Multiple sequence alignment - TraesCS4D01G039000

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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 TraesCS4D01G039000 chr4D 100.000 4819 0 0 1 4819 16792673 16797491 0.000000e+00 8900.0
1 TraesCS4D01G039000 chr4A 92.523 2247 114 20 675 2907 583763768 583761562 0.000000e+00 3169.0
2 TraesCS4D01G039000 chr4A 88.028 994 73 23 3222 4183 583760862 583759883 0.000000e+00 1134.0
3 TraesCS4D01G039000 chr4A 85.714 392 48 7 1048 1438 744427107 744427491 1.610000e-109 407.0
4 TraesCS4D01G039000 chr4A 85.953 299 29 9 2896 3189 583761154 583760864 1.680000e-79 307.0
5 TraesCS4D01G039000 chr4A 87.313 134 11 3 4686 4819 583759378 583759251 1.080000e-31 148.0
6 TraesCS4D01G039000 chr4B 94.572 1179 59 4 1981 3155 28712257 28713434 0.000000e+00 1818.0
7 TraesCS4D01G039000 chr4B 94.479 1123 37 15 3155 4258 28713539 28714655 0.000000e+00 1707.0
8 TraesCS4D01G039000 chr4B 91.559 1244 53 19 675 1889 28711021 28712241 0.000000e+00 1668.0
9 TraesCS4D01G039000 chr4B 85.714 574 42 19 4257 4815 28714686 28715234 1.950000e-158 569.0
10 TraesCS4D01G039000 chr1A 78.879 535 77 27 6 511 516170201 516170728 3.600000e-86 329.0
11 TraesCS4D01G039000 chr1A 78.476 525 63 33 6 507 238653029 238653526 1.010000e-76 298.0
12 TraesCS4D01G039000 chr1A 84.106 151 21 3 368 516 219383746 219383895 5.030000e-30 143.0
13 TraesCS4D01G039000 chr1A 73.930 257 42 18 432 676 360402743 360402500 4.000000e-11 80.5
14 TraesCS4D01G039000 chr5A 79.130 345 58 12 77 417 521748528 521748862 4.850000e-55 226.0
15 TraesCS4D01G039000 chr5D 78.736 348 60 11 73 417 410248026 410248362 2.260000e-53 220.0
16 TraesCS4D01G039000 chr5D 93.443 122 8 0 425 546 506596705 506596584 1.070000e-41 182.0
17 TraesCS4D01G039000 chr3D 93.443 122 8 0 425 546 302991785 302991664 1.070000e-41 182.0
18 TraesCS4D01G039000 chr3D 73.864 264 51 12 423 675 602053623 602053367 6.640000e-14 89.8
19 TraesCS4D01G039000 chr6A 77.570 321 49 16 372 675 85253701 85253387 6.410000e-39 172.0
20 TraesCS4D01G039000 chr6A 75.379 264 44 15 423 676 224249503 224249755 1.830000e-19 108.0
21 TraesCS4D01G039000 chr5B 75.665 263 45 12 422 668 297975810 297976069 3.940000e-21 113.0
22 TraesCS4D01G039000 chr7A 75.094 265 43 17 423 676 686230918 686230666 8.530000e-18 102.0
23 TraesCS4D01G039000 chr7A 85.106 94 10 4 426 516 497653934 497654026 5.140000e-15 93.5
24 TraesCS4D01G039000 chr7A 74.436 266 45 17 423 677 639295268 639295521 5.140000e-15 93.5
25 TraesCS4D01G039000 chr7A 74.330 261 44 17 423 672 3959257 3959505 6.640000e-14 89.8
26 TraesCS4D01G039000 chr7A 73.881 268 41 21 423 676 233341351 233341603 4.000000e-11 80.5


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 TraesCS4D01G039000 chr4D 16792673 16797491 4818 False 8900.0 8900 100.00000 1 4819 1 chr4D.!!$F1 4818
1 TraesCS4D01G039000 chr4A 583759251 583763768 4517 True 1189.5 3169 88.45425 675 4819 4 chr4A.!!$R1 4144
2 TraesCS4D01G039000 chr4B 28711021 28715234 4213 False 1440.5 1818 91.58100 675 4815 4 chr4B.!!$F1 4140
3 TraesCS4D01G039000 chr1A 516170201 516170728 527 False 329.0 329 78.87900 6 511 1 chr1A.!!$F3 505

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
629 678 0.031857 CTGATCTGACGGCTAGCCAG 59.968 60.0 32.47 25.43 35.37 4.85 F
1707 1799 0.037326 TAGAATGCGCCGATGGATCC 60.037 55.0 4.18 4.20 0.00 3.36 F
2486 2581 0.251564 CACCAACCCTGCCCAATACA 60.252 55.0 0.00 0.00 0.00 2.29 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2349 2444 0.034670 AAGCTCTCATCAGTTGGGGC 60.035 55.000 0.00 0.00 0.00 5.80 R
3437 4067 0.245266 TGCGTCTTGCTATCGGTTGA 59.755 50.000 0.00 0.00 46.63 3.18 R
4013 4656 2.979813 GCAACGGTAACTGCAATTTCAG 59.020 45.455 3.36 3.36 37.67 3.02 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
71 72 2.281484 GCAACACGCAGGGGAGAA 60.281 61.111 0.00 0.00 41.79 2.87
74 75 3.553095 AACACGCAGGGGAGAAGCC 62.553 63.158 0.00 0.00 0.00 4.35
102 138 3.423154 GGCGGAACTCGGTGCTTG 61.423 66.667 0.00 0.00 39.69 4.01
106 142 1.741770 GGAACTCGGTGCTTGCGAT 60.742 57.895 0.00 0.00 0.00 4.58
141 178 2.537560 GGATCCCGTGCTTGCGATG 61.538 63.158 0.00 0.00 0.00 3.84
142 179 3.173390 GATCCCGTGCTTGCGATGC 62.173 63.158 0.00 0.00 0.00 3.91
152 189 0.649475 CTTGCGATGCAGCTACTCAC 59.351 55.000 0.00 0.00 40.61 3.51
153 190 0.247460 TTGCGATGCAGCTACTCACT 59.753 50.000 0.00 0.00 40.61 3.41
155 192 1.150567 GCGATGCAGCTACTCACTGG 61.151 60.000 0.00 0.00 35.62 4.00
156 193 0.174389 CGATGCAGCTACTCACTGGT 59.826 55.000 0.00 0.00 35.62 4.00
157 194 1.649664 GATGCAGCTACTCACTGGTG 58.350 55.000 0.00 0.00 35.62 4.17
158 195 1.205655 GATGCAGCTACTCACTGGTGA 59.794 52.381 0.00 3.34 35.62 4.02
159 196 1.047801 TGCAGCTACTCACTGGTGAA 58.952 50.000 4.94 0.00 39.39 3.18
164 201 1.555075 GCTACTCACTGGTGAATCCCA 59.445 52.381 4.94 0.00 39.39 4.37
182 219 4.481112 GCGTTGCAAGCCGGATGG 62.481 66.667 5.05 0.00 38.77 3.51
184 221 3.451894 GTTGCAAGCCGGATGGGG 61.452 66.667 5.05 0.00 35.78 4.96
205 242 3.372730 CCATGGTGCACGGGGTTG 61.373 66.667 11.45 3.64 0.00 3.77
218 256 3.737172 GGTTGTTGGCGCTGCGAT 61.737 61.111 28.07 0.00 0.00 4.58
