTAAGAT 59.284 44.000 0.00 0.00 0.00 2.40
371 372 5.075493 GGACGGAGGGAGTATAATGTAAGA 58.925 45.833 0.00 0.00 0.00 2.10
372 373 4.220163 GGGACGGAGGGAGTATAATGTAAG 59.780 50.000 0.00 0.00 0.00 2.34
373 374 4.154942 GGGACGGAGGGAGTATAATGTAA 58.845 47.826 0.00 0.00 0.00 2.41
374 375 3.140707 TGGGACGGAGGGAGTATAATGTA 59.859 47.826 0.00 0.00 0.00 2.29
375 376 2.090943 TGGGACGGAGGGAGTATAATGT 60.091 50.000 0.00 0.00 0.00 2.71
376 377 2.605257 TGGGACGGAGGGAGTATAATG 58.395 52.381 0.00 0.00 0.00 1.90
377 378 3.339713 TTGGGACGGAGGGAGTATAAT 57.660 47.619 0.00 0.00 0.00 1.28
378 379 2.852714 TTGGGACGGAGGGAGTATAA 57.147 50.000 0.00 0.00 0.00 0.98
379 380 2.852714 TTTGGGACGGAGGGAGTATA 57.147 50.000 0.00 0.00 0.00 1.47
380 381 1.961133 TTTTGGGACGGAGGGAGTAT 58.039 50.000 0.00 0.00 0.00 2.12
381 382 1.961133 ATTTTGGGACGGAGGGAGTA 58.039 50.000 0.00 0.00 0.00 2.59
382 383 1.961133 TATTTTGGGACGGAGGGAGT 58.039 50.000 0.00 0.00 0.00 3.85
383 384 3.359695 TTTATTTTGGGACGGAGGGAG 57.640 47.619 0.00 0.00 0.00 4.30
384 385 3.010808 ACATTTATTTTGGGACGGAGGGA 59.989 43.478 0.00 0.00 0.00 4.20
385 386 3.361786 ACATTTATTTTGGGACGGAGGG 58.638 45.455 0.00 0.00 0.00 4.30
386 387 4.270008 AGACATTTATTTTGGGACGGAGG 58.730 43.478 0.00 0.00 0.00 4.30
387 388 4.941263 TGAGACATTTATTTTGGGACGGAG 59.059 41.667 0.00 0.00 0.00 4.63
388 389 4.912586 TGAGACATTTATTTTGGGACGGA 58.087 39.130 0.00 0.00 0.00 4.69
389 390 5.637006 TTGAGACATTTATTTTGGGACGG 57.363 39.130 0.00 0.00 0.00 4.79
390 391 5.095490 GCTTGAGACATTTATTTTGGGACG 58.905 41.667 0.00 0.00 0.00 4.79
391 392 6.272822 AGCTTGAGACATTTATTTTGGGAC 57.727 37.500 0.00 0.00 0.00 4.46
392 393 6.916360 AAGCTTGAGACATTTATTTTGGGA 57.084 33.333 0.00 0.00 0.00 4.37
393 394 7.830739 ACTAAGCTTGAGACATTTATTTTGGG 58.169 34.615 9.86 0.00 0.00 4.12
442 443 9.179909 TGTTCCAAAATAAGTGTCTCAACTTTA 57.820 29.630 0.00 0.00 40.77 1.85
443 444 8.062065 TGTTCCAAAATAAGTGTCTCAACTTT 57.938 30.769 0.00 0.00 40.77 2.66
444 445 7.556275 TCTGTTCCAAAATAAGTGTCTCAACTT 59.444 33.333 0.00 0.00 42.89 2.66
445 446 7.054124 TCTGTTCCAAAATAAGTGTCTCAACT 58.946 34.615 0.00 0.00 0.00 3.16
446 447 7.259290 TCTGTTCCAAAATAAGTGTCTCAAC 57.741 36.000 0.00 0.00 0.00 3.18
