Multiple sequence alignment - TraesCS4D01G133800

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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 TraesCS4D01G133800 chr4D 100.000 4759 0 0 1 4759 120834590 120829832 0.000000e+00 8789.0
1 TraesCS4D01G133800 chr4D 98.077 156 3 0 484 639 455598193 455598038 6.070000e-69 272.0
2 TraesCS4D01G133800 chr4A 96.133 2715 81 7 2026 4717 452070193 452067480 0.000000e+00 4410.0
3 TraesCS4D01G133800 chr4A 93.011 1345 68 14 645 1970 452071542 452070205 0.000000e+00 1940.0
4 TraesCS4D01G133800 chr4A 87.755 784 78 9 3780 4559 236533076 236532307 0.000000e+00 900.0
5 TraesCS4D01G133800 chr4A 82.133 347 27 16 147 477 452071868 452071541 1.020000e-66 265.0
6 TraesCS4D01G133800 chr4A 92.857 140 10 0 3772 3911 236533311 236533172 2.250000e-48 204.0
7 TraesCS4D01G133800 chr4A 92.857 140 10 0 3772 3911 236533538 236533399 2.250000e-48 204.0
8 TraesCS4D01G133800 chr4B 93.966 2668 107 15 2026 4651 183561200 183558545 0.000000e+00 3986.0
9 TraesCS4D01G133800 chr4B 94.156 770 39 3 640 1403 183562587 183561818 0.000000e+00 1168.0
10 TraesCS4D01G133800 chr4B 94.434 557 25 3 1419 1975 183561749 183561199 0.000000e+00 852.0
11 TraesCS4D01G133800 chr4B 94.694 490 17 6 2 483 183563066 183562578 0.000000e+00 752.0
12 TraesCS4D01G133800 chr4B 95.556 45 1 1 4674 4717 183558544 183558500 2.380000e-08 71.3
13 TraesCS4D01G133800 chr1A 87.296 795 76 14 3772 4559 548729671 548730447 0.000000e+00 885.0
14 TraesCS4D01G133800 chr1A 91.429 140 12 0 3772 3911 548729444 548729583 4.860000e-45 193.0
15 TraesCS4D01G133800 chr6D 86.871 815 74 18 3772 4576 262405953 262405162 0.000000e+00 881.0
16 TraesCS4D01G133800 chr5B 87.667 600 59 8 3743 4341 119892250 119892835 0.000000e+00 684.0
17 TraesCS4D01G133800 chr7B 96.795 156 5 0 484 639 4920078 4920233 1.310000e-65 261.0
18 TraesCS4D01G133800 chr7B 96.129 155 6 0 484 638 680543564 680543718 2.200000e-63 254.0
19 TraesCS4D01G133800 chr3B 95.597 159 7 0 484 642 736318226 736318068 6.110000e-64 255.0
20 TraesCS4D01G133800 chr1D 96.154 156 6 0 484 639 112771399 112771554 6.110000e-64 255.0
21 TraesCS4D01G133800 chr7A 95.513 156 7 0 484 639 662667646 662667801 2.840000e-62 250.0
22 TraesCS4D01G133800 chr7A 91.279 172 14 1 474 645 690200206 690200376 2.860000e-57 233.0
23 TraesCS4D01G133800 chr6B 94.444 162 9 0 478 639 702214383 702214544 2.840000e-62 250.0
24 TraesCS4D01G133800 chr6B 96.364 55 2 0 1973 2027 672534932 672534986 1.820000e-14 91.6
25 TraesCS4D01G133800 chr5A 95.513 156 7 0 484 639 30666620 30666465 2.840000e-62 250.0
26 TraesCS4D01G133800 chr5A 98.182 55 1 0 1974 2028 575688885 575688939 3.920000e-16 97.1
27 TraesCS4D01G133800 chr5D 100.000 57 0 0 1974 2030 451882164 451882108 6.510000e-19 106.0
28 TraesCS4D01G133800 chr1B 98.148 54 1 0 1974 2027 27084824 27084877 1.410000e-15 95.3
29 TraesCS4D01G133800 chr1B 98.148 54 1 0 1974 2027 661577902 661577955 1.410000e-15 95.3
30 TraesCS4D01G133800 chr7D 94.915 59 3 0 1970 2028 27417279 27417337 5.070000e-15 93.5
31 TraesCS4D01G133800 chr3D 95.000 60 2 1 1974 2032 475441935 475441994 5.070000e-15 93.5
32 TraesCS4D01G133800 chr3D 94.915 59 1 2 1974 2031 591356878 591356935 1.820000e-14 91.6
33 TraesCS4D01G133800 chr2D 91.935 62 3 2 1974 2035 631557356 631557415 8.490000e-13 86.1


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 TraesCS4D01G133800 chr4D 120829832 120834590 4758 True 8789.00 8789 100.000000 1 4759 1 chr4D.!!$R1 4758
1 TraesCS4D01G133800 chr4A 452067480 452071868 4388 True 2205.00 4410 90.425667 147 4717 3 chr4A.!!$R2 4570
2 TraesCS4D01G133800 chr4A 236532307 236533538 1231 True 436.00 900 91.156333 3772 4559 3 chr4A.!!$R1 787
3 TraesCS4D01G133800 chr4B 183558500 183563066 4566 True 1365.86 3986 94.561200 2 4717 5 chr4B.!!$R1 4715
4 TraesCS4D01G133800 chr1A 548729444 548730447 1003 False 539.00 885 89.362500 3772 4559 2 chr1A.!!$F1 787
5 TraesCS4D01G133800 chr6D 262405162 262405953 791 True 881.00 881 86.871000 3772 4576 1 chr6D.!!$R1 804
6 TraesCS4D01G133800 chr5B 119892250 119892835 585 False 684.00 684 87.667000 3743 4341 1 chr5B.!!$F1 598

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
511 533 0.100682 TCTGCGTACGATGCCTTCTC 59.899 55.000 21.65 0.0 0.00 2.87 F
520 542 0.108804 GATGCCTTCTCGTCGGACAA 60.109 55.000 9.10 0.0 0.00 3.18 F
1068 1095 0.255033 TCCTCGTCTCCTCCGATCAA 59.745 55.000 0.00 0.0 33.27 2.57 F
1130 1157 0.530211 CTTGATCAGCTGCTCCTCCG 60.530 60.000 14.69 0.0 0.00 4.63 F
1797 1886 1.135315 GGCATGTTGTTGACGCATGAT 60.135 47.619 16.99 0.0 41.62 2.45 F
2952 3042 2.025969 CACTGTCTCTGCCACAGCG 61.026 63.158 0.00 0.0 44.50 5.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1408 1443 1.000233 TGGGGCAGGCTGGTTATTG 60.000 57.895 17.64 0.0 0.00 1.90 R
2385 2474 1.374343 CCTGCAGCGCATCATCAAGT 61.374 55.000 11.47 0.0 38.13 3.16 R
2928 3018 0.038251 TGGCAGAGACAGTGTTAGCG 60.038 55.000 0.00 0.0 0.00 4.26 R
3093 3183 0.322456 ATGGATTGACACCCACACCG 60.322 55.000 0.00 0.0 34.92 4.94 R
3454 3544 2.100197 GTTAAATGTGGAAGGGGAGGC 58.900 52.381 0.00 0.0 0.00 4.70 R
4738 5112 0.465705 TGGATGCTCTCGCCCTAAAG 59.534 55.000 0.00 0.0 34.43 1.85 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
