Multiple sequence alignment - TraesCS6A01G210200

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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 TraesCS6A01G210200 chr6A 100.000 4696 0 0 1 4696 381084041 381079346 0.000000e+00 8672.0
1 TraesCS6A01G210200 chr6A 97.436 195 5 0 3843 4037 381035779 381035585 2.710000e-87 333.0
2 TraesCS6A01G210200 chr6A 88.000 50 6 0 4190 4239 313958978 313959027 5.070000e-05 60.2
3 TraesCS6A01G210200 chr6D 94.532 3438 105 30 600 3999 267527792 267524400 0.000000e+00 5230.0
4 TraesCS6A01G210200 chr6D 90.588 510 24 7 11 520 267528276 267527791 0.000000e+00 654.0
5 TraesCS6A01G210200 chr6D 100.000 31 0 0 536 566 117639585 117639615 1.830000e-04 58.4
6 TraesCS6A01G210200 chr6D 100.000 30 0 0 4008 4037 267520785 267520756 6.560000e-04 56.5
7 TraesCS6A01G210200 chr6B 89.733 3000 188 51 603 3552 415873408 415870479 0.000000e+00 3723.0
8 TraesCS6A01G210200 chr6B 92.885 520 33 3 3 522 415873923 415873408 0.000000e+00 752.0
9 TraesCS6A01G210200 chr6B 87.307 323 26 9 3548 3870 415870447 415870140 5.780000e-94 355.0
10 TraesCS6A01G210200 chr6B 79.310 377 60 12 907 1280 281337340 281337701 1.010000e-61 248.0
11 TraesCS6A01G210200 chr6B 93.197 147 7 2 3856 3999 415870120 415869974 3.680000e-51 213.0
12 TraesCS6A01G210200 chr6B 77.358 265 54 5 4359 4620 114320262 114320523 8.140000e-33 152.0
13 TraesCS6A01G210200 chr7A 89.555 584 51 7 3421 3997 7136824 7136244 0.000000e+00 732.0
14 TraesCS6A01G210200 chr7A 78.843 605 104 19 4097 4690 342845607 342846198 2.050000e-103 387.0
15 TraesCS6A01G210200 chr7D 79.775 623 100 20 4085 4696 318825458 318826065 3.360000e-116 429.0
16 TraesCS6A01G210200 chr1B 81.644 365 49 14 17 375 48279611 48279963 2.140000e-73 287.0
17 TraesCS6A01G210200 chr5B 76.234 547 111 14 4106 4646 547157793 547157260 5.990000e-69 272.0
18 TraesCS6A01G210200 chr5B 79.330 179 26 10 4358 4530 16077089 16077262 1.070000e-21 115.0
19 TraesCS6A01G210200 chr5A 81.935 155 16 8 4188 4338 173449094 173449240 2.300000e-23 121.0
20 TraesCS6A01G210200 chr7B 84.848 66 5 4 4200 4264 348902783 348902844 1.410000e-05 62.1
21 TraesCS6A01G210200 chrUn 92.500 40 3 0 4190 4229 326663941 326663902 1.830000e-04 58.4
22 TraesCS6A01G210200 chrUn 92.500 40 3 0 4190 4229 326673067 326673028 1.830000e-04 58.4
23 TraesCS6A01G210200 chr4A 92.500 40 3 0 4200 4239 2565329 2565290 1.830000e-04 58.4
24 TraesCS6A01G210200 chr4A 90.698 43 4 0 4197 4239 624362978 624363020 1.830000e-04 58.4


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 TraesCS6A01G210200 chr6A 381079346 381084041 4695 True 8672.000000 8672 100.0000 1 4696 1 chr6A.!!$R2 4695
1 TraesCS6A01G210200 chr6D 267520756 267528276 7520 True 1980.166667 5230 95.0400 11 4037 3 chr6D.!!$R1 4026
2 TraesCS6A01G210200 chr6B 415869974 415873923 3949 True 1260.750000 3723 90.7805 3 3999 4 chr6B.!!$R1 3996
3 TraesCS6A01G210200 chr7A 7136244 7136824 580 True 732.000000 732 89.5550 3421 3997 1 chr7A.!!$R1 576
4 TraesCS6A01G210200 chr7A 342845607 342846198 591 False 387.000000 387 78.8430 4097 4690 1 chr7A.!!$F1 593
5 TraesCS6A01G210200 chr7D 318825458 318826065 607 False 429.000000 429 79.7750 4085 4696 1 chr7D.!!$F1 611
6 TraesCS6A01G210200 chr5B 547157260 547157793 533 True 272.000000 272 76.2340 4106 4646 1 chr5B.!!$R1 540