447 448 6.486657 CCTCTGTTCCAAAATAAGTGTCTCAA 59.513 38.462 0.00 0.00 0.00 3.02
448 449 5.997746 CCTCTGTTCCAAAATAAGTGTCTCA 59.002 40.000 0.00 0.00 0.00 3.27
449 450 5.412904 CCCTCTGTTCCAAAATAAGTGTCTC 59.587 44.000 0.00 0.00 0.00 3.36
450 451 5.073144 TCCCTCTGTTCCAAAATAAGTGTCT 59.927 40.000 0.00 0.00 0.00 3.41
451 452 5.313712 TCCCTCTGTTCCAAAATAAGTGTC 58.686 41.667 0.00 0.00 0.00 3.67
452 453 5.163088 ACTCCCTCTGTTCCAAAATAAGTGT 60.163 40.000 0.00 0.00 0.00 3.55
453 454 5.316987 ACTCCCTCTGTTCCAAAATAAGTG 58.683 41.667 0.00 0.00 0.00 3.16
454 455 5.584551 ACTCCCTCTGTTCCAAAATAAGT 57.415 39.130 0.00 0.00 0.00 2.24
455 456 6.472887 TGTACTCCCTCTGTTCCAAAATAAG 58.527 40.000 0.00 0.00 0.00 1.73
456 457 6.442541 TGTACTCCCTCTGTTCCAAAATAA 57.557 37.500 0.00 0.00 0.00 1.40
457 458 6.636454 ATGTACTCCCTCTGTTCCAAAATA 57.364 37.500 0.00 0.00 0.00 1.40
458 459 4.993705 TGTACTCCCTCTGTTCCAAAAT 57.006 40.909 0.00 0.00 0.00 1.82
459 460 4.993705 ATGTACTCCCTCTGTTCCAAAA 57.006 40.909 0.00 0.00 0.00 2.44
460 461 4.993705 AATGTACTCCCTCTGTTCCAAA 57.006 40.909 0.00 0.00 0.00 3.28
461 462 4.104102 ACAAATGTACTCCCTCTGTTCCAA 59.896 41.667 0.00 0.00 0.00 3.53
462 463 3.650942 ACAAATGTACTCCCTCTGTTCCA 59.349 43.478 0.00 0.00 0.00 3.53
463 464 4.287766 ACAAATGTACTCCCTCTGTTCC 57.712 45.455 0.00 0.00 0.00 3.62
464 465 5.869888 CACTACAAATGTACTCCCTCTGTTC 59.130 44.000 0.00 0.00 0.00 3.18
465 466 5.794894 CACTACAAATGTACTCCCTCTGTT 58.205 41.667 0.00 0.00 0.00 3.16
466 467 4.322801 GCACTACAAATGTACTCCCTCTGT 60.323 45.833 0.00 0.00 0.00 3.41
467 468 4.081420 AGCACTACAAATGTACTCCCTCTG 60.081 45.833 0.00 0.00 0.00 3.35
468 469 4.097418 AGCACTACAAATGTACTCCCTCT 58.903 43.478 0.00 0.00 0.00 3.69
469 470 4.473477 AGCACTACAAATGTACTCCCTC 57.527 45.455 0.00 0.00 0.00 4.30
470 471 6.368779 TTTAGCACTACAAATGTACTCCCT 57.631 37.500 0.00 0.00 0.00 4.20
471 472 6.458342 GCATTTAGCACTACAAATGTACTCCC 60.458 42.308 8.37 0.00 41.87 4.30
472 473 6.487103 GCATTTAGCACTACAAATGTACTCC 58.513 40.000 8.37 0.00 41.87 3.85
491 492 8.844244 GTTAATCAGGAGACATCATTAGCATTT 58.156 33.333 0.00 0.00 0.00 2.32
536 537 8.929827 TTTTTATGCATCCATAACAATGACAG 57.070 30.769 0.19 0.00 42.11 3.51
549 550 9.185192 GACATATTTGTAGCTTTTTATGCATCC 57.815 33.333 0.19 0.00 35.79 3.51