229 267 1.359117 GCTGCGATGCAATGCTCAT 59.641 52.632 6.82 0.00 38.41 2.90
242 280 4.193334 CTCATCAGCGGCCGTCGA 62.193 66.667 28.70 23.17 42.43 4.20
243 281 4.492160 TCATCAGCGGCCGTCGAC 62.492 66.667 28.70 10.05 42.43 4.20
263 301 2.885113 TGCGATGCAGCTACTCGT 59.115 55.556 8.31 0.00 38.13 4.18
266 304 1.352056 CGATGCAGCTACTCGTCGA 59.648 57.895 15.22 0.00 42.46 4.20
273 311 2.462782 GCTACTCGTCGACGGCTCT 61.463 63.158 35.05 18.06 40.29 4.09
279 317 1.154016 CGTCGACGGCTCTTGATGT 60.154 57.895 29.70 0.00 35.37 3.06
280 318 0.732880 CGTCGACGGCTCTTGATGTT 60.733 55.000 29.70 0.00 35.37 2.71
281 319 0.716108 GTCGACGGCTCTTGATGTTG 59.284 55.000 0.00 0.00 0.00 3.33
282 320 0.317160 TCGACGGCTCTTGATGTTGT 59.683 50.000 0.00 0.00 0.00 3.32
283 321 0.439985 CGACGGCTCTTGATGTTGTG 59.560 55.000 0.00 0.00 0.00 3.33
285 323 0.534877 ACGGCTCTTGATGTTGTGCA 60.535 50.000 0.00 0.00 0.00 4.57
286 324 0.592637 CGGCTCTTGATGTTGTGCAA 59.407 50.000 0.00 0.00 0.00 4.08
328 366 0.171007 CAGGGTAATTGTTGCTGCGG 59.829 55.000 0.00 0.00 0.00 5.69
352 390 3.200593 GCTCATCACTGGCTGCCG 61.201 66.667 14.98 11.36 0.00 5.69
354 392 3.320879 CTCATCACTGGCTGCCGGT 62.321 63.158 27.12 27.12 45.12 5.28
364 402 3.204827 CTGCCGGTGGTGCTATGC 61.205 66.667 1.90 0.00 0.00 3.14
386 432 2.101770 GCTGCAATGGAGCTTCGC 59.898 61.111 19.55 0.00 33.37 4.70
398 444 4.116328 CTTCGCCGGAGCTGTCGA 62.116 66.667 5.05 0.00 36.60 4.20
402 448 4.521062 GCCGGAGCTGTCGATGCT 62.521 66.667 5.05 14.32 44.24 3.79
403 449 2.584418 CCGGAGCTGTCGATGCTG 60.584 66.667 18.33 7.06 41.30 4.41
412 458 1.738099 GTCGATGCTGCGTTGGAGT 60.738 57.895 9.16 0.00 0.00 3.85
438 484 3.885521 GGCTGCAATGGAGCTCGC 61.886 66.667 25.07 6.23 36.63 5.03
439 485 2.823147 GCTGCAATGGAGCTCGCT 60.823 61.111 19.55 0.00 33.37 4.93
452 499 1.300971 GCTCGCTGGAGTTGCAATGA 61.301 55.000 0.59 0.00 42.53 2.57
467 515 4.760047 TGAAGCTTCGCCGGAGCC 62.760 66.667 15.06 0.00 34.57 4.70
483 531 2.962786 CCGTCGGTGTTGCGTTGA 60.963 61.111 2.08 0.00 0.00 3.18
487 535 2.051345 CGGTGTTGCGTTGAAGCC 60.051 61.111 0.00 0.00 36.02 4.35
488 536 2.335011 GGTGTTGCGTTGAAGCCC 59.665 61.111 0.00 0.00 36.02 5.19
489 537 2.485795 GGTGTTGCGTTGAAGCCCA 61.486 57.895 0.00 0.00 36.02 5.36
507 556 4.431131 CCGGGGCTGCAATGGAGT 62.431 66.667 3.24 0.00 0.00 3.85
511 560 1.675641 GGGCTGCAATGGAGTTCGT 60.676 57.895 3.24 0.00 0.00 3.85
512 561 1.648467 GGGCTGCAATGGAGTTCGTC 61.648 60.000 3.24 0.00 0.00 4.20
513 562 1.421485 GCTGCAATGGAGTTCGTCG 59.579 57.895 3.24 0.00 0.00 5.12
514 563 1.970917 GCTGCAATGGAGTTCGTCGG 61.971 60.000 3.24 0.00 0.00 4.79
515 564 0.389817 CTGCAATGGAGTTCGTCGGA 60.390 55.000 0.00 0.00 0.00 4.55
516 565 0.669318 TGCAATGGAGTTCGTCGGAC 60.669 55.000 0.00 0.00 0.00 4.79
517 566 0.669318 GCAATGGAGTTCGTCGGACA 60.669 55.000 6.41 0.00 0.00 4.02
518 567 2.007049 GCAATGGAGTTCGTCGGACAT 61.007 52.381 6.41 0.00 0.00 3.06
519 568 2.346803 CAATGGAGTTCGTCGGACATT 58.653 47.619 6.41 0.00 0.00 2.71
520 569 3.517602 CAATGGAGTTCGTCGGACATTA 58.482 45.455 6.41 0.00 0.00 1.90
521 570 2.642139 TGGAGTTCGTCGGACATTAC 57.358 50.000 6.41 2.87 0.00 1.89
522 571 1.203052 TGGAGTTCGTCGGACATTACC 59.797 52.381 6.41 4.58 0.00 2.85
523 572 1.203052 GGAGTTCGTCGGACATTACCA 59.797 52.381 6.41 0.00 0.00 3.25
524 573 2.527100 GAGTTCGTCGGACATTACCAG 58.473 52.381 6.41 0.00 0.00 4.00
525 574 1.891150 AGTTCGTCGGACATTACCAGT 59.109 47.619 6.41 0.00 0.00 4.00
526 575 3.084039 AGTTCGTCGGACATTACCAGTA 58.916 45.455 6.41 0.00 0.00 2.74
527 576 3.119708 AGTTCGTCGGACATTACCAGTAC 60.120 47.826 6.41 0.00 0.00 2.73
528 577 2.715046 TCGTCGGACATTACCAGTACT 58.285 47.619 9.10 0.00 0.00 2.73
529 578 2.421073 TCGTCGGACATTACCAGTACTG 59.579 50.000 16.34 16.34 0.00 2.74
530 579 2.537401 GTCGGACATTACCAGTACTGC 58.463 52.381 17.86 1.61 0.00 4.40
531 580 1.133598 TCGGACATTACCAGTACTGCG 59.866 52.381 17.86 12.43 0.00 5.18
532 581 1.135199 CGGACATTACCAGTACTGCGT 60.135 52.381 17.86 17.63 0.00 5.24
533 582 2.673043 CGGACATTACCAGTACTGCGTT 60.673 50.000 17.86 6.25 0.00 4.84
534 583 2.671396 GGACATTACCAGTACTGCGTTG 59.329 50.000 17.86 13.85 0.00 4.10
535 584 2.671396 GACATTACCAGTACTGCGTTGG 59.329 50.000 17.86 6.95 37.98 3.77
536 585 2.300723 ACATTACCAGTACTGCGTTGGA 59.699 45.455 17.86 0.00 35.89 3.53
537 586 2.736144 TTACCAGTACTGCGTTGGAG 57.264 50.000 17.86 4.48 35.89 3.86
538 587 0.245539 TACCAGTACTGCGTTGGAGC 59.754 55.000 17.86 0.00 35.89 4.70
539 588 1.293498 CCAGTACTGCGTTGGAGCT 59.707 57.895 17.86 0.00 38.13 4.09
540 589 0.737715 CCAGTACTGCGTTGGAGCTC 60.738 60.000 17.86 4.71 38.13 4.09
541 590 1.073216 CAGTACTGCGTTGGAGCTCG 61.073 60.000 10.54 0.00 38.13 5.03
547 596 2.185350 CGTTGGAGCTCGCAGGAT 59.815 61.111 7.83 0.00 0.00 3.24
548 597 2.169789 CGTTGGAGCTCGCAGGATG 61.170 63.158 7.83 0.00 40.87 3.51
549 598 1.078848 GTTGGAGCTCGCAGGATGT 60.079 57.895 7.83 0.00 39.31 3.06
559 608 2.103538 CAGGATGTGCAATGCCGC 59.896 61.111 1.53 0.00 0.00 6.53
560 609 2.044650 AGGATGTGCAATGCCGCT 60.045 55.556 1.53 0.00 0.00 5.52
561 610 2.103538 GGATGTGCAATGCCGCTG 59.896 61.111 1.53 0.00 0.00 5.18
562 611 2.581409 GATGTGCAATGCCGCTGC 60.581 61.111 1.53 0.00 40.35 5.25
563 612 4.485834 ATGTGCAATGCCGCTGCG 62.486 61.111 16.34 16.34 42.97 5.18