41 42 1.781786 TCCAATTCCCCTCTCTCTCG 58.218 55.000 0.00 0.00 0.00 4.04
53 54 4.365723 CCTCTCTCTCGTAGTCTCTGTAC 58.634 52.174 0.00 0.00 0.00 2.90
98 99 2.425668 CAATCCATTACCCCGTTTGTCC 59.574 50.000 0.00 0.00 0.00 4.02
121 122 3.446799 TGCTTGATTTGTTTCTGCACAC 58.553 40.909 0.00 0.00 0.00 3.82
230 236 3.720949 ATGCATACACAATGGCATGAC 57.279 42.857 0.00 0.00 35.99 3.06
299 305 8.740123 TCCGGCTAATGTAATTTCAAAAGATA 57.260 30.769 0.00 0.00 37.87 1.98
326 342 3.914426 AGGATCCGTGTTTATTCTGCT 57.086 42.857 5.98 0.00 0.00 4.24
334 350 4.391830 CCGTGTTTATTCTGCTTGCTCTAA 59.608 41.667 0.00 0.00 0.00 2.10
402 424 7.010738 GGTTGCTTGTACATAACATACATACGT 59.989 37.037 15.57 0.00 38.10 3.57
494 516 6.864360 CTATAGTAGCACCGAAACTACTCT 57.136 41.667 12.52 7.70 44.48 3.24
495 517 3.851976 AGTAGCACCGAAACTACTCTG 57.148 47.619 5.66 0.00 44.48 3.35
496 518 2.094649 AGTAGCACCGAAACTACTCTGC 60.095 50.000 5.66 0.00 44.48 4.26
497 519 0.388649 AGCACCGAAACTACTCTGCG 60.389 55.000 0.00 0.00 0.00 5.18
498 520 0.666577 GCACCGAAACTACTCTGCGT 60.667 55.000 0.00 0.00 0.00 5.24
499 521 1.401931 GCACCGAAACTACTCTGCGTA 60.402 52.381 0.00 0.00 0.00 4.42
500 522 2.248487 CACCGAAACTACTCTGCGTAC 58.752 52.381 0.00 0.00 0.00 3.67
501 523 1.135859 ACCGAAACTACTCTGCGTACG 60.136 52.381 11.84 11.84 0.00 3.67
502 524 1.129251 CCGAAACTACTCTGCGTACGA 59.871 52.381 21.65 3.19 0.00 3.43
503 525 2.223203 CCGAAACTACTCTGCGTACGAT 60.223 50.000 21.65 0.40 0.00 3.73
504 526 2.776765 CGAAACTACTCTGCGTACGATG 59.223 50.000 21.65 10.55 0.00 3.84
505 527 2.190325 AACTACTCTGCGTACGATGC 57.810 50.000 21.65 1.15 0.00 3.91
506 528 0.381089 ACTACTCTGCGTACGATGCC 59.619 55.000 21.65 0.89 0.00 4.40
507 529 0.663688 CTACTCTGCGTACGATGCCT 59.336 55.000 21.65 0.00 0.00 4.75
508 530 1.065701 CTACTCTGCGTACGATGCCTT 59.934 52.381 21.65 0.00 0.00 4.35
509 531 0.179134 ACTCTGCGTACGATGCCTTC 60.179 55.000 21.65 0.00 0.00 3.46
510 532 0.101399 CTCTGCGTACGATGCCTTCT 59.899 55.000 21.65 0.00 0.00 2.85
511 533 0.100682 TCTGCGTACGATGCCTTCTC 59.899 55.000 21.65 0.00 0.00 2.87
512 534 1.202973 CTGCGTACGATGCCTTCTCG 61.203 60.000 21.65 0.00 41.77 4.04
514 536 1.201098 GCGTACGATGCCTTCTCGTC 61.201 60.000 21.65 0.00 45.63 4.20
515 537 0.924363 CGTACGATGCCTTCTCGTCG 60.924 60.000 10.44 4.12 45.63 5.12
516 538 0.591741 GTACGATGCCTTCTCGTCGG 60.592 60.000 1.17 0.00 45.63 4.79
517 539 0.745486 TACGATGCCTTCTCGTCGGA 60.745 55.000 1.17 0.00 45.63 4.55
518 540 1.586564 CGATGCCTTCTCGTCGGAC 60.587 63.158 0.00 0.00 40.65 4.79
519 541 1.511305 GATGCCTTCTCGTCGGACA 59.489 57.895 9.10 0.00 0.00 4.02
520 542 0.108804 GATGCCTTCTCGTCGGACAA 60.109 55.000 9.10 0.00 0.00 3.18
521 543 0.389948 ATGCCTTCTCGTCGGACAAC 60.390 55.000 9.10 0.00 0.00 3.32
522 544 1.006571 GCCTTCTCGTCGGACAACA 60.007 57.895 9.10 0.00 0.00 3.33
523 545 1.009389 GCCTTCTCGTCGGACAACAG 61.009 60.000 9.10 0.95 0.00 3.16
524 546 0.314302 CCTTCTCGTCGGACAACAGT 59.686 55.000 9.10 0.00 0.00 3.55
525 547 1.538512 CCTTCTCGTCGGACAACAGTA 59.461 52.381 9.10 0.00 0.00 2.74
526 548 2.582687 CTTCTCGTCGGACAACAGTAC 58.417 52.381 9.10 0.00 0.00 2.73
527 549 0.514255 TCTCGTCGGACAACAGTACG 59.486 55.000 9.10 0.00 40.95 3.67
528 550 0.514255 CTCGTCGGACAACAGTACGA 59.486 55.000 9.10 0.00 45.76 3.43
532 554 2.913777 TCGGACAACAGTACGATCAG 57.086 50.000 0.00 0.00 43.28 2.90
533 555 2.429478 TCGGACAACAGTACGATCAGA 58.571 47.619 0.00 0.00 43.28 3.27
534 556 2.161012 TCGGACAACAGTACGATCAGAC 59.839 50.000 0.00 0.00 43.28 3.51
535 557 2.161808 CGGACAACAGTACGATCAGACT 59.838 50.000 0.00 0.00 42.17 3.24
536 558 3.502920 GGACAACAGTACGATCAGACTG 58.497 50.000 18.12 18.12 46.95 3.51
537 559 3.190744 GGACAACAGTACGATCAGACTGA 59.809 47.826 23.92 7.80 44.88 3.41
538 560 4.407818 GACAACAGTACGATCAGACTGAG 58.592 47.826 23.92 18.43 44.88 3.35
539 561 4.072839 ACAACAGTACGATCAGACTGAGA 58.927 43.478 23.92 0.00 44.88 3.27
540 562 4.702612 ACAACAGTACGATCAGACTGAGAT 59.297 41.667 23.92 11.23 44.88 2.75
541 563 5.163703 ACAACAGTACGATCAGACTGAGATC 60.164 44.000 23.92 3.73 44.88 2.75
542 564 4.518249 ACAGTACGATCAGACTGAGATCA 58.482 43.478 23.92 0.00 44.88 2.92
543 565 5.129634 ACAGTACGATCAGACTGAGATCAT 58.870 41.667 23.92 0.00 44.88 2.45
544 566 5.238432 ACAGTACGATCAGACTGAGATCATC 59.762 44.000 23.92 2.27 44.88 2.92
545 567 5.469760 CAGTACGATCAGACTGAGATCATCT 59.530 44.000 15.74 0.00 44.88 2.90
546 568 5.700832 AGTACGATCAGACTGAGATCATCTC 59.299 44.000 11.52 7.83 43.65 2.75
547 569 4.717877 ACGATCAGACTGAGATCATCTCT 58.282 43.478 15.89 0.00 43.73 3.10
548 570 5.863965 ACGATCAGACTGAGATCATCTCTA 58.136 41.667 15.89 1.86 43.73 2.43
549 571 6.295249 ACGATCAGACTGAGATCATCTCTAA 58.705 40.000 15.89 0.00 43.73 2.10
550 572 6.770303 ACGATCAGACTGAGATCATCTCTAAA 59.230 38.462 15.89 0.00 43.73 1.85
551 573 7.448161 ACGATCAGACTGAGATCATCTCTAAAT 59.552 37.037 15.89 0.00 43.73 1.40
552 574 8.945057 CGATCAGACTGAGATCATCTCTAAATA 58.055 37.037 15.89 0.00 43.73 1.40
554 576 9.812347 ATCAGACTGAGATCATCTCTAAATACT 57.188 33.333 15.89 4.38 43.73 2.12
557 579 9.739276 AGACTGAGATCATCTCTAAATACTAGG 57.261 37.037 15.89 0.00 43.73 3.02
558 580 8.877864 ACTGAGATCATCTCTAAATACTAGGG 57.122 38.462 15.89 0.00 43.73 3.53