568 569 7.684670 CAACGCAACTGTTGTATAGACATATT 58.315 34.615 20.57 0.41 43.28 1.28
594 596 3.071479 ACAACGCGACTGTCCAATAATT 58.929 40.909 15.93 0.00 0.00 1.40
603 605 1.735571 AGAAACAAACAACGCGACTGT 59.264 42.857 15.93 13.36 0.00 3.55
605 607 2.223180 GGAAGAAACAAACAACGCGACT 60.223 45.455 15.93 0.00 0.00 4.18
606 608 2.106418 GGAAGAAACAAACAACGCGAC 58.894 47.619 15.93 0.00 0.00 5.19
607 609 1.064357 GGGAAGAAACAAACAACGCGA 59.936 47.619 15.93 0.00 0.00 5.87
609 611 2.357952 AGAGGGAAGAAACAAACAACGC 59.642 45.455 0.00 0.00 0.00 4.84
610 612 4.632538 AAGAGGGAAGAAACAAACAACG 57.367 40.909 0.00 0.00 0.00 4.10
614 616 6.163476 ACAACAAAAGAGGGAAGAAACAAAC 58.837 36.000 0.00 0.00 0.00 2.93
615 617 6.353404 ACAACAAAAGAGGGAAGAAACAAA 57.647 33.333 0.00 0.00 0.00 2.83
616 618 5.993748 ACAACAAAAGAGGGAAGAAACAA 57.006 34.783 0.00 0.00 0.00 2.83
617 619 5.105513 GGAACAACAAAAGAGGGAAGAAACA 60.106 40.000 0.00 0.00 0.00 2.83
618 620 5.127194 AGGAACAACAAAAGAGGGAAGAAAC 59.873 40.000 0.00 0.00 0.00 2.78
619 621 5.127031 CAGGAACAACAAAAGAGGGAAGAAA 59.873 40.000 0.00 0.00 0.00 2.52
620 622 4.644685 CAGGAACAACAAAAGAGGGAAGAA 59.355 41.667 0.00 0.00 0.00 2.52
621 623 4.080015 TCAGGAACAACAAAAGAGGGAAGA 60.080 41.667 0.00 0.00 0.00 2.87
622 624 4.036852 GTCAGGAACAACAAAAGAGGGAAG 59.963 45.833 0.00 0.00 0.00 3.46
623 625 3.951680 GTCAGGAACAACAAAAGAGGGAA 59.048 43.478 0.00 0.00 0.00 3.97
625 627 2.290641 CGTCAGGAACAACAAAAGAGGG 59.709 50.000 0.00 0.00 0.00 4.30
627 629 3.374058 ACACGTCAGGAACAACAAAAGAG 59.626 43.478 0.00 0.00 0.00 2.85
631 648 2.980568 AGACACGTCAGGAACAACAAA 58.019 42.857 0.00 0.00 0.00 2.83
634 651 3.909430 TCATAGACACGTCAGGAACAAC 58.091 45.455 0.00 0.00 0.00 3.32
642 659 1.404181 GCAGCCTTCATAGACACGTCA 60.404 52.381 0.00 0.00 0.00 4.35
659 676 4.968181 CGCAAAAGAACATGATCTATGCAG 59.032 41.667 27.80 20.85 40.05 4.41
663 680 4.202441 AGCCGCAAAAGAACATGATCTAT 58.798 39.130 5.85 0.00 0.00 1.98
670 687 1.818060 TGCATAGCCGCAAAAGAACAT 59.182 42.857 0.00 0.00 39.45 2.71
685 702 6.543465 CCTTTCTATGTGACCAATCTTGCATA 59.457 38.462 0.00 0.00 0.00 3.14
686 703 5.359009 CCTTTCTATGTGACCAATCTTGCAT 59.641 40.000 0.00 0.00 0.00 3.96