569 618 4.088762 AATGCCGCTGCGTTGACG 62.089 61.111 21.59 6.08 44.90 4.35
580 629 4.077188 GTTGACGCTGCCACGCTC 62.077 66.667 0.00 0.00 36.19 5.03
591 640 2.816958 CACGCTCGCTGCTTCCAT 60.817 61.111 0.00 0.00 40.11 3.41
592 641 2.510238 ACGCTCGCTGCTTCCATC 60.510 61.111 0.00 0.00 40.11 3.51
593 642 3.267860 CGCTCGCTGCTTCCATCC 61.268 66.667 0.00 0.00 40.11 3.51
594 643 2.124983 GCTCGCTGCTTCCATCCA 60.125 61.111 0.00 0.00 38.95 3.41
595 644 1.746615 GCTCGCTGCTTCCATCCAA 60.747 57.895 0.00 0.00 38.95 3.53
596 645 1.986575 GCTCGCTGCTTCCATCCAAC 61.987 60.000 0.00 0.00 38.95 3.77
597 646 1.699656 CTCGCTGCTTCCATCCAACG 61.700 60.000 0.00 0.00 0.00 4.10
598 647 2.753966 CGCTGCTTCCATCCAACGG 61.754 63.158 0.00 0.00 0.00 4.44
599 648 3.056313 GCTGCTTCCATCCAACGGC 62.056 63.158 0.00 0.00 0.00 5.68
600 649 2.361104 TGCTTCCATCCAACGGCC 60.361 61.111 0.00 0.00 0.00 6.13
601 650 2.361104 GCTTCCATCCAACGGCCA 60.361 61.111 2.24 0.00 0.00 5.36
602 651 2.700773 GCTTCCATCCAACGGCCAC 61.701 63.158 2.24 0.00 0.00 5.01
603 652 1.002134 CTTCCATCCAACGGCCACT 60.002 57.895 2.24 0.00 0.00 4.00
604 653 0.251916 CTTCCATCCAACGGCCACTA 59.748 55.000 2.24 0.00 0.00 2.74
605 654 0.693622 TTCCATCCAACGGCCACTAA 59.306 50.000 2.24 0.00 0.00 2.24
606 655 0.035820 TCCATCCAACGGCCACTAAC 60.036 55.000 2.24 0.00 0.00 2.34
607 656 0.322098 CCATCCAACGGCCACTAACA 60.322 55.000 2.24 0.00 0.00 2.41
608 657 0.802494 CATCCAACGGCCACTAACAC 59.198 55.000 2.24 0.00 0.00 3.32
609 658 0.398696 ATCCAACGGCCACTAACACA 59.601 50.000 2.24 0.00 0.00 3.72
610 659 0.533308 TCCAACGGCCACTAACACAC 60.533 55.000 2.24 0.00 0.00 3.82
611 660 0.534203 CCAACGGCCACTAACACACT 60.534 55.000 2.24 0.00 0.00 3.55
612 661 0.586319 CAACGGCCACTAACACACTG 59.414 55.000 2.24 0.00 0.00 3.66
613 662 0.466543 AACGGCCACTAACACACTGA 59.533 50.000 2.24 0.00 0.00 3.41
614 663 0.685097 ACGGCCACTAACACACTGAT 59.315 50.000 2.24 0.00 0.00 2.90
615 664 1.337823 ACGGCCACTAACACACTGATC 60.338 52.381 2.24 0.00 0.00 2.92
616 665 1.066858 CGGCCACTAACACACTGATCT 60.067 52.381 2.24 0.00 0.00 2.75
617 666 2.350522 GGCCACTAACACACTGATCTG 58.649 52.381 0.00 0.00 0.00 2.90
618 667 2.028112 GGCCACTAACACACTGATCTGA 60.028 50.000 6.60 0.00 0.00 3.27
619 668 2.996621 GCCACTAACACACTGATCTGAC 59.003 50.000 6.60 0.00 0.00 3.51
620 669 3.245797 CCACTAACACACTGATCTGACG 58.754 50.000 6.60 0.00 0.00 4.35
621 670 3.245797 CACTAACACACTGATCTGACGG 58.754 50.000 6.60 0.00 0.00 4.79
622 671 2.263077 CTAACACACTGATCTGACGGC 58.737 52.381 6.60 0.00 0.00 5.68
623 672 0.681733 AACACACTGATCTGACGGCT 59.318 50.000 6.60 0.00 0.00 5.52
624 673 1.545841 ACACACTGATCTGACGGCTA 58.454 50.000 6.60 0.00 0.00 3.93
625 674 1.474478 ACACACTGATCTGACGGCTAG 59.526 52.381 6.60 0.00 0.00 3.42
626 675 0.457851 ACACTGATCTGACGGCTAGC 59.542 55.000 6.04 6.04 0.00 3.42
627 676 0.249238 CACTGATCTGACGGCTAGCC 60.249 60.000 24.75 24.75 0.00 3.93
628 677 0.684479 ACTGATCTGACGGCTAGCCA 60.684 55.000 32.47 14.01 35.37 4.75
629 678 0.031857 CTGATCTGACGGCTAGCCAG 59.968 60.000 32.47 25.43 35.37 4.85
630 679 1.365633 GATCTGACGGCTAGCCAGG 59.634 63.158 32.47 19.84 35.37 4.45
631 680 2.707529 GATCTGACGGCTAGCCAGGC 62.708 65.000 32.47 25.95 43.81 4.85
637 686 3.550431 GGCTAGCCAGGCGGATGA 61.550 66.667 29.33 0.00 37.63 2.92
638 687 2.746359 GCTAGCCAGGCGGATGAT 59.254 61.111 5.55 0.00 29.71 2.45
639 688 1.375268 GCTAGCCAGGCGGATGATC 60.375 63.158 5.55 0.00 29.71 2.92
640 689 1.825281 GCTAGCCAGGCGGATGATCT 61.825 60.000 5.55 0.00 29.71 2.75
641 690 1.550327 CTAGCCAGGCGGATGATCTA 58.450 55.000 5.55 0.00 29.71 1.98
642 691 1.895798 CTAGCCAGGCGGATGATCTAA 59.104 52.381 5.55 0.00 29.71 2.10
643 692 0.683973 AGCCAGGCGGATGATCTAAG 59.316 55.000 5.55 0.00 0.00 2.18
644 693 0.681733 GCCAGGCGGATGATCTAAGA 59.318 55.000 0.00 0.00 0.00 2.10
645 694 1.070758 GCCAGGCGGATGATCTAAGAA 59.929 52.381 0.00 0.00 0.00 2.52
646 695 2.485479 GCCAGGCGGATGATCTAAGAAA 60.485 50.000 0.00 0.00 0.00 2.52
647 696 3.808618 GCCAGGCGGATGATCTAAGAAAT 60.809 47.826 0.00 0.00 0.00 2.17
648 697 3.999663 CCAGGCGGATGATCTAAGAAATC 59.000 47.826 0.00 0.00 0.00 2.17
649 698 4.503817 CCAGGCGGATGATCTAAGAAATCA 60.504 45.833 0.00 0.00 37.53 2.57
650 699 5.243981 CAGGCGGATGATCTAAGAAATCAT 58.756 41.667 0.00 0.00 44.52 2.45
656 705 4.963318 TGATCTAAGAAATCATCCGGCT 57.037 40.909 0.00 0.00 0.00 5.52
657 706 4.635223 TGATCTAAGAAATCATCCGGCTG 58.365 43.478 0.00 0.00 0.00 4.85
658 707 4.344968 TGATCTAAGAAATCATCCGGCTGA 59.655 41.667 10.98 10.98 0.00 4.26
659 708 4.963318 TCTAAGAAATCATCCGGCTGAT 57.037 40.909 15.02 15.02 37.47 2.90
660 709 5.296151 TCTAAGAAATCATCCGGCTGATT 57.704 39.130 24.37 24.37 45.48 2.57
666 715 1.953559 TCATCCGGCTGATTTGTAGC 58.046 50.000 3.28 0.00 40.41 3.58
667 716 1.209261 TCATCCGGCTGATTTGTAGCA 59.791 47.619 3.28 0.00 42.88 3.49
668 717 2.016318 CATCCGGCTGATTTGTAGCAA 58.984 47.619 0.00 0.00 42.88 3.91
669 718 1.737838 TCCGGCTGATTTGTAGCAAG 58.262 50.000 0.00 0.00 42.88 4.01
670 719 0.099436 CCGGCTGATTTGTAGCAAGC 59.901 55.000 0.00 0.00 42.88 4.01
671 720 0.099436 CGGCTGATTTGTAGCAAGCC 59.901 55.000 1.85 1.85 42.88 4.35