559 581 7.396055 ACTGAGATCATCTCTAAATACTAGGGC 59.604 40.741 15.89 0.00 43.73 5.19
560 582 6.665680 TGAGATCATCTCTAAATACTAGGGCC 59.334 42.308 15.89 0.00 43.73 5.80
561 583 5.961421 AGATCATCTCTAAATACTAGGGCCC 59.039 44.000 16.46 16.46 30.26 5.80
562 584 5.087923 TCATCTCTAAATACTAGGGCCCA 57.912 43.478 27.56 9.36 0.00 5.36
563 585 4.838986 TCATCTCTAAATACTAGGGCCCAC 59.161 45.833 27.56 0.00 0.00 4.61
564 586 4.274794 TCTCTAAATACTAGGGCCCACA 57.725 45.455 27.56 10.69 0.00 4.17
565 587 4.627015 TCTCTAAATACTAGGGCCCACAA 58.373 43.478 27.56 8.08 0.00 3.33
566 588 5.034200 TCTCTAAATACTAGGGCCCACAAA 58.966 41.667 27.56 7.01 0.00 2.83
567 589 5.104652 TCTCTAAATACTAGGGCCCACAAAC 60.105 44.000 27.56 0.00 0.00 2.93
568 590 4.786454 TCTAAATACTAGGGCCCACAAACT 59.214 41.667 27.56 3.89 0.00 2.66
569 591 3.366052 AATACTAGGGCCCACAAACTG 57.634 47.619 27.56 7.80 0.00 3.16
570 592 2.032965 TACTAGGGCCCACAAACTGA 57.967 50.000 27.56 0.00 0.00 3.41
571 593 1.145571 ACTAGGGCCCACAAACTGAA 58.854 50.000 27.56 0.00 0.00 3.02
572 594 1.710809 ACTAGGGCCCACAAACTGAAT 59.289 47.619 27.56 0.25 0.00 2.57
573 595 2.290960 ACTAGGGCCCACAAACTGAATC 60.291 50.000 27.56 0.00 0.00 2.52
574 596 0.482446 AGGGCCCACAAACTGAATCA 59.518 50.000 27.56 0.00 0.00 2.57
575 597 1.077663 AGGGCCCACAAACTGAATCAT 59.922 47.619 27.56 0.00 0.00 2.45
576 598 1.478105 GGGCCCACAAACTGAATCATC 59.522 52.381 19.95 0.00 0.00 2.92
577 599 1.478105 GGCCCACAAACTGAATCATCC 59.522 52.381 0.00 0.00 0.00 3.51
578 600 2.170166 GCCCACAAACTGAATCATCCA 58.830 47.619 0.00 0.00 0.00 3.41
579 601 2.762327 GCCCACAAACTGAATCATCCAT 59.238 45.455 0.00 0.00 0.00 3.41
580 602 3.429822 GCCCACAAACTGAATCATCCATG 60.430 47.826 0.00 0.00 0.00 3.66
581 603 3.131577 CCCACAAACTGAATCATCCATGG 59.868 47.826 4.97 4.97 0.00 3.66
582 604 3.429822 CCACAAACTGAATCATCCATGGC 60.430 47.826 6.96 0.00 0.00 4.40
583 605 3.446161 CACAAACTGAATCATCCATGGCT 59.554 43.478 6.96 0.00 0.00 4.75
584 606 3.446161 ACAAACTGAATCATCCATGGCTG 59.554 43.478 9.41 9.41 0.00 4.85
585 607 3.377253 AACTGAATCATCCATGGCTGT 57.623 42.857 15.03 3.77 0.00 4.40
586 608 2.928334 ACTGAATCATCCATGGCTGTC 58.072 47.619 15.03 7.28 0.00 3.51
587 609 2.508716 ACTGAATCATCCATGGCTGTCT 59.491 45.455 15.03 3.91 0.00 3.41
588 610 3.139850 CTGAATCATCCATGGCTGTCTC 58.860 50.000 15.03 12.53 0.00 3.36
589 611 2.775960 TGAATCATCCATGGCTGTCTCT 59.224 45.455 15.03 0.00 0.00 3.10
590 612 3.969312 TGAATCATCCATGGCTGTCTCTA 59.031 43.478 15.03 0.00 0.00 2.43
591 613 4.409901 TGAATCATCCATGGCTGTCTCTAA 59.590 41.667 15.03 0.00 0.00 2.10
592 614 5.072736 TGAATCATCCATGGCTGTCTCTAAT 59.927 40.000 15.03 0.00 0.00 1.73
593 615 4.613925 TCATCCATGGCTGTCTCTAATC 57.386 45.455 15.03 0.00 0.00 1.75
594 616 3.006217 TCATCCATGGCTGTCTCTAATCG 59.994 47.826 15.03 0.00 0.00 3.34
595 617 2.388735 TCCATGGCTGTCTCTAATCGT 58.611 47.619 6.96 0.00 0.00 3.73
596 618 3.562182 TCCATGGCTGTCTCTAATCGTA 58.438 45.455 6.96 0.00 0.00 3.43
597 619 4.152647 TCCATGGCTGTCTCTAATCGTAT 58.847 43.478 6.96 0.00 0.00 3.06
598 620 4.021981 TCCATGGCTGTCTCTAATCGTATG 60.022 45.833 6.96 0.00 0.00 2.39
599 621 4.240888 CATGGCTGTCTCTAATCGTATGG 58.759 47.826 0.00 0.00 0.00 2.74
600 622 3.562182 TGGCTGTCTCTAATCGTATGGA 58.438 45.455 0.00 0.00 0.00 3.41
601 623 3.570125 TGGCTGTCTCTAATCGTATGGAG 59.430 47.826 0.00 0.00 0.00 3.86
602 624 3.570550 GGCTGTCTCTAATCGTATGGAGT 59.429 47.826 4.22 0.00 0.00 3.85
603 625 4.541779 GCTGTCTCTAATCGTATGGAGTG 58.458 47.826 4.22 0.00 0.00 3.51
604 626 4.036971 GCTGTCTCTAATCGTATGGAGTGT 59.963 45.833 4.22 0.00 0.00 3.55
605 627 5.450688 GCTGTCTCTAATCGTATGGAGTGTT 60.451 44.000 4.22 0.00 0.00 3.32
606 628 6.132791 TGTCTCTAATCGTATGGAGTGTTC 57.867 41.667 4.22 0.00 0.00 3.18
607 629 5.206299 GTCTCTAATCGTATGGAGTGTTCG 58.794 45.833 4.22 0.00 0.00 3.95
608 630 4.275196 TCTCTAATCGTATGGAGTGTTCGG 59.725 45.833 4.22 0.00 0.00 4.30
609 631 1.935933 AATCGTATGGAGTGTTCGGC 58.064 50.000 0.00 0.00 0.00 5.54
610 632 0.821517 ATCGTATGGAGTGTTCGGCA 59.178 50.000 0.00 0.00 0.00 5.69
635 657 6.964246 CGAATTTATCGTACGTATAGCAAGG 58.036 40.000 16.05 0.00 46.52 3.61
636 658 6.580041 CGAATTTATCGTACGTATAGCAAGGT 59.420 38.462 16.05 0.00 46.52 3.50
637 659 7.113965 CGAATTTATCGTACGTATAGCAAGGTT 59.886 37.037 16.05 0.00 46.52 3.50
638 660 7.864307 ATTTATCGTACGTATAGCAAGGTTC 57.136 36.000 16.05 0.00 0.00 3.62
639 661 4.906065 ATCGTACGTATAGCAAGGTTCA 57.094 40.909 16.05 0.00 0.00 3.18
640 662 4.906065 TCGTACGTATAGCAAGGTTCAT 57.094 40.909 16.05 0.00 0.00 2.57
641 663 6.564709 ATCGTACGTATAGCAAGGTTCATA 57.435 37.500 16.05 0.00 0.00 2.15
642 664 5.993891 TCGTACGTATAGCAAGGTTCATAG 58.006 41.667 16.05 0.00 0.00 2.23
643 665 5.528690 TCGTACGTATAGCAAGGTTCATAGT 59.471 40.000 16.05 0.00 0.00 2.12
644 666 6.705825 TCGTACGTATAGCAAGGTTCATAGTA 59.294 38.462 16.05 0.00 0.00 1.82
645 667 7.014115 CGTACGTATAGCAAGGTTCATAGTAG 58.986 42.308 7.22 0.00 0.00 2.57
646 668 5.770417 ACGTATAGCAAGGTTCATAGTAGC 58.230 41.667 0.00 0.00 0.00 3.58
647 669 5.301045 ACGTATAGCAAGGTTCATAGTAGCA 59.699 40.000 0.00 0.00 0.00 3.49
648 670 5.629849 CGTATAGCAAGGTTCATAGTAGCAC 59.370 44.000 0.00 0.00 0.00 4.40