687 704 4.701651 CCTTTCTATGTGACCAATCTTGCA 59.298 41.667 0.00 0.00 0.00 4.08
688 705 4.096984 CCCTTTCTATGTGACCAATCTTGC 59.903 45.833 0.00 0.00 0.00 4.01
689 706 5.500234 TCCCTTTCTATGTGACCAATCTTG 58.500 41.667 0.00 0.00 0.00 3.02
690 707 5.488919 TCTCCCTTTCTATGTGACCAATCTT 59.511 40.000 0.00 0.00 0.00 2.40
691 708 5.032846 TCTCCCTTTCTATGTGACCAATCT 58.967 41.667 0.00 0.00 0.00 2.40
692 709 5.359194 TCTCCCTTTCTATGTGACCAATC 57.641 43.478 0.00 0.00 0.00 2.67
693 710 5.779241 TTCTCCCTTTCTATGTGACCAAT 57.221 39.130 0.00 0.00 0.00 3.16
694 711 5.779241 ATTCTCCCTTTCTATGTGACCAA 57.221 39.130 0.00 0.00 0.00 3.67
695 712 5.500234 CAATTCTCCCTTTCTATGTGACCA 58.500 41.667 0.00 0.00 0.00 4.02
696 713 4.336713 GCAATTCTCCCTTTCTATGTGACC 59.663 45.833 0.00 0.00 0.00 4.02
697 714 5.065731 CAGCAATTCTCCCTTTCTATGTGAC 59.934 44.000 0.00 0.00 0.00 3.67
698 715 5.188434 CAGCAATTCTCCCTTTCTATGTGA 58.812 41.667 0.00 0.00 0.00 3.58
699 716 4.201990 GCAGCAATTCTCCCTTTCTATGTG 60.202 45.833 0.00 0.00 0.00 3.21
700 717 3.950395 GCAGCAATTCTCCCTTTCTATGT 59.050 43.478 0.00 0.00 0.00 2.29
701 718 3.317430 GGCAGCAATTCTCCCTTTCTATG 59.683 47.826 0.00 0.00 0.00 2.23
702 719 3.053395 TGGCAGCAATTCTCCCTTTCTAT 60.053 43.478 0.00 0.00 0.00 1.98
703 720 2.308570 TGGCAGCAATTCTCCCTTTCTA 59.691 45.455 0.00 0.00 0.00 2.10
704 721 1.076024 TGGCAGCAATTCTCCCTTTCT 59.924 47.619 0.00 0.00 0.00 2.52
705 722 1.549203 TGGCAGCAATTCTCCCTTTC 58.451 50.000 0.00 0.00 0.00 2.62
706 723 2.105766 GATGGCAGCAATTCTCCCTTT 58.894 47.619 0.00 0.00 0.00 3.11
707 724 1.772836 GATGGCAGCAATTCTCCCTT 58.227 50.000 0.00 0.00 0.00 3.95
708 725 0.465097 CGATGGCAGCAATTCTCCCT 60.465 55.000 2.73 0.00 0.00 4.20
709 726 0.464373 TCGATGGCAGCAATTCTCCC 60.464 55.000 2.73 0.00 0.00 4.30
710 727 1.382522 TTCGATGGCAGCAATTCTCC 58.617 50.000 2.73 0.00 0.00 3.71
711 728 3.369385 CAATTCGATGGCAGCAATTCTC 58.631 45.455 2.73 0.00 0.00 2.87
712 729 2.100252 CCAATTCGATGGCAGCAATTCT 59.900 45.455 2.73 0.00 32.78 2.40
713 730 2.466846 CCAATTCGATGGCAGCAATTC 58.533 47.619 2.73 0.00 32.78 2.17
714 731 2.589798 CCAATTCGATGGCAGCAATT 57.410 45.000 2.73 5.52 32.78 2.32
722 739 3.243301 CCTGAAGATTGCCAATTCGATGG 60.243 47.826 0.37 0.37 43.70 3.51