672 721 0.457443 GGCTGATTTGTAGCAAGCCC 59.543 55.000 0.39 0.00 42.88 5.19
673 722 0.457443 GCTGATTTGTAGCAAGCCCC 59.543 55.000 0.00 0.00 40.81 5.80
716 765 3.834726 CACGGTTGGTGCCTTTGA 58.165 55.556 0.00 0.00 40.33 2.69
1283 1357 1.826709 GCCTCCTCAAGTAGGGCTC 59.173 63.158 0.00 0.00 46.55 4.70
1284 1358 0.978146 GCCTCCTCAAGTAGGGCTCA 60.978 60.000 0.00 0.00 46.55 4.26
1367 1441 4.579869 ACTGCGGAATGTAGTTTGAATCT 58.420 39.130 0.00 0.00 41.09 2.40
1409 1492 6.814146 AGGTTTCGATTTGATCTAGTGAGTTC 59.186 38.462 0.00 0.00 0.00 3.01
1430 1513 3.057174 TCCGGTTTCGATTGGGATTTTTG 60.057 43.478 0.00 0.00 39.00 2.44
1521 1607 1.267235 CGATGCAAGCACGAGACAATC 60.267 52.381 0.00 0.00 0.00 2.67
1543 1629 4.278170 TCAGGAAATAAACAGCAAGGTGTG 59.722 41.667 5.59 0.00 0.00 3.82
1563 1653 5.568296 GTGTGTACTAGTTTCGCAGTAGAAG 59.432 44.000 0.00 0.00 33.09 2.85
1569 1659 3.422796 AGTTTCGCAGTAGAAGAGAGGA 58.577 45.455 0.00 0.00 0.00 3.71
1574 1664 6.716934 TTCGCAGTAGAAGAGAGGAAATAT 57.283 37.500 0.00 0.00 0.00 1.28
1658 1748 6.204688 TGCGAAACAATATTCTGAACTTCACT 59.795 34.615 0.00 0.00 0.00 3.41
1678 1768 5.301551 TCACTGTATTGTTGGTTTGCTTGAT 59.698 36.000 0.00 0.00 0.00 2.57
1707 1799 0.037326 TAGAATGCGCCGATGGATCC 60.037 55.000 4.18 4.20 0.00 3.36
1729 1821 5.908831 TCCCCATTGTACTTACTCACCATAT 59.091 40.000 0.00 0.00 0.00 1.78
1743 1835 6.051717 ACTCACCATATTCTAGTGCATTCAC 58.948 40.000 0.00 0.00 43.44 3.18
1850 1945 8.994429 ATCAGGATCGAATCATTAAGATACAC 57.006 34.615 0.00 0.00 35.39 2.90
1889 1984 8.942338 TTTACAGGCAGTACTAAATACATGAG 57.058 34.615 0.00 0.00 36.09 2.90
1891 1986 4.752101 CAGGCAGTACTAAATACATGAGCC 59.248 45.833 0.00 0.00 38.75 4.70
1908 2003 6.441604 ACATGAGCCCTTCCTTTTATGATTTT 59.558 34.615 0.00 0.00 0.00 1.82
1912 2007 7.122650 TGAGCCCTTCCTTTTATGATTTTGTAG 59.877 37.037 0.00 0.00 0.00 2.74
1914 2009 6.350949 GCCCTTCCTTTTATGATTTTGTAGCA 60.351 38.462 0.00 0.00 0.00 3.49
1928 2023 9.866798 TGATTTTGTAGCAATTTTATGTATGCA 57.133 25.926 0.00 0.00 41.18 3.96
2102 2197 6.380560 TCTTCATGCAAACATTTATGATCCCA 59.619 34.615 0.00 0.00 32.87 4.37
2105 2200 3.705579 TGCAAACATTTATGATCCCAGGG 59.294 43.478 0.00 0.00 0.00 4.45
2160 2255 1.149782 TGGGGTGATTAAAGGGGGCA 61.150 55.000 0.00 0.00 0.00 5.36
2349 2444 7.149973 TGGCAATCTTTTTCTTGAGATCTTTG 58.850 34.615 0.00 0.00 31.63 2.77
2486 2581 0.251564 CACCAACCCTGCCCAATACA 60.252 55.000 0.00 0.00 0.00 2.29
2507 2602 4.518970 ACATTCATAAATATGGCGTCACCC 59.481 41.667 0.00 0.00 37.83 4.61
2629 2724 9.330063 CAGTGATCTTATATTTTGGCTCAGTTA 57.670 33.333 0.00 0.00 0.00 2.24
2681 2777 9.425248 ACCAGAATCCATGTTATATGTTCAAAT 57.575 29.630 0.00 0.00 0.00 2.32
2712 2808 7.915293 TGAAAATGGACTAGAATCGCTTAAA 57.085 32.000 0.00 0.00 0.00 1.52
2714 2810 7.606456 TGAAAATGGACTAGAATCGCTTAAACT 59.394 33.333 0.00 0.00 0.00 2.66
2810 2907 1.965414 TTGGGGTCTGGATGCTCTTA 58.035 50.000 0.00 0.00 0.00 2.10
2814 2911 2.224402 GGGGTCTGGATGCTCTTACATC 60.224 54.545 0.00 0.00 44.73 3.06
2828 2925 6.432162 TGCTCTTACATCTTTCTTTTGCTGAT 59.568 34.615 0.00 0.00 0.00 2.90
2867 2964 3.964031 TCAAAAATGGGTAGTTGGTTGCT 59.036 39.130 0.00 0.00 0.00 3.91
2914 3432 8.798859 AGTATACCGGTGTTATAGTACCTATG 57.201 38.462 19.93 0.00 34.77 2.23
2915 3433 4.861102 ACCGGTGTTATAGTACCTATGC 57.139 45.455 6.12 0.00 34.77 3.14
2972 3492 6.700960 CCACATAAAACAACTGCTTTGATTGA 59.299 34.615 5.73 0.00 38.73 2.57
2982 3502 9.362539 ACAACTGCTTTGATTGATTCAATAATC 57.637 29.630 11.79 2.07 43.73 1.75
3023 3547 2.098614 TGTTGAAGTTTGCTGGCTTCA 58.901 42.857 11.40 11.40 46.23 3.02
3027 3551 4.019792 TGAAGTTTGCTGGCTTCATAGA 57.980 40.909 11.40 0.00 44.01 1.98
3130 3654 7.809806 GCAAGGAATATGGCAGAATATTGTTAC 59.190 37.037 0.00 0.00 33.77 2.50
3294 3922 8.738064 AGGAAACCACCTAAGCTTTACTAGCG 62.738 46.154 3.20 0.00 45.77 4.26
3400 4030 1.981256 TTGGCTTCCTTTGTGTCTCC 58.019 50.000 0.00 0.00 0.00 3.71
3413 4043 0.920763 TGTCTCCCCATGGCAGGATT 60.921 55.000 6.09 0.00 0.00 3.01
3414 4044 0.259938 GTCTCCCCATGGCAGGATTT 59.740 55.000 6.09 0.00 0.00 2.17
3648 4278 4.082845 TGGCTTAATTTCCGGACAATGAA 58.917 39.130 1.83 6.33 0.00 2.57
3677 4310 4.454504 ACCTGCTAACTATTGTTTTCCACG 59.545 41.667 0.00 0.00 37.59 4.94
3773 4406 3.588842 TCCTGTTCCTCATTGGATCTGTT 59.411 43.478 0.00 0.00 45.68 3.16
3875 4512 1.437986 CCAGCGTGTACTAGCCTCC 59.562 63.158 9.02 0.00 0.00 4.30
3959 4600 1.075536 AGAAACGGAATGGCTCCCTTT 59.924 47.619 0.00 0.00 41.87 3.11
4013 4656 2.284190 GCTGTATCTGCTTCCCTGTTC 58.716 52.381 0.00 0.00 0.00 3.18
4265 4998 9.137459 TCAAATGTACCCTTGTGAAAAATTCTA 57.863 29.630 0.00 0.00 0.00 2.10
4270 5003 9.757227 TGTACCCTTGTGAAAAATTCTAATTTG 57.243 29.630 1.61 0.00 38.53 2.32
4280 5013 9.171877 TGAAAAATTCTAATTTGTTTGGCAACT 57.828 25.926 0.00 0.00 38.53 3.16
4365 5101 4.024133 GGCGGAAAAACAAATTTGATGCTT 60.024 37.500 24.64 9.98 0.00 3.91
4381 5117 6.774354 TGATGCTTCAAAAAGATTTTCTGC 57.226 33.333 0.00 0.00 34.14 4.26
4447 5183 9.512435 CTCCAAGAATGTGATTTCATCATTAAC 57.488 33.333 7.75 0.00 42.04 2.01
4475 5211 5.788055 CATGCATGCAAAAGAATTAGCAA 57.212 34.783 26.68 0.00 41.48 3.91
4485 5224 9.852091 TGCAAAAGAATTAGCAATTTTTGTTTT 57.148 22.222 9.03 0.00 36.50 2.43