1011 1038 1.075212 TGTCATTCCATGCAACCAGGA 59.925 47.619 0.00 0.00 0.00 3.86
1021 1048 0.811281 GCAACCAGGAATACTGCACC 59.189 55.000 0.00 0.00 46.14 5.01
1037 1064 3.062466 CCGTCTCGGCTCACAGGA 61.062 66.667 0.00 0.00 41.17 3.86
1053 1080 0.450983 AGGAATCGTCGTTCGTCCTC 59.549 55.000 8.26 3.04 39.71 3.71
1068 1095 0.255033 TCCTCGTCTCCTCCGATCAA 59.745 55.000 0.00 0.00 33.27 2.57
1071 1098 1.064803 CTCGTCTCCTCCGATCAAGTG 59.935 57.143 0.00 0.00 33.27 3.16
1130 1157 0.530211 CTTGATCAGCTGCTCCTCCG 60.530 60.000 14.69 0.00 0.00 4.63
1216 1243 8.902806 ACAAGTTCAATGTGAGAATCTTAACAA 58.097 29.630 4.25 0.00 34.92 2.83
1268 1303 6.719829 ACACATATACATACATTCGGAGGAGA 59.280 38.462 0.00 0.00 0.00 3.71
1284 1319 6.378564 TCGGAGGAGAAATAGATAGCTAATGG 59.621 42.308 0.00 0.00 0.00 3.16
1343 1378 2.140717 CCACTCTTTACACAACCCGAC 58.859 52.381 0.00 0.00 0.00 4.79
1371 1406 6.199937 AGTACAATGCTTTCTTTGCCATAG 57.800 37.500 0.00 0.00 32.42 2.23
1397 1432 8.337532 GTTTCAAAATGTCATTTTCCTTTCTGG 58.662 33.333 18.62 7.30 40.27 3.86
1403 1438 4.344679 TGTCATTTTCCTTTCTGGTGCAAT 59.655 37.500 0.00 0.00 37.07 3.56
1408 1443 8.250332 TCATTTTCCTTTCTGGTGCAATATAAC 58.750 33.333 0.00 0.00 37.07 1.89
1411 1499 7.716799 TTCCTTTCTGGTGCAATATAACAAT 57.283 32.000 0.00 0.00 37.07 2.71
1624 1712 3.103447 TCTATGCAAGAGAAGGCGATG 57.897 47.619 0.00 0.00 0.00 3.84
1651 1739 4.641396 TCTTGTCAAGGTCGTCAATCATT 58.359 39.130 12.66 0.00 0.00 2.57
1758 1847 1.607148 CTGCATGCCCTCACACATATG 59.393 52.381 16.68 0.00 0.00 1.78
1768 1857 1.136891 TCACACATATGGACAGCCTCG 59.863 52.381 7.80 0.00 34.31 4.63
1797 1886 1.135315 GGCATGTTGTTGACGCATGAT 60.135 47.619 16.99 0.00 41.62 2.45
1936 2025 6.773976 TTTCAACAAAGACACATCCTTTCT 57.226 33.333 0.00 0.00 32.04 2.52
1947 2036 4.965532 ACACATCCTTTCTATAGACAGGCT 59.034 41.667 24.65 15.76 40.82 4.58
1980 2069 9.533831 AAAGAAAATTCATACAACATACTCCCT 57.466 29.630 0.00 0.00 0.00 4.20
1981 2070 8.738645 AGAAAATTCATACAACATACTCCCTC 57.261 34.615 0.00 0.00 0.00 4.30
1982 2071 7.775561 AGAAAATTCATACAACATACTCCCTCC 59.224 37.037 0.00 0.00 0.00 4.30
1983 2072 4.665833 TTCATACAACATACTCCCTCCG 57.334 45.455 0.00 0.00 0.00 4.63
1984 2073 3.638860 TCATACAACATACTCCCTCCGT 58.361 45.455 0.00 0.00 0.00 4.69
1985 2074 4.795469 TCATACAACATACTCCCTCCGTA 58.205 43.478 0.00 0.00 0.00 4.02
1986 2075 5.202765 TCATACAACATACTCCCTCCGTAA 58.797 41.667 0.00 0.00 0.00 3.18
1987 2076 5.657745 TCATACAACATACTCCCTCCGTAAA 59.342 40.000 0.00 0.00 0.00 2.01
1988 2077 4.467198 ACAACATACTCCCTCCGTAAAG 57.533 45.455 0.00 0.00 0.00 1.85
1989 2078 4.091549 ACAACATACTCCCTCCGTAAAGA 58.908 43.478 0.00 0.00 0.00 2.52
1990 2079 4.529377 ACAACATACTCCCTCCGTAAAGAA 59.471 41.667 0.00 0.00 0.00 2.52
1991 2080 5.012354 ACAACATACTCCCTCCGTAAAGAAA 59.988 40.000 0.00 0.00 0.00 2.52
1992 2081 5.952347 ACATACTCCCTCCGTAAAGAAAT 57.048 39.130 0.00 0.00 0.00 2.17
1993 2082 7.093201 ACAACATACTCCCTCCGTAAAGAAATA 60.093 37.037 0.00 0.00 0.00 1.40
1994 2083 7.613551 ACATACTCCCTCCGTAAAGAAATAT 57.386 36.000 0.00 0.00 0.00 1.28
1995 2084 8.716674 ACATACTCCCTCCGTAAAGAAATATA 57.283 34.615 0.00 0.00 0.00 0.86
1996 2085 9.151177 ACATACTCCCTCCGTAAAGAAATATAA 57.849 33.333 0.00 0.00 0.00 0.98
1997 2086 9.991906 CATACTCCCTCCGTAAAGAAATATAAA 57.008 33.333 0.00 0.00 0.00 1.40
1998 2087 9.993454 ATACTCCCTCCGTAAAGAAATATAAAC 57.007 33.333 0.00 0.00 0.00 2.01
1999 2088 6.982724 ACTCCCTCCGTAAAGAAATATAAACG 59.017 38.462 0.00 0.00 0.00 3.60
2000 2089 5.754890 TCCCTCCGTAAAGAAATATAAACGC 59.245 40.000 0.00 0.00 0.00 4.84
2001 2090 5.756833 CCCTCCGTAAAGAAATATAAACGCT 59.243 40.000 0.00 0.00 0.00 5.07
2002 2091 6.073927 CCCTCCGTAAAGAAATATAAACGCTC 60.074 42.308 0.00 0.00 0.00 5.03
2003 2092 6.700520 CCTCCGTAAAGAAATATAAACGCTCT 59.299 38.462 0.00 0.00 0.00 4.09
2004 2093 7.224167 CCTCCGTAAAGAAATATAAACGCTCTT 59.776 37.037 0.00 0.00 0.00 2.85
2005 2094 9.241317 CTCCGTAAAGAAATATAAACGCTCTTA 57.759 33.333 0.00 0.00 0.00 2.10
2006 2095 9.754382 TCCGTAAAGAAATATAAACGCTCTTAT 57.246 29.630 0.00 0.00 0.00 1.73
2021 2110 8.649973 AACGCTCTTATATTTCTTTACAGAGG 57.350 34.615 0.00 0.00 0.00 3.69
2022 2111 7.210873 ACGCTCTTATATTTCTTTACAGAGGG 58.789 38.462 8.36 8.36 42.53 4.30
2023 2112 7.069578 ACGCTCTTATATTTCTTTACAGAGGGA 59.930 37.037 14.96 0.00 40.49 4.20
2024 2113 7.596995 CGCTCTTATATTTCTTTACAGAGGGAG 59.403 40.741 4.76 0.00 40.49 4.30
2079 2168 7.792374 TTCTAACTGAATCATAATCAGGCAC 57.208 36.000 8.26 0.00 46.81 5.01
2332 2421 9.909644 CAGTTGTTGTCCTAGGTATATGTATAC 57.090 37.037 9.08 0.00 38.21 1.47
2626 2716 5.382618 ACTGCTTTCCTGATGAATGTTTC 57.617 39.130 0.00 0.00 31.67 2.78
2952 3042 2.025969 CACTGTCTCTGCCACAGCG 61.026 63.158 0.00 0.00 44.50 5.18
3072 3162 3.402110 CAATGTGCCACAGACAGTAGAA 58.598 45.455 3.00 0.00 0.00 2.10
3093 3183 5.179555 AGAACACTCGCTTTTCTTTACCATC 59.820 40.000 0.00 0.00 0.00 3.51
3162 3252 2.036992 GGTGGGCACAATCAACAATTCA 59.963 45.455 0.00 0.00 0.00 2.57
3316 3406 2.490902 ACCATGAAAGGAACCAGGGTTC 60.491 50.000 20.44 20.44 43.95 3.62
3604 3709 5.068067 CCCTACTGCTTACTAGAAGGAGTTC 59.932 48.000 23.51 3.51 44.82 3.01
3665 3773 1.237285 GCCATTTCGAGGTGCACACT 61.237 55.000 20.43 13.33 0.00 3.55
3698 3806 3.074390 TCAAGATGGTCTTTGTGGTGGAT 59.926 43.478 0.00 0.00 33.78 3.41