723 740 3.379372 ACCTGAAGATTGCCAATTCGATG 59.621 43.478 0.00 0.00 0.00 3.84
724 741 3.379372 CACCTGAAGATTGCCAATTCGAT 59.621 43.478 0.00 0.00 0.00 3.59
733 750 1.246056 TGCCTGCACCTGAAGATTGC 61.246 55.000 0.00 0.00 36.76 3.56
752 769 1.837439 TGTCCAGTCCACTTGAACAGT 59.163 47.619 0.00 0.00 35.35 3.55
753 770 2.620251 TGTCCAGTCCACTTGAACAG 57.380 50.000 0.00 0.00 0.00 3.16
754 771 2.238646 ACTTGTCCAGTCCACTTGAACA 59.761 45.455 0.00 0.00 0.00 3.18
755 772 2.919228 ACTTGTCCAGTCCACTTGAAC 58.081 47.619 0.00 0.00 0.00 3.18
756 773 3.199946 AGAACTTGTCCAGTCCACTTGAA 59.800 43.478 0.00 0.00 32.94 2.69
757 774 2.771943 AGAACTTGTCCAGTCCACTTGA 59.228 45.455 0.00 0.00 32.94 3.02
758 775 2.874701 CAGAACTTGTCCAGTCCACTTG 59.125 50.000 0.00 0.00 32.94 3.16
759 776 2.771943 TCAGAACTTGTCCAGTCCACTT 59.228 45.455 0.00 0.00 32.94 3.16
760 777 2.366916 CTCAGAACTTGTCCAGTCCACT 59.633 50.000 0.00 0.00 32.94 4.00
761 778 2.760374 CTCAGAACTTGTCCAGTCCAC 58.240 52.381 0.00 0.00 32.94 4.02
762 779 1.070758 GCTCAGAACTTGTCCAGTCCA 59.929 52.381 0.00 0.00 32.94 4.02
763 780 1.609320 GGCTCAGAACTTGTCCAGTCC 60.609 57.143 0.00 0.00 32.94 3.85
764 781 1.802069 GGCTCAGAACTTGTCCAGTC 58.198 55.000 0.00 0.00 32.94 3.51
765 782 0.034059 CGGCTCAGAACTTGTCCAGT 59.966 55.000 0.00 0.00 37.30 4.00
766 783 0.034059 ACGGCTCAGAACTTGTCCAG 59.966 55.000 0.00 0.00 0.00 3.86
767 784 0.468226 AACGGCTCAGAACTTGTCCA 59.532 50.000 0.00 0.00 0.00 4.02
768 785 0.868406 CAACGGCTCAGAACTTGTCC 59.132 55.000 0.00 0.00 0.00 4.02
769 786 0.235926 GCAACGGCTCAGAACTTGTC 59.764 55.000 0.00 0.00 36.96 3.18
770 787 2.321213 GCAACGGCTCAGAACTTGT 58.679 52.632 0.00 0.00 36.96 3.16
790 807 3.793144 CAGGAAAGAGCGCGCACC 61.793 66.667 35.10 24.96 0.00 5.01
791 808 2.738521 TCAGGAAAGAGCGCGCAC 60.739 61.111 35.10 28.25 0.00 5.34
812 829 9.559958 GTAACAAGAAACTTGGACATCATATTG 57.440 33.333 14.51 0.00 0.00 1.90
817 834 6.038161 CACTGTAACAAGAAACTTGGACATCA 59.962 38.462 14.51 6.67 0.00 3.07
819 836 5.885912 ACACTGTAACAAGAAACTTGGACAT 59.114 36.000 14.51 6.98 0.00 3.06
823 840 4.798387 GCAACACTGTAACAAGAAACTTGG 59.202 41.667 14.51 1.15 0.00 3.61
846 863 0.097674 GTTGCTCAATGCTGCTACCG 59.902 55.000 0.00 0.00 43.37 4.02