4538 5278 5.852282 ACTTTTTGGGATATTGGGATTCG 57.148 39.130 0.00 0.00 0.00 3.34
4654 5394 4.442753 GGCAAAACCCTTTCACAATTGAGA 60.443 41.667 13.59 7.01 31.71 3.27
4680 5420 3.399330 CCGAAACTCTGAGTGGCTTTTA 58.601 45.455 11.71 0.00 0.00 1.52
4681 5421 3.433615 CCGAAACTCTGAGTGGCTTTTAG 59.566 47.826 11.71 2.05 0.00 1.85
4707 5458 0.243907 GTAGGCTCAGCGACACTTCA 59.756 55.000 0.00 0.00 0.00 3.02
4741 5492 0.978907 AAAATCAAGCCCAAGCCCAG 59.021 50.000 0.00 0.00 41.25 4.45
4748 5499 4.403502 CCCAAGCCCAGGCCCAAT 62.404 66.667 4.70 0.00 43.17 3.16
4749 5500 2.689175 CCAAGCCCAGGCCCAATA 59.311 61.111 4.70 0.00 43.17 1.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
89 90 1.421485 CATCGCAAGCACCGAGTTC 59.579 57.895 0.00 0.00 38.20 3.01
91 92 3.121030 GCATCGCAAGCACCGAGT 61.121 61.111 0.00 0.00 38.20 4.18
93 94 3.120385 CTGCATCGCAAGCACCGA 61.120 61.111 0.00 0.00 38.41 4.69
122 158 4.812476 TCGCAAGCACGGGATCCG 62.812 66.667 5.45 4.67 46.26 4.18
124 160 3.017323 CATCGCAAGCACGGGATC 58.983 61.111 0.00 0.00 36.51 3.36
141 178 2.275318 GATTCACCAGTGAGTAGCTGC 58.725 52.381 0.00 0.00 41.13 5.25
142 179 2.419297 GGGATTCACCAGTGAGTAGCTG 60.419 54.545 0.00 0.00 41.13 4.24
153 190 1.971167 GCAACGCTGGGATTCACCA 60.971 57.895 0.00 0.00 41.20 4.17
155 192 0.109597 CTTGCAACGCTGGGATTCAC 60.110 55.000 0.00 0.00 0.00 3.18
156 193 1.865788 GCTTGCAACGCTGGGATTCA 61.866 55.000 11.98 0.00 0.00 2.57
157 194 1.153958 GCTTGCAACGCTGGGATTC 60.154 57.895 11.98 0.00 0.00 2.52
158 195 2.639327 GGCTTGCAACGCTGGGATT 61.639 57.895 16.77 0.00 0.00 3.01
159 196 3.064324 GGCTTGCAACGCTGGGAT 61.064 61.111 16.77 0.00 0.00 3.85
164 201 3.434319 CATCCGGCTTGCAACGCT 61.434 61.111 16.77 0.49 0.00 5.07
168 205 4.757355 CCCCCATCCGGCTTGCAA 62.757 66.667 0.00 0.00 0.00 4.08
202 239 2.502510 CATCGCAGCGCCAACAAC 60.503 61.111 10.87 0.00 0.00 3.32
205 242 3.688475 ATTGCATCGCAGCGCCAAC 62.688 57.895 10.87 0.00 40.61 3.77
211 249 0.660595 GATGAGCATTGCATCGCAGC 60.661 55.000 11.91 2.65 40.61 5.25
215 253 0.384353 CGCTGATGAGCATTGCATCG 60.384 55.000 11.91 4.42 46.62 3.84
218 256 2.767445 GCCGCTGATGAGCATTGCA 61.767 57.895 11.91 0.00 46.62 4.08
246 284 1.226688 GACGAGTAGCTGCATCGCA 60.227 57.895 18.23 0.00 40.02 5.10
247 285 2.289375 CGACGAGTAGCTGCATCGC 61.289 63.158 18.23 12.36 40.02 4.58
248 286 0.926174 GTCGACGAGTAGCTGCATCG 60.926 60.000 17.24 17.24 42.04 3.84
249 287 0.926174 CGTCGACGAGTAGCTGCATC 60.926 60.000 33.35 0.00 43.02 3.91
250 288 1.062685 CGTCGACGAGTAGCTGCAT 59.937 57.895 33.35 0.00 43.02 3.96
251 289 2.479198 CGTCGACGAGTAGCTGCA 59.521 61.111 33.35 0.00 43.02 4.41
252 290 2.277373 CCGTCGACGAGTAGCTGC 60.277 66.667 37.65 0.00 43.02 5.25
253 291 2.277373 GCCGTCGACGAGTAGCTG 60.277 66.667 37.65 20.24 43.02 4.24
254 292 2.436292 AGCCGTCGACGAGTAGCT 60.436 61.111 37.65 31.46 43.02 3.32
255 293 1.979831 AAGAGCCGTCGACGAGTAGC 61.980 60.000 37.65 29.86 43.02 3.58
256 294 0.247735 CAAGAGCCGTCGACGAGTAG 60.248 60.000 37.65 22.06 43.02 2.57
257 295 0.671472 TCAAGAGCCGTCGACGAGTA 60.671 55.000 37.65 13.37 43.02 2.59
258 296 1.306642 ATCAAGAGCCGTCGACGAGT 61.307 55.000 37.65 24.10 43.02 4.18
263 301 0.317160 ACAACATCAAGAGCCGTCGA 59.683 50.000 0.00 0.00 0.00 4.20
266 304 0.534877 TGCACAACATCAAGAGCCGT 60.535 50.000 0.00 0.00 0.00 5.68
273 311 0.821301 TCCGGCTTGCACAACATCAA 60.821 50.000 0.00 0.00 0.00 2.57
279 317 2.676121 CCCATCCGGCTTGCACAA 60.676 61.111 0.00 0.00 0.00 3.33
280 318 4.738998 CCCCATCCGGCTTGCACA 62.739 66.667 0.00 0.00 0.00 4.57
301 339 1.677300 CAATTACCCTGCACCGCCA 60.677 57.895 0.00 0.00 0.00 5.69
309 347 0.171007 CCGCAGCAACAATTACCCTG 59.829 55.000 0.00 0.00 0.00 4.45
328 366 1.499056 CCAGTGATGAGCGTTGCAC 59.501 57.895 0.00 0.00 0.00 4.57
333 371 2.435586 GCAGCCAGTGATGAGCGT 60.436 61.111 0.00 0.00 0.00 5.07
352 390 4.875713 CCCCCGCATAGCACCACC 62.876 72.222 0.00 0.00 0.00 4.61
360 398 2.519063 CATTGCAGCCCCCGCATA 60.519 61.111 0.00 0.00 39.58 3.14
365 403 3.970746 AAGCTCCATTGCAGCCCCC 62.971 63.158 0.00 0.00 37.63 5.40
368 414 2.796651 CGAAGCTCCATTGCAGCC 59.203 61.111 0.00 0.00 37.63 4.85
386 432 2.584418 CAGCATCGACAGCTCCGG 60.584 66.667 10.96 0.00 41.14 5.14
393 439 1.737735 CTCCAACGCAGCATCGACA 60.738 57.895 4.64 0.00 0.00 4.35
398 444 2.034879 CGGAACTCCAACGCAGCAT 61.035 57.895 0.00 0.00 35.14 3.79
401 447 3.423154 GCCGGAACTCCAACGCAG 61.423 66.667 5.05 0.00 35.14 5.18
412 458 4.408821 ATTGCAGCCTCGCCGGAA 62.409 61.111 5.05 0.00 33.16 4.30
438 484 2.413765 CGAAGCTTCATTGCAACTCCAG 60.414 50.000 25.47 1.22 34.99 3.86
439 485 1.536766 CGAAGCTTCATTGCAACTCCA 59.463 47.619 25.47 0.00 34.99 3.86
467 515 1.083657 CTTCAACGCAACACCGACG 60.084 57.895 0.00 0.00 0.00 5.12
488 536 4.738998 TCCATTGCAGCCCCGGTG 62.739 66.667 0.00 0.00 0.00 4.94
489 537 4.431131 CTCCATTGCAGCCCCGGT 62.431 66.667 0.00 0.00 0.00 5.28
494 543 1.796796 GACGAACTCCATTGCAGCC 59.203 57.895 0.00 0.00 0.00 4.85
496 545 0.389817 TCCGACGAACTCCATTGCAG 60.390 55.000 0.00 0.00 0.00 4.41
507 556 3.084039 AGTACTGGTAATGTCCGACGAA 58.916 45.455 0.00 0.00 0.00 3.85
511 560 1.133598 CGCAGTACTGGTAATGTCCGA 59.866 52.381 23.95 0.00 34.05 4.55
512 561 1.135199 ACGCAGTACTGGTAATGTCCG 60.135 52.381 23.95 17.23 41.94 4.79