3737 3845 2.761208 CGAGACTCTAATTCCACCACCT 59.239 50.000 0.03 0.00 0.00 4.00
3856 3964 3.593834 GCTTTTGCTTGACCCCTTG 57.406 52.632 0.00 0.00 43.35 3.61
3880 3989 4.083802 GGTCACACATTTTCCTTTCTCTCG 60.084 45.833 0.00 0.00 0.00 4.04
3935 4271 5.005779 GTGTATACAGGAGCAAAAGACATCG 59.994 44.000 5.62 0.00 0.00 3.84
4039 4377 6.684686 TGAATTTGAGAATTGGAGAAAGCTG 58.315 36.000 0.00 0.00 35.65 4.24
4051 4389 2.304470 GAGAAAGCTGAGTCCCTCCTTT 59.696 50.000 0.00 0.00 29.38 3.11
4114 4454 7.339953 CGGCTAACGTATAACTGAATTTTACC 58.660 38.462 0.00 0.00 37.93 2.85
4357 4702 9.334947 CCTGCTCAAATCAATCTAATCTAAGAA 57.665 33.333 0.00 0.00 0.00 2.52
4483 4836 2.203640 TGTGCGAGGAGGTGGAGT 60.204 61.111 0.00 0.00 0.00 3.85
4519 4872 3.708220 CTTGTCGAGGCGGAGGAGC 62.708 68.421 0.00 0.00 0.00 4.70
4667 5041 2.748058 CTACTGCAACGGCTTGGGGT 62.748 60.000 0.00 0.00 41.91 4.95
4671 5045 2.912025 CAACGGCTTGGGGTTGCT 60.912 61.111 0.00 0.00 37.34 3.91
4746 5120 6.216569 GCAAATATAGCCTTTTCTTTAGGGC 58.783 40.000 0.00 0.00 44.38 5.19
4750 5124 2.109425 GCCTTTTCTTTAGGGCGAGA 57.891 50.000 0.00 0.00 35.08 4.04
4751 5125 2.010497 GCCTTTTCTTTAGGGCGAGAG 58.990 52.381 0.00 0.00 35.08 3.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.936956 GGATTTAGCCTAGGACATGAAGATG 59.063 44.000 14.75 0.00 35.49 2.90
9 10 4.399219 GGGAATTGGATTTAGCCTAGGAC 58.601 47.826 14.75 3.76 0.00 3.85
41 42 4.519730 AGTTGTCAGGTGTACAGAGACTAC 59.480 45.833 19.50 19.50 35.96 2.73
53 54 1.014044 ATGCGCGTAGTTGTCAGGTG 61.014 55.000 8.43 0.00 0.00 4.00
98 99 3.054878 GTGCAGAAACAAATCAAGCAGG 58.945 45.455 0.00 0.00 34.66 4.85
121 122 0.039527 GCTAGTGGCCGGTTTTTGTG 60.040 55.000 1.90 0.00 34.27 3.33
209 212 3.447944 TGTCATGCCATTGTGTATGCATT 59.552 39.130 3.54 0.00 32.38 3.56
230 236 0.097674 GCTTAGTGGCGTGCAGAATG 59.902 55.000 0.00 0.00 40.87 2.67
299 305 0.110486 AAACACGGATCCTTGTGGCT 59.890 50.000 23.40 6.44 40.39 4.75
326 342 5.129485 AGCCTAGCATTAGAGTTTAGAGCAA 59.871 40.000 0.00 0.00 0.00 3.91
334 350 7.290248 TGAACCTTATAGCCTAGCATTAGAGTT 59.710 37.037 0.00 0.00 0.00 3.01
402 424 3.146066 GTCCACTTCCATGTACTGCAAA 58.854 45.455 0.00 0.00 0.00 3.68
483 505 2.515641 TCGTACGCAGAGTAGTTTCG 57.484 50.000 11.24 0.00 35.72 3.46
484 506 2.530700 GCATCGTACGCAGAGTAGTTTC 59.469 50.000 11.24 0.00 35.72 2.78
485 507 2.527100 GCATCGTACGCAGAGTAGTTT 58.473 47.619 11.24 0.00 35.72 2.66
486 508 1.202268 GGCATCGTACGCAGAGTAGTT 60.202 52.381 11.24 0.00 35.72 2.24
487 509 0.381089 GGCATCGTACGCAGAGTAGT 59.619 55.000 11.24 0.00 35.72 2.73
488 510 0.663688 AGGCATCGTACGCAGAGTAG 59.336 55.000 11.24 0.00 35.72 2.57
489 511 1.065102 GAAGGCATCGTACGCAGAGTA 59.935 52.381 11.24 0.00 0.00 2.59
490 512 0.179134 GAAGGCATCGTACGCAGAGT 60.179 55.000 11.24 0.00 0.00 3.24
491 513 0.101399 AGAAGGCATCGTACGCAGAG 59.899 55.000 11.24 1.01 0.00 3.35
492 514 0.100682 GAGAAGGCATCGTACGCAGA 59.899 55.000 11.24 0.00 0.00 4.26
493 515 1.202973 CGAGAAGGCATCGTACGCAG 61.203 60.000 11.24 6.40 35.48 5.18
494 516 1.226575 CGAGAAGGCATCGTACGCA 60.227 57.895 11.24 0.00 35.48 5.24
495 517 3.601981 CGAGAAGGCATCGTACGC 58.398 61.111 11.24 0.00 35.48 4.42
500 522 1.586564 GTCCGACGAGAAGGCATCG 60.587 63.158 0.00 5.42 45.54 3.84
501 523 0.108804 TTGTCCGACGAGAAGGCATC 60.109 55.000 0.00 0.00 0.00 3.91
502 524 0.389948 GTTGTCCGACGAGAAGGCAT 60.390 55.000 0.00 0.00 0.00 4.40
503 525 1.006571 GTTGTCCGACGAGAAGGCA 60.007 57.895 0.00 0.00 0.00 4.75
504 526 1.006571 TGTTGTCCGACGAGAAGGC 60.007 57.895 0.00 0.00 0.00 4.35
505 527 0.314302 ACTGTTGTCCGACGAGAAGG 59.686 55.000 0.00 0.00 0.00 3.46
506 528 2.582687 GTACTGTTGTCCGACGAGAAG 58.417 52.381 0.00 0.00 0.00 2.85
507 529 1.069703 CGTACTGTTGTCCGACGAGAA 60.070 52.381 0.00 0.00 35.59 2.87
508 530 0.514255 CGTACTGTTGTCCGACGAGA 59.486 55.000 0.00 0.00 35.59 4.04
509 531 0.514255 TCGTACTGTTGTCCGACGAG 59.486 55.000 0.00 0.00 37.60 4.18
510 532 1.129251 GATCGTACTGTTGTCCGACGA 59.871 52.381 0.00 4.02 45.54 4.20
511 533 1.135888 TGATCGTACTGTTGTCCGACG 60.136 52.381 0.00 0.00 37.36 5.12
512 534 2.161012 TCTGATCGTACTGTTGTCCGAC 59.839 50.000 0.00 0.00 37.36 4.79
513 535 2.161012 GTCTGATCGTACTGTTGTCCGA 59.839 50.000 0.00 0.00 38.80 4.55
514 536 2.161808 AGTCTGATCGTACTGTTGTCCG 59.838 50.000 0.00 0.00 0.00 4.79
515 537 3.190744 TCAGTCTGATCGTACTGTTGTCC 59.809 47.826 20.54 0.00 42.96 4.02
516 538 4.154375 TCTCAGTCTGATCGTACTGTTGTC 59.846 45.833 20.54 0.00 42.96 3.18
517 539 4.072839 TCTCAGTCTGATCGTACTGTTGT 58.927 43.478 20.54 0.00 42.96 3.32
518 540 4.686839 TCTCAGTCTGATCGTACTGTTG 57.313 45.455 20.54 16.00 42.96 3.33
519 541 4.944317 TGATCTCAGTCTGATCGTACTGTT 59.056 41.667 20.54 11.11 42.96 3.16
520 542 4.518249 TGATCTCAGTCTGATCGTACTGT 58.482 43.478 20.54 7.52 42.96 3.55
521 543 5.469760 AGATGATCTCAGTCTGATCGTACTG 59.530 44.000 17.11 17.11 42.18 2.74
522 544 5.620206 AGATGATCTCAGTCTGATCGTACT 58.380 41.667 2.22 0.00 42.18 2.73
523 545 5.700832 AGAGATGATCTCAGTCTGATCGTAC 59.299 44.000 23.17 0.00 45.73 3.67
524 546 5.863965 AGAGATGATCTCAGTCTGATCGTA 58.136 41.667 23.17 0.00 45.73 3.43
525 547 4.717877 AGAGATGATCTCAGTCTGATCGT 58.282 43.478 23.17 0.25 45.73 3.73
526 548 6.799926 TTAGAGATGATCTCAGTCTGATCG 57.200 41.667 23.17 0.00 45.73 3.69