885 904 0.686769 AGGGTTAGGTAGGAGTGCCG 60.687 60.000 0.00 0.00 39.96 5.69
890 909 0.105090 GGGGGAGGGTTAGGTAGGAG 60.105 65.000 0.00 0.00 0.00 3.69
912 933 1.338769 GCTCCTTGGTTCCGCTTTAGA 60.339 52.381 0.00 0.00 0.00 2.10
921 942 0.721718 CAATCGTCGCTCCTTGGTTC 59.278 55.000 0.00 0.00 0.00 3.62
935 956 2.484264 GTGGGGAGAAGTCAAACAATCG 59.516 50.000 0.00 0.00 0.00 3.34
952 973 0.679002 CCTGTGCAGATTCTGGTGGG 60.679 60.000 15.28 0.00 31.21 4.61
967 988 0.250901 CCTACTGGTTTGCTGCCTGT 60.251 55.000 0.00 8.64 40.49 4.00
971 992 0.039165 GTTGCCTACTGGTTTGCTGC 60.039 55.000 0.00 0.00 35.27 5.25
980 1001 0.610174 TGCTGGAGAGTTGCCTACTG 59.390 55.000 0.00 0.00 37.17 2.74
983 1004 1.065199 CCATTGCTGGAGAGTTGCCTA 60.065 52.381 0.00 0.00 46.37 3.93
1066 1087 3.901797 AAACCAGAAGCTCGGGCGG 62.902 63.158 0.00 0.00 44.37 6.13
1067 1088 2.358737 AAACCAGAAGCTCGGGCG 60.359 61.111 0.00 0.00 44.37 6.13
1068 1089 2.391389 CGAAACCAGAAGCTCGGGC 61.391 63.158 0.00 0.00 34.97 6.13
1069 1090 1.004918 ACGAAACCAGAAGCTCGGG 60.005 57.895 0.00 0.00 37.75 5.14
1070 1091 1.344942 CGACGAAACCAGAAGCTCGG 61.345 60.000 0.00 0.00 35.64 4.63
1071 1092 1.945776 GCGACGAAACCAGAAGCTCG 61.946 60.000 0.00 0.00 37.33 5.03
1072 1093 1.782181 GCGACGAAACCAGAAGCTC 59.218 57.895 0.00 0.00 0.00 4.09
1073 1094 2.022129 CGCGACGAAACCAGAAGCT 61.022 57.895 0.00 0.00 0.00 3.74
1074 1095 2.308039 ACGCGACGAAACCAGAAGC 61.308 57.895 15.93 0.00 0.00 3.86
1103 1124 1.052124 AAACACTCACCGGGTCAGGA 61.052 55.000 6.32 0.00 34.73 3.86
1104 1125 0.884704 CAAACACTCACCGGGTCAGG 60.885 60.000 6.32 0.00 37.30 3.86
1105 1126 0.105964 TCAAACACTCACCGGGTCAG 59.894 55.000 6.32 0.00 0.00 3.51
1106 1127 0.762418 ATCAAACACTCACCGGGTCA 59.238 50.000 6.32 0.00 0.00 4.02
1108 1129 1.604604 CAATCAAACACTCACCGGGT 58.395 50.000 6.32 0.00 0.00 5.28
1109 1130 0.240945 GCAATCAAACACTCACCGGG 59.759 55.000 6.32 0.00 0.00 5.73
1110 1131 0.110238 CGCAATCAAACACTCACCGG 60.110 55.000 0.00 0.00 0.00 5.28
1111 1132 0.586319 ACGCAATCAAACACTCACCG 59.414 50.000 0.00 0.00 0.00 4.94
1112 1133 1.925946 GCACGCAATCAAACACTCACC 60.926 52.381 0.00 0.00 0.00 4.02
1114 1135 1.002576 CTGCACGCAATCAAACACTCA 60.003 47.619 0.00 0.00 0.00 3.41