513 562 2.667473 ACGCAGTACTGGTAATGTCC 57.333 50.000 23.95 4.05 41.94 4.02
514 563 2.671396 CCAACGCAGTACTGGTAATGTC 59.329 50.000 23.95 4.78 45.00 3.06
515 564 2.300723 TCCAACGCAGTACTGGTAATGT 59.699 45.455 23.95 3.30 45.00 2.71
516 565 2.930040 CTCCAACGCAGTACTGGTAATG 59.070 50.000 23.95 14.50 45.00 1.90
517 566 2.677037 GCTCCAACGCAGTACTGGTAAT 60.677 50.000 23.95 4.28 45.00 1.89
518 567 1.337447 GCTCCAACGCAGTACTGGTAA 60.337 52.381 23.95 8.77 45.00 2.85
519 568 0.245539 GCTCCAACGCAGTACTGGTA 59.754 55.000 23.95 5.39 45.00 3.25
520 569 1.004918 GCTCCAACGCAGTACTGGT 60.005 57.895 23.95 16.47 45.00 4.00
521 570 0.737715 GAGCTCCAACGCAGTACTGG 60.738 60.000 23.95 15.85 45.00 4.00
522 571 1.073216 CGAGCTCCAACGCAGTACTG 61.073 60.000 18.93 18.93 45.00 2.74
523 572 1.213013 CGAGCTCCAACGCAGTACT 59.787 57.895 8.47 0.00 45.00 2.73
524 573 3.768632 CGAGCTCCAACGCAGTAC 58.231 61.111 8.47 0.00 45.00 2.73
530 579 2.169789 CATCCTGCGAGCTCCAACG 61.170 63.158 8.47 0.00 0.00 4.10
531 580 1.078848 ACATCCTGCGAGCTCCAAC 60.079 57.895 8.47 0.00 0.00 3.77
532 581 1.078918 CACATCCTGCGAGCTCCAA 60.079 57.895 8.47 0.00 0.00 3.53
533 582 2.580815 CACATCCTGCGAGCTCCA 59.419 61.111 8.47 6.43 0.00 3.86
534 583 2.894387 GCACATCCTGCGAGCTCC 60.894 66.667 8.47 1.40 35.72 4.70
542 591 2.103538 GCGGCATTGCACATCCTG 59.896 61.111 11.39 0.00 34.15 3.86
543 592 2.044650 AGCGGCATTGCACATCCT 60.045 55.556 11.39 0.00 37.31 3.24
544 593 2.103538 CAGCGGCATTGCACATCC 59.896 61.111 11.39 0.00 37.31 3.51
545 594 2.581409 GCAGCGGCATTGCACATC 60.581 61.111 11.39 0.00 41.17 3.06
546 595 4.485834 CGCAGCGGCATTGCACAT 62.486 61.111 7.00 0.00 41.59 3.21
548 597 4.705519 AACGCAGCGGCATTGCAC 62.706 61.111 21.15 1.70 41.59 4.57
549 598 4.703799 CAACGCAGCGGCATTGCA 62.704 61.111 21.15 0.00 36.32 4.08
550 599 4.403137 TCAACGCAGCGGCATTGC 62.403 61.111 21.15 3.11 42.61 3.56
551 600 2.502510 GTCAACGCAGCGGCATTG 60.503 61.111 21.15 11.46 44.15 2.82
552 601 4.088762 CGTCAACGCAGCGGCATT 62.089 61.111 21.15 0.76 41.24 3.56
563 612 4.077188 GAGCGTGGCAGCGTCAAC 62.077 66.667 10.30 0.00 43.00 3.18
577 626 1.746615 TTGGATGGAAGCAGCGAGC 60.747 57.895 0.00 0.00 46.19 5.03
578 627 1.699656 CGTTGGATGGAAGCAGCGAG 61.700 60.000 0.00 0.00 0.00 5.03
579 628 1.741401 CGTTGGATGGAAGCAGCGA 60.741 57.895 0.00 0.00 0.00 4.93
580 629 2.753966 CCGTTGGATGGAAGCAGCG 61.754 63.158 0.00 0.00 0.00 5.18
581 630 3.056313 GCCGTTGGATGGAAGCAGC 62.056 63.158 0.00 0.00 0.00 5.25
582 631 2.409870 GGCCGTTGGATGGAAGCAG 61.410 63.158 0.00 0.00 0.00 4.24
583 632 2.361104 GGCCGTTGGATGGAAGCA 60.361 61.111 0.00 0.00 0.00 3.91
584 633 2.361104 TGGCCGTTGGATGGAAGC 60.361 61.111 0.00 0.00 0.00 3.86
585 634 0.251916 TAGTGGCCGTTGGATGGAAG 59.748 55.000 0.00 0.00 0.00 3.46
586 635 0.693622 TTAGTGGCCGTTGGATGGAA 59.306 50.000 0.00 0.00 0.00 3.53
587 636 0.035820 GTTAGTGGCCGTTGGATGGA 60.036 55.000 0.00 0.00 0.00 3.41
588 637 0.322098 TGTTAGTGGCCGTTGGATGG 60.322 55.000 0.00 0.00 0.00 3.51
589 638 0.802494 GTGTTAGTGGCCGTTGGATG 59.198 55.000 0.00 0.00 0.00 3.51
590 639 0.398696 TGTGTTAGTGGCCGTTGGAT 59.601 50.000 0.00 0.00 0.00 3.41
591 640 0.533308 GTGTGTTAGTGGCCGTTGGA 60.533 55.000 0.00 0.00 0.00 3.53
592 641 0.534203 AGTGTGTTAGTGGCCGTTGG 60.534 55.000 0.00 0.00 0.00 3.77
593 642 0.586319 CAGTGTGTTAGTGGCCGTTG 59.414 55.000 0.00 0.00 0.00 4.10
594 643 0.466543 TCAGTGTGTTAGTGGCCGTT 59.533 50.000 0.00 0.00 0.00 4.44
595 644 0.685097 ATCAGTGTGTTAGTGGCCGT 59.315 50.000 0.00 0.00 0.00 5.68
596 645 1.066858 AGATCAGTGTGTTAGTGGCCG 60.067 52.381 0.00 0.00 0.00 6.13
597 646 2.028112 TCAGATCAGTGTGTTAGTGGCC 60.028 50.000 0.00 0.00 0.00 5.36
598 647 2.996621 GTCAGATCAGTGTGTTAGTGGC 59.003 50.000 0.00 0.00 0.00 5.01
599 648 3.245797 CGTCAGATCAGTGTGTTAGTGG 58.754 50.000 0.00 0.00 0.00 4.00
600 649 3.245797 CCGTCAGATCAGTGTGTTAGTG 58.754 50.000 0.00 0.00 0.00 2.74
601 650 2.352814 GCCGTCAGATCAGTGTGTTAGT 60.353 50.000 0.00 0.00 0.00 2.24
602 651 2.094494 AGCCGTCAGATCAGTGTGTTAG 60.094 50.000 0.00 0.00 0.00 2.34
603 652 1.893137 AGCCGTCAGATCAGTGTGTTA 59.107 47.619 0.00 0.00 0.00 2.41
604 653 0.681733 AGCCGTCAGATCAGTGTGTT 59.318 50.000 0.00 0.00 0.00 3.32
605 654 1.474478 CTAGCCGTCAGATCAGTGTGT 59.526 52.381 0.00 0.00 0.00 3.72
606 655 1.800655 GCTAGCCGTCAGATCAGTGTG 60.801 57.143 2.29 0.00 0.00 3.82
607 656 0.457851 GCTAGCCGTCAGATCAGTGT 59.542 55.000 2.29 0.00 0.00 3.55
608 657 0.249238 GGCTAGCCGTCAGATCAGTG 60.249 60.000 20.16 0.00 0.00 3.66
609 658 0.684479 TGGCTAGCCGTCAGATCAGT 60.684 55.000 28.28 0.00 39.42 3.41
610 659 2.119009 TGGCTAGCCGTCAGATCAG 58.881 57.895 28.28 0.00 39.42 2.90
611 660 4.355151 TGGCTAGCCGTCAGATCA 57.645 55.556 28.28 5.61 39.42 2.92
615 664 4.880537 CGCCTGGCTAGCCGTCAG 62.881 72.222 28.28 19.59 45.03 3.51
619 668 4.976925 CATCCGCCTGGCTAGCCG 62.977 72.222 28.28 21.44 39.42 5.52
620 669 2.794820 GATCATCCGCCTGGCTAGCC 62.795 65.000 27.71 27.71 34.14 3.93
621 670 1.375268 GATCATCCGCCTGGCTAGC 60.375 63.158 17.92 6.04 34.14 3.42
622 671 1.550327 TAGATCATCCGCCTGGCTAG 58.450 55.000 17.92 8.21 34.14 3.42
623 672 1.895798 CTTAGATCATCCGCCTGGCTA 59.104 52.381 17.92 4.99 34.14 3.93