528 550 9.812347 AGTATTTAGAGATGATCTCAGTCTGAT 57.188 33.333 23.17 10.76 45.73 2.90
531 553 9.739276 CCTAGTATTTAGAGATGATCTCAGTCT 57.261 37.037 23.17 13.82 45.73 3.24
532 554 8.956426 CCCTAGTATTTAGAGATGATCTCAGTC 58.044 40.741 23.17 8.17 45.73 3.51
533 555 7.396055 GCCCTAGTATTTAGAGATGATCTCAGT 59.604 40.741 23.17 7.28 45.73 3.41
534 556 7.147915 GGCCCTAGTATTTAGAGATGATCTCAG 60.148 44.444 23.17 9.64 45.73 3.35
535 557 6.665680 GGCCCTAGTATTTAGAGATGATCTCA 59.334 42.308 23.17 7.71 45.73 3.27
536 558 6.097696 GGGCCCTAGTATTTAGAGATGATCTC 59.902 46.154 17.04 14.47 43.70 2.75
537 559 5.961421 GGGCCCTAGTATTTAGAGATGATCT 59.039 44.000 17.04 0.00 42.47 2.75
538 560 5.721960 TGGGCCCTAGTATTTAGAGATGATC 59.278 44.000 25.70 0.00 0.00 2.92
539 561 5.485708 GTGGGCCCTAGTATTTAGAGATGAT 59.514 44.000 25.70 0.00 0.00 2.45
540 562 4.838986 GTGGGCCCTAGTATTTAGAGATGA 59.161 45.833 25.70 0.00 0.00 2.92
541 563 4.593206 TGTGGGCCCTAGTATTTAGAGATG 59.407 45.833 25.70 0.00 0.00 2.90
542 564 4.827789 TGTGGGCCCTAGTATTTAGAGAT 58.172 43.478 25.70 0.00 0.00 2.75
543 565 4.274794 TGTGGGCCCTAGTATTTAGAGA 57.725 45.455 25.70 0.00 0.00 3.10
544 566 5.104485 AGTTTGTGGGCCCTAGTATTTAGAG 60.104 44.000 25.70 0.00 0.00 2.43
545 567 4.786454 AGTTTGTGGGCCCTAGTATTTAGA 59.214 41.667 25.70 0.00 0.00 2.10
546 568 4.881850 CAGTTTGTGGGCCCTAGTATTTAG 59.118 45.833 25.70 1.34 0.00 1.85
547 569 4.536888 TCAGTTTGTGGGCCCTAGTATTTA 59.463 41.667 25.70 0.00 0.00 1.40
548 570 3.332485 TCAGTTTGTGGGCCCTAGTATTT 59.668 43.478 25.70 0.00 0.00 1.40
549 571 2.916934 TCAGTTTGTGGGCCCTAGTATT 59.083 45.455 25.70 1.47 0.00 1.89
550 572 2.557869 TCAGTTTGTGGGCCCTAGTAT 58.442 47.619 25.70 1.19 0.00 2.12
551 573 2.032965 TCAGTTTGTGGGCCCTAGTA 57.967 50.000 25.70 0.00 0.00 1.82
552 574 1.145571 TTCAGTTTGTGGGCCCTAGT 58.854 50.000 25.70 5.80 0.00 2.57
553 575 2.290896 TGATTCAGTTTGTGGGCCCTAG 60.291 50.000 25.70 4.84 0.00 3.02
554 576 1.707989 TGATTCAGTTTGTGGGCCCTA 59.292 47.619 25.70 9.60 0.00 3.53
555 577 0.482446 TGATTCAGTTTGTGGGCCCT 59.518 50.000 25.70 0.00 0.00 5.19
556 578 1.478105 GATGATTCAGTTTGTGGGCCC 59.522 52.381 17.59 17.59 0.00 5.80
557 579 1.478105 GGATGATTCAGTTTGTGGGCC 59.522 52.381 0.00 0.00 0.00 5.80
558 580 2.170166 TGGATGATTCAGTTTGTGGGC 58.830 47.619 0.00 0.00 0.00 5.36
559 581 3.131577 CCATGGATGATTCAGTTTGTGGG 59.868 47.826 5.56 0.00 0.00 4.61
560 582 3.429822 GCCATGGATGATTCAGTTTGTGG 60.430 47.826 18.40 0.00 0.00 4.17
561 583 3.446161 AGCCATGGATGATTCAGTTTGTG 59.554 43.478 18.40 0.00 0.00 3.33
562 584 3.446161 CAGCCATGGATGATTCAGTTTGT 59.554 43.478 26.03 0.00 32.62 2.83
563 585 3.446161 ACAGCCATGGATGATTCAGTTTG 59.554 43.478 35.60 6.03 35.26 2.93
564 586 3.698040 GACAGCCATGGATGATTCAGTTT 59.302 43.478 35.60 11.26 35.26 2.66
565 587 3.053842 AGACAGCCATGGATGATTCAGTT 60.054 43.478 35.60 12.07 35.26 3.16
566 588 2.508716 AGACAGCCATGGATGATTCAGT 59.491 45.455 35.60 12.88 35.26 3.41
567 589 3.139850 GAGACAGCCATGGATGATTCAG 58.860 50.000 35.60 9.22 35.26 3.02
568 590 2.775960 AGAGACAGCCATGGATGATTCA 59.224 45.455 35.60 0.00 35.26 2.57
569 591 3.488778 AGAGACAGCCATGGATGATTC 57.511 47.619 35.60 27.72 35.26 2.52
570 592 5.558818 GATTAGAGACAGCCATGGATGATT 58.441 41.667 35.60 21.99 35.26 2.57
571 593 4.322574 CGATTAGAGACAGCCATGGATGAT 60.323 45.833 35.60 22.84 35.26 2.45
572 594 3.006217 CGATTAGAGACAGCCATGGATGA 59.994 47.826 35.60 13.24 35.26 2.92
573 595 3.244009 ACGATTAGAGACAGCCATGGATG 60.244 47.826 28.12 28.12 37.56 3.51
574 596 2.968574 ACGATTAGAGACAGCCATGGAT 59.031 45.455 18.40 6.18 0.00 3.41
575 597 2.388735 ACGATTAGAGACAGCCATGGA 58.611 47.619 18.40 0.00 0.00 3.41
576 598 2.898729 ACGATTAGAGACAGCCATGG 57.101 50.000 7.63 7.63 0.00 3.66
577 599 4.021981 TCCATACGATTAGAGACAGCCATG 60.022 45.833 0.00 0.00 0.00 3.66
578 600 4.152647 TCCATACGATTAGAGACAGCCAT 58.847 43.478 0.00 0.00 0.00 4.40
579 601 3.562182 TCCATACGATTAGAGACAGCCA 58.438 45.455 0.00 0.00 0.00 4.75
580 602 3.570550 ACTCCATACGATTAGAGACAGCC 59.429 47.826 0.00 0.00 0.00 4.85
581 603 4.036971 ACACTCCATACGATTAGAGACAGC 59.963 45.833 0.00 0.00 0.00 4.40
582 604 5.759506 ACACTCCATACGATTAGAGACAG 57.240 43.478 0.00 0.00 0.00 3.51
583 605 5.220796 CGAACACTCCATACGATTAGAGACA 60.221 44.000 0.00 0.00 0.00 3.41
584 606 5.206299 CGAACACTCCATACGATTAGAGAC 58.794 45.833 0.00 0.00 0.00 3.36
585 607 4.275196 CCGAACACTCCATACGATTAGAGA 59.725 45.833 0.00 0.00 0.00 3.10
586 608 4.537965 CCGAACACTCCATACGATTAGAG 58.462 47.826 0.00 0.00 0.00 2.43
587 609 3.243301 GCCGAACACTCCATACGATTAGA 60.243 47.826 0.00 0.00 0.00 2.10
588 610 3.050619 GCCGAACACTCCATACGATTAG 58.949 50.000 0.00 0.00 0.00 1.73
589 611 2.427812 TGCCGAACACTCCATACGATTA 59.572 45.455 0.00 0.00 0.00 1.75
590 612 1.206132 TGCCGAACACTCCATACGATT 59.794 47.619 0.00 0.00 0.00 3.34
591 613 0.821517 TGCCGAACACTCCATACGAT 59.178 50.000 0.00 0.00 0.00 3.73
592 614 0.108992 GTGCCGAACACTCCATACGA 60.109 55.000 0.00 0.00 46.41 3.43
593 615 2.369870 GTGCCGAACACTCCATACG 58.630 57.895 1.75 0.00 46.41 3.06
612 634 7.864307 ACCTTGCTATACGTACGATAAATTC 57.136 36.000 24.41 5.14 0.00 2.17
613 635 7.922278 TGAACCTTGCTATACGTACGATAAATT 59.078 33.333 24.41 0.00 0.00 1.82