1115 1136 1.678360 CTGCACGCAATCAAACACTC 58.322 50.000 0.00 0.00 0.00 3.51
1116 1137 0.318107 GCTGCACGCAATCAAACACT 60.318 50.000 0.00 0.00 38.92 3.55
1330 1388 5.977489 TTCGGATCAAAGTTGAGAGTAGA 57.023 39.130 0.00 0.00 41.08 2.59
1438 1523 1.225855 GTGAATTGTGTGAGCGGTGA 58.774 50.000 0.00 0.00 0.00 4.02
1442 1527 1.980844 GCATTGTGAATTGTGTGAGCG 59.019 47.619 0.00 0.00 0.00 5.03
1453 1538 2.813754 GTTAGGCTGTCAGCATTGTGAA 59.186 45.455 25.68 7.70 44.75 3.18
1479 1564 2.047179 GACCACCCTGCGGACTTC 60.047 66.667 0.00 0.00 0.00 3.01
1480 1565 4.003788 CGACCACCCTGCGGACTT 62.004 66.667 0.00 0.00 0.00 3.01
1481 1566 4.988716 TCGACCACCCTGCGGACT 62.989 66.667 0.00 0.00 0.00 3.85
1485 1570 4.803426 GCTCTCGACCACCCTGCG 62.803 72.222 0.00 0.00 0.00 5.18
1622 1707 1.682684 GACGCCCTTCCTCTCCAGA 60.683 63.158 0.00 0.00 0.00 3.86
1815 1900 1.152546 GGGGCAAAGTGAAGGGTGT 60.153 57.895 0.00 0.00 0.00 4.16
1816 1901 0.542702 ATGGGGCAAAGTGAAGGGTG 60.543 55.000 0.00 0.00 0.00 4.61
1838 1923 2.936919 TCTTTGCAAGCTTCAGAGGA 57.063 45.000 0.00 0.00 0.00 3.71
1844 1929 5.065090 ACCAAAACAATTCTTTGCAAGCTTC 59.935 36.000 0.00 0.00 36.22 3.86
1845 1930 4.943093 ACCAAAACAATTCTTTGCAAGCTT 59.057 33.333 0.00 0.00 36.22 3.74
1883 1994 5.885352 TCAGACACCTTCAAAACAAGATGAA 59.115 36.000 0.00 0.00 34.57 2.57
1898 2021 2.544721 ACAGTGGATGATCAGACACCT 58.455 47.619 22.01 11.44 34.50 4.00
1902 2025 4.201891 GCAATGAACAGTGGATGATCAGAC 60.202 45.833 0.09 0.00 43.14 3.51
1920 2043 6.521151 AAAGAAGAGATTAACAGGGCAATG 57.479 37.500 0.00 0.00 0.00 2.82
1926 2049 5.995446 AGGCCTAAAGAAGAGATTAACAGG 58.005 41.667 1.29 0.00 0.00 4.00
1937 2060 0.804989 CGCACCAAGGCCTAAAGAAG 59.195 55.000 5.16 0.00 0.00 2.85
1986 2109 7.280205 CCCAGACCAAATATAACTACACTTGAC 59.720 40.741 0.00 0.00 0.00 3.18
2065 2188 8.362639 ACTGCATTTCTTGATATGTGTTTTCTT 58.637 29.630 0.00 0.00 0.00 2.52
2066 2189 7.889469 ACTGCATTTCTTGATATGTGTTTTCT 58.111 30.769 0.00 0.00 0.00 2.52
2090 2213 1.419387 AGCAGATATGGGCCTCAGAAC 59.581 52.381 4.53 0.00 0.00 3.01
2120 2243 1.134965 CGTAGCTTAGCACCTTGAGCT 60.135 52.381 7.07 2.10 46.40 4.09
2179 2302 6.928492 TGCAAAAATACCCTTTTCTTGCTTAG 59.072 34.615 5.59 0.00 35.72 2.18
2355 2478 5.757886 TCAGATAACGAAGCAAACCAAAAG 58.242 37.500 0.00 0.00 0.00 2.27