624 673 0.683973 CTTAGATCATCCGCCTGGCT 59.316 55.000 17.92 0.00 34.14 4.75
625 674 0.681733 TCTTAGATCATCCGCCTGGC 59.318 55.000 9.11 9.11 34.14 4.85
626 675 3.475566 TTTCTTAGATCATCCGCCTGG 57.524 47.619 0.00 0.00 0.00 4.45
627 676 4.635223 TGATTTCTTAGATCATCCGCCTG 58.365 43.478 0.00 0.00 0.00 4.85
628 677 4.963318 TGATTTCTTAGATCATCCGCCT 57.037 40.909 0.00 0.00 0.00 5.52
634 683 5.012458 TCAGCCGGATGATTTCTTAGATCAT 59.988 40.000 20.59 0.00 44.62 2.45
635 684 4.344968 TCAGCCGGATGATTTCTTAGATCA 59.655 41.667 20.59 0.00 37.86 2.92
636 685 4.887748 TCAGCCGGATGATTTCTTAGATC 58.112 43.478 20.59 0.00 0.00 2.75
637 686 4.963318 TCAGCCGGATGATTTCTTAGAT 57.037 40.909 20.59 0.00 0.00 1.98
638 687 4.963318 ATCAGCCGGATGATTTCTTAGA 57.037 40.909 29.04 1.31 36.50 2.10
646 695 2.158769 TGCTACAAATCAGCCGGATGAT 60.159 45.455 29.04 29.04 41.72 2.45
647 696 1.209261 TGCTACAAATCAGCCGGATGA 59.791 47.619 26.87 26.87 38.29 2.92
648 697 1.667236 TGCTACAAATCAGCCGGATG 58.333 50.000 15.12 15.12 38.29 3.51
649 698 2.292267 CTTGCTACAAATCAGCCGGAT 58.708 47.619 5.05 0.00 38.29 4.18
650 699 1.737838 CTTGCTACAAATCAGCCGGA 58.262 50.000 5.05 0.00 38.29 5.14
651 700 0.099436 GCTTGCTACAAATCAGCCGG 59.901 55.000 0.00 0.00 38.29 6.13
652 701 0.099436 GGCTTGCTACAAATCAGCCG 59.901 55.000 0.00 0.00 38.29 5.52
653 702 0.457443 GGGCTTGCTACAAATCAGCC 59.543 55.000 0.00 0.00 38.29 4.85
654 703 0.457443 GGGGCTTGCTACAAATCAGC 59.543 55.000 0.00 0.00 39.56 4.26
655 704 1.106285 GGGGGCTTGCTACAAATCAG 58.894 55.000 0.00 0.00 0.00 2.90
656 705 0.407528 TGGGGGCTTGCTACAAATCA 59.592 50.000 0.00 0.00 0.00 2.57
657 706 1.478105 CTTGGGGGCTTGCTACAAATC 59.522 52.381 0.00 0.00 0.00 2.17
658 707 1.203174 ACTTGGGGGCTTGCTACAAAT 60.203 47.619 0.00 0.00 0.00 2.32
659 708 0.187361 ACTTGGGGGCTTGCTACAAA 59.813 50.000 0.00 0.00 0.00 2.83
660 709 0.539438 CACTTGGGGGCTTGCTACAA 60.539 55.000 0.00 0.00 0.00 2.41
661 710 1.074775 CACTTGGGGGCTTGCTACA 59.925 57.895 0.00 0.00 0.00 2.74
662 711 0.034089 ATCACTTGGGGGCTTGCTAC 60.034 55.000 0.00 0.00 0.00 3.58
663 712 1.590591 TATCACTTGGGGGCTTGCTA 58.409 50.000 0.00 0.00 0.00 3.49
664 713 0.929244 ATATCACTTGGGGGCTTGCT 59.071 50.000 0.00 0.00 0.00 3.91
665 714 1.133668 AGATATCACTTGGGGGCTTGC 60.134 52.381 5.32 0.00 0.00 4.01
666 715 2.173356 TGAGATATCACTTGGGGGCTTG 59.827 50.000 5.32 0.00 0.00 4.01
667 716 2.173569 GTGAGATATCACTTGGGGGCTT 59.826 50.000 13.23 0.00 37.62 4.35
668 717 1.771255 GTGAGATATCACTTGGGGGCT 59.229 52.381 13.23 0.00 37.62 5.19
669 718 1.202818 GGTGAGATATCACTTGGGGGC 60.203 57.143 19.26 0.00 40.28 5.80
670 719 1.421646 GGGTGAGATATCACTTGGGGG 59.578 57.143 19.26 0.00 40.28 5.40
671 720 1.070758 CGGGTGAGATATCACTTGGGG 59.929 57.143 19.26 2.20 40.28 4.96
672 721 1.762957 ACGGGTGAGATATCACTTGGG 59.237 52.381 19.26 9.13 40.28 4.12
673 722 2.483714 CCACGGGTGAGATATCACTTGG 60.484 54.545 19.26 17.69 40.28 3.61
714 763 6.210784 GGTAGTAGGATATACTGTTGCCATCA 59.789 42.308 0.00 0.00 0.00 3.07
716 765 6.014499 GTGGTAGTAGGATATACTGTTGCCAT 60.014 42.308 11.65 0.00 0.00 4.40
730 779 0.677731 CGGTGTCCGTGGTAGTAGGA 60.678 60.000 0.00 0.00 42.73 2.94
1283 1357 2.982130 CGTGGGAGGGGAAGAGTG 59.018 66.667 0.00 0.00 0.00 3.51
1284 1358 3.003763 GCGTGGGAGGGGAAGAGT 61.004 66.667 0.00 0.00 0.00 3.24
1313 1387 1.416813 CGCGATCCAGAAGACACAGC 61.417 60.000 0.00 0.00 0.00 4.40
1345 1419 4.579869 AGATTCAAACTACATTCCGCAGT 58.420 39.130 0.00 0.00 0.00 4.40
1367 1441 1.881973 ACCTCACTTCGCGTGTAGTAA 59.118 47.619 5.77 0.00 44.16 2.24
1375 1452 1.068474 AATCGAAACCTCACTTCGCG 58.932 50.000 0.00 0.00 44.14 5.87
1387 1464 5.805486 CGGAACTCACTAGATCAAATCGAAA 59.195 40.000 0.00 0.00 0.00 3.46
1388 1465 5.340803 CGGAACTCACTAGATCAAATCGAA 58.659 41.667 0.00 0.00 0.00 3.71
1409 1492 3.057174 TCAAAAATCCCAATCGAAACCGG 60.057 43.478 0.00 0.00 0.00 5.28
1430 1513 1.591619 GCTTACCTACCGCGACAAATC 59.408 52.381 8.23 0.00 0.00 2.17
1515 1601 6.095377 CCTTGCTGTTTATTTCCTGATTGTC 58.905 40.000 0.00 0.00 0.00 3.18
1521 1607 4.037923 ACACACCTTGCTGTTTATTTCCTG 59.962 41.667 0.00 0.00 0.00 3.86
1543 1629 6.419980 TCTCTTCTACTGCGAAACTAGTAC 57.580 41.667 0.00 0.00 0.00 2.73
1563 1653 8.361139 TCTTCGGATGAACTAATATTTCCTCTC 58.639 37.037 0.00 0.00 0.00 3.20
1569 1659 7.648510 GTCGTCTCTTCGGATGAACTAATATTT 59.351 37.037 0.00 0.00 33.70 1.40
1574 1664 3.754850 TGTCGTCTCTTCGGATGAACTAA 59.245 43.478 0.00 0.00 33.70 2.24
1658 1748 5.069648 TGGAATCAAGCAAACCAACAATACA 59.930 36.000 0.00 0.00 0.00 2.29
1678 1768 1.405526 GGCGCATTCTAGTGTCTGGAA 60.406 52.381 10.83 0.00 35.57 3.53
1707 1799 7.509546 AGAATATGGTGAGTAAGTACAATGGG 58.490 38.462 0.00 0.00 0.00 4.00
1889 1984 6.042777 GCTACAAAATCATAAAAGGAAGGGC 58.957 40.000 0.00 0.00 0.00 5.19
1891 1986 9.657419 AATTGCTACAAAATCATAAAAGGAAGG 57.343 29.630 0.00 0.00 0.00 3.46
1967 2062 8.861086 AGGAATGTCAGTATACGAATTCAGTAT 58.139 33.333 19.52 19.52 38.27 2.12
1968 2063 8.234136 AGGAATGTCAGTATACGAATTCAGTA 57.766 34.615 6.22 9.09 0.00 2.74
1969 2064 7.113658 AGGAATGTCAGTATACGAATTCAGT 57.886 36.000 6.22 7.16 0.00 3.41
1970 2065 8.425577 AAAGGAATGTCAGTATACGAATTCAG 57.574 34.615 6.22 1.11 0.00 3.02