614 636 7.428020 TGAACCTTGCTATACGTACGATAAAT 58.572 34.615 24.41 11.69 0.00 1.40
615 637 6.794374 TGAACCTTGCTATACGTACGATAAA 58.206 36.000 24.41 4.52 0.00 1.40
616 638 6.375945 TGAACCTTGCTATACGTACGATAA 57.624 37.500 24.41 7.24 0.00 1.75
617 639 6.564709 ATGAACCTTGCTATACGTACGATA 57.435 37.500 24.41 13.69 0.00 2.92
618 640 4.906065 TGAACCTTGCTATACGTACGAT 57.094 40.909 24.41 13.27 0.00 3.73
619 641 4.906065 ATGAACCTTGCTATACGTACGA 57.094 40.909 24.41 6.04 0.00 3.43
620 642 5.755813 ACTATGAACCTTGCTATACGTACG 58.244 41.667 15.01 15.01 0.00 3.67
621 643 6.800892 GCTACTATGAACCTTGCTATACGTAC 59.199 42.308 0.00 0.00 0.00 3.67
622 644 6.487668 TGCTACTATGAACCTTGCTATACGTA 59.512 38.462 0.00 0.00 0.00 3.57
623 645 5.301045 TGCTACTATGAACCTTGCTATACGT 59.699 40.000 0.00 0.00 0.00 3.57
624 646 5.629849 GTGCTACTATGAACCTTGCTATACG 59.370 44.000 0.00 0.00 0.00 3.06
625 647 6.642950 CAGTGCTACTATGAACCTTGCTATAC 59.357 42.308 0.00 0.00 0.00 1.47
626 648 6.239317 CCAGTGCTACTATGAACCTTGCTATA 60.239 42.308 0.00 0.00 0.00 1.31
627 649 5.453903 CCAGTGCTACTATGAACCTTGCTAT 60.454 44.000 0.00 0.00 0.00 2.97
628 650 4.141937 CCAGTGCTACTATGAACCTTGCTA 60.142 45.833 0.00 0.00 0.00 3.49
629 651 3.369892 CCAGTGCTACTATGAACCTTGCT 60.370 47.826 0.00 0.00 0.00 3.91
630 652 2.939103 CCAGTGCTACTATGAACCTTGC 59.061 50.000 0.00 0.00 0.00 4.01
631 653 2.939103 GCCAGTGCTACTATGAACCTTG 59.061 50.000 0.00 0.00 33.53 3.61
632 654 2.092914 GGCCAGTGCTACTATGAACCTT 60.093 50.000 0.00 0.00 37.74 3.50
633 655 1.486726 GGCCAGTGCTACTATGAACCT 59.513 52.381 0.00 0.00 37.74 3.50
634 656 1.806623 CGGCCAGTGCTACTATGAACC 60.807 57.143 2.24 0.00 37.74 3.62
635 657 1.571919 CGGCCAGTGCTACTATGAAC 58.428 55.000 2.24 0.00 37.74 3.18
636 658 0.464036 CCGGCCAGTGCTACTATGAA 59.536 55.000 2.24 0.00 37.74 2.57
637 659 0.686441 ACCGGCCAGTGCTACTATGA 60.686 55.000 0.00 0.00 37.74 2.15
638 660 0.178068 AACCGGCCAGTGCTACTATG 59.822 55.000 0.00 0.00 37.74 2.23
639 661 1.784358 TAACCGGCCAGTGCTACTAT 58.216 50.000 0.00 0.00 37.74 2.12
640 662 1.205417 GTTAACCGGCCAGTGCTACTA 59.795 52.381 0.00 0.00 37.74 1.82
641 663 0.036671 GTTAACCGGCCAGTGCTACT 60.037 55.000 0.00 0.00 37.74 2.57
642 664 0.320946 TGTTAACCGGCCAGTGCTAC 60.321 55.000 0.00 0.00 37.74 3.58
643 665 0.036765 CTGTTAACCGGCCAGTGCTA 60.037 55.000 0.00 0.00 37.74 3.49
644 666 1.302511 CTGTTAACCGGCCAGTGCT 60.303 57.895 0.00 0.00 37.74 4.40
645 667 2.978018 GCTGTTAACCGGCCAGTGC 61.978 63.158 0.00 0.00 39.74 4.40
646 668 3.263941 GCTGTTAACCGGCCAGTG 58.736 61.111 0.00 0.00 39.74 3.66
1021 1048 0.526524 GATTCCTGTGAGCCGAGACG 60.527 60.000 0.00 0.00 0.00 4.18
1037 1064 0.179205 GACGAGGACGAACGACGATT 60.179 55.000 0.00 0.00 45.77 3.34
1053 1080 0.101399 CCACTTGATCGGAGGAGACG 59.899 60.000 1.59 0.00 0.00 4.18
1253 1283 7.617723 AGCTATCTATTTCTCCTCCGAATGTAT 59.382 37.037 0.00 0.00 0.00 2.29
1259 1289 6.378564 CCATTAGCTATCTATTTCTCCTCCGA 59.621 42.308 0.00 0.00 0.00 4.55
1284 1319 2.086869 TGGCTACATGCAGAAAAGAGC 58.913 47.619 0.00 0.00 45.15 4.09
1343 1378 4.860907 GCAAAGAAAGCATTGTACTCCATG 59.139 41.667 0.00 0.00 0.00 3.66
1371 1406 8.337532 CCAGAAAGGAAAATGACATTTTGAAAC 58.662 33.333 26.73 14.12 42.15 2.78
1397 1432 6.208644 CAGGCTGGTTATTGTTATATTGCAC 58.791 40.000 6.61 0.00 0.00 4.57
1403 1438 3.435890 GGGGCAGGCTGGTTATTGTTATA 60.436 47.826 17.64 0.00 0.00 0.98
1408 1443 1.000233 TGGGGCAGGCTGGTTATTG 60.000 57.895 17.64 0.00 0.00 1.90
1411 1499 3.338250 CCTGGGGCAGGCTGGTTA 61.338 66.667 17.64 0.00 45.13 2.85
1624 1712 1.785430 GACGACCTTGACAAGAACGTC 59.215 52.381 30.48 30.48 43.26 4.34
1651 1739 2.289195 GGATGGTAACGTTGTGAGGTGA 60.289 50.000 11.99 0.00 42.51 4.02
1758 1847 1.472376 CCAGAAAGATCGAGGCTGTCC 60.472 57.143 0.00 0.00 0.00 4.02
1768 1857 4.479619 GTCAACAACATGCCAGAAAGATC 58.520 43.478 0.00 0.00 0.00 2.75
1797 1886 9.107177 TCTTCTTTTGCAGCAAATGAAAAATTA 57.893 25.926 32.62 19.50 43.97 1.40
1970 2059 5.952347 ATTTCTTTACGGAGGGAGTATGT 57.048 39.130 0.00 0.00 0.00 2.29
1971 2060 9.991906 TTTATATTTCTTTACGGAGGGAGTATG 57.008 33.333 0.00 0.00 0.00 2.39
1975 2064 6.073927 GCGTTTATATTTCTTTACGGAGGGAG 60.074 42.308 0.00 0.00 0.00 4.30
1976 2065 5.754890 GCGTTTATATTTCTTTACGGAGGGA 59.245 40.000 0.00 0.00 0.00 4.20
1977 2066 5.756833 AGCGTTTATATTTCTTTACGGAGGG 59.243 40.000 0.00 0.00 0.00 4.30
1978 2067 6.700520 AGAGCGTTTATATTTCTTTACGGAGG 59.299 38.462 0.00 0.00 0.00 4.30
1980 2069 9.754382 ATAAGAGCGTTTATATTTCTTTACGGA 57.246 29.630 0.00 0.00 31.19 4.69
1995 2084 9.099454 CCTCTGTAAAGAAATATAAGAGCGTTT 57.901 33.333 0.00 0.00 0.00 3.60
1996 2085 7.711339 CCCTCTGTAAAGAAATATAAGAGCGTT 59.289 37.037 0.00 0.00 0.00 4.84
1997 2086 7.069578 TCCCTCTGTAAAGAAATATAAGAGCGT 59.930 37.037 0.00 0.00 0.00 5.07
1998 2087 7.434492 TCCCTCTGTAAAGAAATATAAGAGCG 58.566 38.462 0.00 0.00 0.00 5.03
1999 2088 8.425703 ACTCCCTCTGTAAAGAAATATAAGAGC 58.574 37.037 0.00 0.00 0.00 4.09
2007 2096 9.343539 GCATAAATACTCCCTCTGTAAAGAAAT 57.656 33.333 0.00 0.00 0.00 2.17
2008 2097 8.325787 TGCATAAATACTCCCTCTGTAAAGAAA 58.674 33.333 0.00 0.00 0.00 2.52
2009 2098 7.857456 TGCATAAATACTCCCTCTGTAAAGAA 58.143 34.615 0.00 0.00 0.00 2.52
2010 2099 7.432148 TGCATAAATACTCCCTCTGTAAAGA 57.568 36.000 0.00 0.00 0.00 2.52