2445 2569 5.645497 AGATCAGTGGTTCAAGTTTATCAGC 59.355 40.000 0.00 0.00 0.00 4.26
2450 2574 9.653287 CTGTAATAGATCAGTGGTTCAAGTTTA 57.347 33.333 0.00 0.00 0.00 2.01
2514 2638 6.403866 TTCTTTGTGTAAACAGAATGCCAT 57.596 33.333 0.00 0.00 42.53 4.40
2535 2659 3.360533 CATGATTGAGCGCATCAGTTTC 58.639 45.455 11.47 9.24 39.68 2.78
2545 2669 1.134580 AGTCCAGTCCATGATTGAGCG 60.135 52.381 0.00 0.00 0.00 5.03
2648 2772 2.029649 CCAAAGCTTGCTTACTGTGCAT 60.030 45.455 8.36 0.00 40.34 3.96
2688 2812 6.985188 TGAATGGAGTTGTTATAAGAGCAC 57.015 37.500 0.00 0.00 0.00 4.40
2710 2834 8.768957 TCAGTTTTTGACATCTCTCTCTTATG 57.231 34.615 0.00 0.00 0.00 1.90
2742 2866 8.699749 GTTAAAACATATGAAGTGAAAACCAGC 58.300 33.333 10.38 0.00 0.00 4.85
3145 3277 7.973048 TCTCCACTAACAAAGGTATATCAGT 57.027 36.000 0.00 0.00 0.00 3.41
3297 3429 2.708861 ACACCACACTAATGAGGGACAA 59.291 45.455 0.00 0.00 40.68 3.18
3306 3438 4.041567 TCCACAATCTCACACCACACTAAT 59.958 41.667 0.00 0.00 0.00 1.73
3393 3525 8.974408 CACATGCCACATTTATTGAATCTATTG 58.026 33.333 0.00 0.00 0.00 1.90
3725 3857 4.012374 ACACTGGAGCTTCAATATGTTGG 58.988 43.478 0.00 0.00 35.99 3.77
3742 3874 5.728471 AGACACCAATAGAGAATCACACTG 58.272 41.667 0.00 0.00 37.82 3.66
3772 3904 8.041323 CCTCAACAACTATAACACCATAACTCT 58.959 37.037 0.00 0.00 0.00 3.24
3907 4039 3.604130 GCACCGAACATGCATACAC 57.396 52.632 0.00 0.00 42.88 2.90
4038 4171 7.772292 CCATACAATGGGTCCTCAATCTATATG 59.228 40.741 0.00 0.00 46.86 1.78
4041 4174 6.131972 CCATACAATGGGTCCTCAATCTAT 57.868 41.667 0.00 0.00 46.86 1.98
4102 4235 1.198867 TGAAGCGCACGCAAATAACAT 59.801 42.857 18.24 0.00 44.88 2.71
4126 4259 2.954318 GTGGTTACTAGCCGAGGATACA 59.046 50.000 0.00 0.00 41.41 2.29
4263 4399 5.371526 TGCAGAGAACTTCAAGAGAAACAT 58.628 37.500 0.00 0.00 32.35 2.71
4264 4400 4.769688 TGCAGAGAACTTCAAGAGAAACA 58.230 39.130 0.00 0.00 32.35 2.83
4265 4401 5.741388 TTGCAGAGAACTTCAAGAGAAAC 57.259 39.130 0.00 0.00 32.35 2.78
4386 4527 3.126000 GCTGCTCACTAAAATCACAGGAC 59.874 47.826 0.00 0.00 0.00 3.85
4544 4692 6.715718 TCGACCAGTTAAAATGAATTACCCAA 59.284 34.615 0.00 0.00 0.00 4.12


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

AutoCloner maintained by Alex Coulton.