1971 2066 8.258007 AGAAAGGAATGTCAGTATACGAATTCA 58.742 33.333 6.22 7.81 0.00 2.57
1972 2067 8.543774 CAGAAAGGAATGTCAGTATACGAATTC 58.456 37.037 0.00 0.00 0.00 2.17
1973 2068 8.258007 TCAGAAAGGAATGTCAGTATACGAATT 58.742 33.333 0.00 0.00 0.00 2.17
1974 2069 7.782049 TCAGAAAGGAATGTCAGTATACGAAT 58.218 34.615 0.00 0.00 0.00 3.34
1975 2070 7.165460 TCAGAAAGGAATGTCAGTATACGAA 57.835 36.000 0.00 0.00 0.00 3.85
1976 2071 6.769134 TCAGAAAGGAATGTCAGTATACGA 57.231 37.500 0.00 0.00 0.00 3.43
1977 2072 7.545965 AGTTTCAGAAAGGAATGTCAGTATACG 59.454 37.037 0.00 0.00 0.00 3.06
1978 2073 8.779354 AGTTTCAGAAAGGAATGTCAGTATAC 57.221 34.615 0.00 0.00 0.00 1.47
1979 2074 9.219603 CAAGTTTCAGAAAGGAATGTCAGTATA 57.780 33.333 0.00 0.00 0.00 1.47
2051 2146 1.302949 GGAGCAATACCCCAGCACA 59.697 57.895 0.00 0.00 0.00 4.57
2102 2197 8.903820 GCAAGTAAAGACATAAATATTGTCCCT 58.096 33.333 2.98 0.00 43.62 4.20
2105 2200 9.722056 CCAGCAAGTAAAGACATAAATATTGTC 57.278 33.333 0.00 0.00 43.05 3.18
2160 2255 1.880027 GGCAGTGAAGACGACCAAAAT 59.120 47.619 0.00 0.00 0.00 1.82
2349 2444 0.034670 AAGCTCTCATCAGTTGGGGC 60.035 55.000 0.00 0.00 0.00 5.80
2486 2581 4.724399 TGGGTGACGCCATATTTATGAAT 58.276 39.130 7.48 0.00 39.65 2.57
2507 2602 7.496529 AATATGGAAAGGTATGTCGACAATG 57.503 36.000 24.13 0.00 0.00 2.82
2629 2724 5.047802 CAGGTAATTGCTTTGTTCCAGACAT 60.048 40.000 0.00 0.00 38.26 3.06
2681 2777 6.313658 CGATTCTAGTCCATTTTCATGTGACA 59.686 38.462 0.00 0.00 35.02 3.58
2712 2808 6.544197 AGTTATGATACTCAGACATCGACAGT 59.456 38.462 0.00 0.00 0.00 3.55
2714 2810 6.944234 AGTTATGATACTCAGACATCGACA 57.056 37.500 0.00 0.00 0.00 4.35
2814 2911 5.118286 ACCCAAAACATCAGCAAAAGAAAG 58.882 37.500 0.00 0.00 0.00 2.62
2828 2925 9.331282 CCATTTTTGACTTATTTACCCAAAACA 57.669 29.630 0.00 0.00 36.73 2.83
2887 2986 7.751768 AGGTACTATAACACCGGTATACTTC 57.248 40.000 6.87 0.00 39.94 3.01
2914 3432 0.811281 AATGCGGTGCCTTTCTAAGC 59.189 50.000 0.00 0.00 0.00 3.09
2915 3433 2.487762 TGAAATGCGGTGCCTTTCTAAG 59.512 45.455 16.60 0.00 41.39 2.18
2937 3455 7.117523 GCAGTTGTTTTATGTGGAAATGCAATA 59.882 33.333 0.00 0.00 0.00 1.90
3023 3547 4.339530 TCGTGCAGCTTCTACTGAATCTAT 59.660 41.667 0.00 0.00 40.25 1.98
3027 3551 2.417924 CCTCGTGCAGCTTCTACTGAAT 60.418 50.000 0.00 0.00 40.25 2.57
3130 3654 6.777213 AGGTAAGAGGTTGTATAGACAGTG 57.223 41.667 0.00 0.00 36.76 3.66
3229 3857 7.336176 GGTAGCCTTTTAGCACTAACAAACTAT 59.664 37.037 0.00 0.00 34.23 2.12
3294 3922 5.766670 ACTAACTTGGTTACCTAAAGTTGCC 59.233 40.000 22.31 0.00 42.51 4.52
3437 4067 0.245266 TGCGTCTTGCTATCGGTTGA 59.755 50.000 0.00 0.00 46.63 3.18
3616 4246 5.242393 CCGGAAATTAAGCCATCATTCAGAT 59.758 40.000 0.00 0.00 37.48 2.90
3627 4257 4.712122 TTCATTGTCCGGAAATTAAGCC 57.288 40.909 5.23 0.00 0.00 4.35
3648 4278 8.903820 GGAAAACAATAGTTAGCAGGTATGAAT 58.096 33.333 0.00 0.00 36.84 2.57
3677 4310 4.106925 CTCCCAGCCTGCAGGACC 62.107 72.222 37.21 19.60 37.39 4.46
3773 4406 3.599285 GATGGTTGGGACGACGGCA 62.599 63.158 1.63 0.00 0.00 5.69
3926 4567 7.415206 GCCATTCCGTTTCTTACATCTTTACAT 60.415 37.037 0.00 0.00 0.00 2.29
3959 4600 8.389603 CCTTTTTATTGCGTAATACCGACTTTA 58.610 33.333 5.37 0.00 0.00 1.85
4013 4656 2.979813 GCAACGGTAACTGCAATTTCAG 59.020 45.455 3.36 3.36 37.67 3.02
4233 4934 3.438087 CACAAGGGTACATTTGAGCTCTG 59.562 47.826 16.19 7.62 0.00 3.35
4234 4935 3.327757 TCACAAGGGTACATTTGAGCTCT 59.672 43.478 16.19 0.00 0.00 4.09
4265 4998 7.335422 TCAACAATGTTAGTTGCCAAACAAATT 59.665 29.630 0.00 0.00 44.50 1.82
4270 5003 6.843069 ATTCAACAATGTTAGTTGCCAAAC 57.157 33.333 0.00 0.00 44.50 2.93
4338 5071 5.263968 TCAAATTTGTTTTTCCGCCTACA 57.736 34.783 17.47 0.00 0.00 2.74
4339 5072 5.389411 GCATCAAATTTGTTTTTCCGCCTAC 60.389 40.000 17.47 0.00 0.00 3.18
4341 5074 3.498018 GCATCAAATTTGTTTTTCCGCCT 59.502 39.130 17.47 0.00 0.00 5.52
4342 5075 3.498018 AGCATCAAATTTGTTTTTCCGCC 59.502 39.130 17.47 0.00 0.00 6.13
4344 5077 6.284475 TGAAGCATCAAATTTGTTTTTCCG 57.716 33.333 17.47 0.00 30.99 4.30
4365 5101 7.556733 AAATGCTTGCAGAAAATCTTTTTGA 57.443 28.000 0.87 0.00 0.00 2.69
4394 5130 5.411053 CCGGGCAAAAATAACAAATCAACAT 59.589 36.000 0.00 0.00 0.00 2.71
4512 5251 9.073475 CGAATCCCAATATCCCAAAAAGTAATA 57.927 33.333 0.00 0.00 0.00 0.98
4517 5256 5.852282 ACGAATCCCAATATCCCAAAAAG 57.148 39.130 0.00 0.00 0.00 2.27
4523 5262 3.260884 TCTGCTACGAATCCCAATATCCC 59.739 47.826 0.00 0.00 0.00 3.85
4528 5268 2.092968 TGCTTCTGCTACGAATCCCAAT 60.093 45.455 0.00 0.00 40.48 3.16
4531 5271 2.246719 ATGCTTCTGCTACGAATCCC 57.753 50.000 0.00 0.00 40.48 3.85
4533 5273 4.784710 GCTCAAATGCTTCTGCTACGAATC 60.785 45.833 0.00 0.00 40.48 2.52
4534 5274 3.064545 GCTCAAATGCTTCTGCTACGAAT 59.935 43.478 0.00 0.00 40.48 3.34
4639 5379 2.160417 GGCTCGTCTCAATTGTGAAAGG 59.840 50.000 11.57 5.25 31.88 3.11
4641 5381 1.798223 CGGCTCGTCTCAATTGTGAAA 59.202 47.619 11.57 3.31 31.88 2.69
4654 5394 0.039074 CACTCAGAGTTTCGGCTCGT 60.039 55.000 0.00 0.00 40.26 4.18
4741 5492 2.203209 CTGCTCCGGTATTGGGCC 60.203 66.667 0.00 0.00 0.00 5.80
4748 5499 2.759973 CTGGAGGCTGCTCCGGTA 60.760 66.667 7.74 0.00 46.18 4.02


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

AutoCloner maintained by Alex Coulton.