2011 2100 6.203723 GCTGCATAAATACTCCCTCTGTAAAG 59.796 42.308 0.00 0.00 0.00 1.85
2012 2101 6.055588 GCTGCATAAATACTCCCTCTGTAAA 58.944 40.000 0.00 0.00 0.00 2.01
2013 2102 5.130311 TGCTGCATAAATACTCCCTCTGTAA 59.870 40.000 0.00 0.00 0.00 2.41
2014 2103 4.653801 TGCTGCATAAATACTCCCTCTGTA 59.346 41.667 0.00 0.00 0.00 2.74
2015 2104 3.455910 TGCTGCATAAATACTCCCTCTGT 59.544 43.478 0.00 0.00 0.00 3.41
2016 2105 3.812053 GTGCTGCATAAATACTCCCTCTG 59.188 47.826 5.27 0.00 0.00 3.35
2017 2106 3.455910 TGTGCTGCATAAATACTCCCTCT 59.544 43.478 5.27 0.00 0.00 3.69
2018 2107 3.561725 GTGTGCTGCATAAATACTCCCTC 59.438 47.826 5.27 0.00 0.00 4.30
2019 2108 3.054434 TGTGTGCTGCATAAATACTCCCT 60.054 43.478 5.27 0.00 0.00 4.20
2020 2109 3.278574 TGTGTGCTGCATAAATACTCCC 58.721 45.455 5.27 0.00 0.00 4.30
2021 2110 5.333339 CGTATGTGTGCTGCATAAATACTCC 60.333 44.000 26.76 10.32 31.54 3.85
2022 2111 5.234329 ACGTATGTGTGCTGCATAAATACTC 59.766 40.000 26.76 10.86 31.54 2.59
2023 2112 5.116180 ACGTATGTGTGCTGCATAAATACT 58.884 37.500 26.76 16.42 31.54 2.12
2024 2113 5.403897 ACGTATGTGTGCTGCATAAATAC 57.596 39.130 22.63 22.63 31.54 1.89
2079 2168 1.822186 CCGGATTTGCCTTACCCCG 60.822 63.158 0.00 0.00 36.98 5.73
2238 2327 4.129380 GCAGTATGACAATAGCACCATGA 58.871 43.478 0.00 0.00 39.69 3.07
2349 2438 8.443937 GCTGAATGGGTTATTCTCGATTAATAC 58.556 37.037 0.00 0.00 44.49 1.89
2385 2474 1.374343 CCTGCAGCGCATCATCAAGT 61.374 55.000 11.47 0.00 38.13 3.16
2626 2716 4.062991 TCGAGATTGAATCCATCTGCATG 58.937 43.478 1.24 0.00 0.00 4.06
2830 2920 1.529244 GGCCAGCACTTTGGTCAGT 60.529 57.895 0.00 0.00 42.50 3.41
2925 3015 2.251893 GCAGAGACAGTGTTAGCGTAC 58.748 52.381 0.00 0.00 0.00 3.67
2928 3018 0.038251 TGGCAGAGACAGTGTTAGCG 60.038 55.000 0.00 0.00 0.00 4.26
3072 3162 3.432252 CGATGGTAAAGAAAAGCGAGTGT 59.568 43.478 0.00 0.00 0.00 3.55
3093 3183 0.322456 ATGGATTGACACCCACACCG 60.322 55.000 0.00 0.00 34.92 4.94
3162 3252 2.687935 GGTGGATGGCATAACGAATGTT 59.312 45.455 0.00 0.00 42.19 2.71
3316 3406 4.945543 TGAAGCATTATATGGCAGCCTATG 59.054 41.667 14.15 9.40 0.00 2.23
3423 3513 2.150014 AATTCCCAACACCCCTCCCG 62.150 60.000 0.00 0.00 0.00 5.14
3454 3544 2.100197 GTTAAATGTGGAAGGGGAGGC 58.900 52.381 0.00 0.00 0.00 4.70
3604 3709 7.012704 CACCTGGAATAGAACAACATATCAAGG 59.987 40.741 0.00 0.00 0.00 3.61
3665 3773 2.239654 GACCATCTTGAGTCCCCATGAA 59.760 50.000 0.00 0.00 0.00 2.57
3698 3806 4.028131 TCTCGCTAGGTCTTTTCCCATTA 58.972 43.478 0.00 0.00 0.00 1.90
3737 3845 3.181329 TCAGCACTGGGGAAGATCTTTA 58.819 45.455 9.87 0.00 0.00 1.85
3794 3902 5.172053 CGTTGAAGTTTCAGCATCTGTTTTC 59.828 40.000 8.97 0.00 38.17 2.29
3851 3959 1.618343 GGAAAATGTGTGACCCAAGGG 59.382 52.381 2.91 2.91 42.03 3.95
3856 3964 4.145052 AGAGAAAGGAAAATGTGTGACCC 58.855 43.478 0.00 0.00 0.00 4.46
3866 3974 7.543756 ACAAATCAAAACGAGAGAAAGGAAAA 58.456 30.769 0.00 0.00 0.00 2.29
3880 3989 5.207033 GCAATCAAGCCAACAAATCAAAAC 58.793 37.500 0.00 0.00 0.00 2.43
4003 4341 3.119280 TCTCAAATTCATGTGCATGCCAG 60.119 43.478 16.68 2.17 38.65 4.85
4081 4421 4.339247 AGTTATACGTTAGCCGCCTTCTAA 59.661 41.667 0.00 0.00 41.42 2.10
4114 4454 4.982295 TGTGTTCTTAATGTCTGTCTGTCG 59.018 41.667 0.00 0.00 0.00 4.35
4197 4540 3.851458 TGATCATGGATCAGGACCAAG 57.149 47.619 4.86 0.00 43.11 3.61
4357 4702 3.057946 GCAGAAAGAAAAACGGCAGATCT 60.058 43.478 0.00 0.00 0.00 2.75
4483 4836 0.998928 AGACTCTCTCCAGCCTCTCA 59.001 55.000 0.00 0.00 0.00 3.27
4667 5041 1.685224 CTGTAGCTTCCCCCAGCAA 59.315 57.895 0.00 0.00 42.84 3.91
4722 5096 6.216569 GCCCTAAAGAAAAGGCTATATTTGC 58.783 40.000 0.00 0.00 42.34 3.68
4723 5097 6.262273 TCGCCCTAAAGAAAAGGCTATATTTG 59.738 38.462 0.00 0.00 43.48 2.32
4724 5098 6.362248 TCGCCCTAAAGAAAAGGCTATATTT 58.638 36.000 0.00 0.00 43.48 1.40
4725 5099 5.937111 TCGCCCTAAAGAAAAGGCTATATT 58.063 37.500 0.00 0.00 43.48 1.28
4726 5100 5.307196 TCTCGCCCTAAAGAAAAGGCTATAT 59.693 40.000 0.00 0.00 43.48 0.86
4727 5101 4.652421 TCTCGCCCTAAAGAAAAGGCTATA 59.348 41.667 0.00 0.00 43.48 1.31
4728 5102 3.454812 TCTCGCCCTAAAGAAAAGGCTAT 59.545 43.478 0.00 0.00 43.48 2.97
4729 5103 2.835764 TCTCGCCCTAAAGAAAAGGCTA 59.164 45.455 0.00 0.00 43.48 3.93
4730 5104 1.628846 TCTCGCCCTAAAGAAAAGGCT 59.371 47.619 0.00 0.00 43.48 4.58
4731 5105 2.010497 CTCTCGCCCTAAAGAAAAGGC 58.990 52.381 0.00 0.00 42.18 4.35
4732 5106 2.010497 GCTCTCGCCCTAAAGAAAAGG 58.990 52.381 0.00 0.00 0.00 3.11
4733 5107 2.699954 TGCTCTCGCCCTAAAGAAAAG 58.300 47.619 0.00 0.00 34.43 2.27
4734 5108 2.851263 TGCTCTCGCCCTAAAGAAAA 57.149 45.000 0.00 0.00 34.43 2.29
4735 5109 2.420129 GGATGCTCTCGCCCTAAAGAAA 60.420 50.000 0.00 0.00 34.43 2.52
4736 5110 1.139058 GGATGCTCTCGCCCTAAAGAA 59.861 52.381 0.00 0.00 34.43 2.52
4737 5111 0.753262 GGATGCTCTCGCCCTAAAGA 59.247 55.000 0.00 0.00 34.43 2.52
4738 5112 0.465705 TGGATGCTCTCGCCCTAAAG 59.534 55.000 0.00 0.00 34.43 1.85
4739 5113 0.908910 TTGGATGCTCTCGCCCTAAA 59.091 50.000 0.00 0.00 34.43 1.85
4740 5114 2.602890 TTGGATGCTCTCGCCCTAA 58.397 52.632 0.00 0.00 34.43 2.69
4741 5115 4.373551 TTGGATGCTCTCGCCCTA 57.626 55.556 0.00 0.00 34.43 3.53


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

AutoCloner maintained by Alex Coulton.