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
988 1008 0.037447 AAAACCTCCTGCCTGAGAGC 59.963 55.0 1.37 0.0 34.11 4.09 F
2515 2577 0.106268 TTTCACCTTGCTGGCCTTCA 60.106 50.0 3.32 0.0 40.22 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2624 2686 0.179094 TAAGAAGTGGTATGCGCCGG 60.179 55.0 4.18 0.0 0.0 6.13 R
4064 7845 0.247460 CTGTCTTGACGATCCTGGCA 59.753 55.0 0.00 0.0 0.0 4.92 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
54 55 4.478206 TCATGCTTTCCTCAAGGTAGAG 57.522 45.455 0.00 0.00 36.34 2.43
78 79 1.915614 GCATCAGGACTTGTGTGCCG 61.916 60.000 6.48 0.00 35.19 5.69
126 127 5.013183 AGACTTGTAGCTAACCAGGATTGTT 59.987 40.000 0.00 0.00 0.00 2.83
129 130 5.499004 TGTAGCTAACCAGGATTGTTCTT 57.501 39.130 0.00 0.00 0.00 2.52
130 131 5.488341 TGTAGCTAACCAGGATTGTTCTTC 58.512 41.667 0.00 0.00 0.00 2.87
139 140 6.004574 ACCAGGATTGTTCTTCTTTTAGGTC 58.995 40.000 0.00 0.00 0.00 3.85
357 358 6.964908 TGCTATCGAAAATGTTCTTGTGAAA 58.035 32.000 0.00 0.00 33.52 2.69
381 382 1.417288 ACATCAGATCGGCATGGAGA 58.583 50.000 0.00 0.00 0.00 3.71
382 383 1.343789 ACATCAGATCGGCATGGAGAG 59.656 52.381 0.00 0.00 0.00 3.20
383 384 0.321021 ATCAGATCGGCATGGAGAGC 59.679 55.000 0.00 0.00 0.00 4.09
384 385 0.758310 TCAGATCGGCATGGAGAGCT 60.758 55.000 0.00 0.00 32.86 4.09
386 387 1.549620 CAGATCGGCATGGAGAGCTAT 59.450 52.381 0.00 0.00 31.31 2.97
387 388 1.824230 AGATCGGCATGGAGAGCTATC 59.176 52.381 0.00 0.00 30.65 2.08
388 389 1.547820 GATCGGCATGGAGAGCTATCA 59.452 52.381 11.08 0.00 0.00 2.15
389 390 0.964700 TCGGCATGGAGAGCTATCAG 59.035 55.000 11.08 0.51 0.00 2.90
435 436 3.063997 CAGTTGGTGCATCTATTTCGTCC 59.936 47.826 0.00 0.00 0.00 4.79
449 450 0.747283 TCGTCCGAGGGAGTAAGCTC 60.747 60.000 0.00 0.00 40.93 4.09
481 482 8.957466 GTGTAACTTATGGAGAAGCCTAAAATT 58.043 33.333 0.00 0.00 37.63 1.82
506 507 8.055279 TGTCTTGAAGATTATTTTGGATGGAC 57.945 34.615 0.00 0.00 0.00 4.02
510 511 7.645058 TGAAGATTATTTTGGATGGACTTCC 57.355 36.000 0.00 0.00 36.24 3.46
522 523 3.695830 TGGACTTCCACCATGTTACTC 57.304 47.619 0.00 0.00 42.01 2.59
523 524 2.304761 TGGACTTCCACCATGTTACTCC 59.695 50.000 0.00 0.00 42.01 3.85
524 525 2.355818 GGACTTCCACCATGTTACTCCC 60.356 54.545 0.00 0.00 35.64 4.30
525 526 2.572104 GACTTCCACCATGTTACTCCCT 59.428 50.000 0.00 0.00 0.00 4.20
526 527 2.572104 ACTTCCACCATGTTACTCCCTC 59.428 50.000 0.00 0.00 0.00 4.30
527 528 1.580059 TCCACCATGTTACTCCCTCC 58.420 55.000 0.00 0.00 0.00 4.30
528 529 0.178068 CCACCATGTTACTCCCTCCG 59.822 60.000 0.00 0.00 0.00 4.63
529 530 1.191535 CACCATGTTACTCCCTCCGA 58.808 55.000 0.00 0.00 0.00 4.55
530 531 1.762957 CACCATGTTACTCCCTCCGAT 59.237 52.381 0.00 0.00 0.00 4.18
531 532 2.040178 ACCATGTTACTCCCTCCGATC 58.960 52.381 0.00 0.00 0.00 3.69
532 533 1.344763 CCATGTTACTCCCTCCGATCC 59.655 57.143 0.00 0.00 0.00 3.36
533 534 2.039418 CATGTTACTCCCTCCGATCCA 58.961 52.381 0.00 0.00 0.00 3.41
534 535 2.241281 TGTTACTCCCTCCGATCCAA 57.759 50.000 0.00 0.00 0.00 3.53
535 536 2.542550 TGTTACTCCCTCCGATCCAAA 58.457 47.619 0.00 0.00 0.00 3.28
536 537 3.112263 TGTTACTCCCTCCGATCCAAAT 58.888 45.455 0.00 0.00 0.00 2.32
537 538 3.521937 TGTTACTCCCTCCGATCCAAATT 59.478 43.478 0.00 0.00 0.00 1.82
538 539 4.717778 TGTTACTCCCTCCGATCCAAATTA 59.282 41.667 0.00 0.00 0.00 1.40
539 540 3.840124 ACTCCCTCCGATCCAAATTAC 57.160 47.619 0.00 0.00 0.00 1.89
540 541 3.385115 ACTCCCTCCGATCCAAATTACT 58.615 45.455 0.00 0.00 0.00 2.24
541 542 3.780850 ACTCCCTCCGATCCAAATTACTT 59.219 43.478 0.00 0.00 0.00 2.24
542 543 4.227527 ACTCCCTCCGATCCAAATTACTTT 59.772 41.667 0.00 0.00 0.00 2.66
543 544 5.187621 TCCCTCCGATCCAAATTACTTTT 57.812 39.130 0.00 0.00 0.00 2.27
544 545 5.190677 TCCCTCCGATCCAAATTACTTTTC 58.809 41.667 0.00 0.00 0.00 2.29
545 546 4.035208 CCCTCCGATCCAAATTACTTTTCG 59.965 45.833 0.00 0.00 0.00 3.46
546 547 4.495844 CCTCCGATCCAAATTACTTTTCGC 60.496 45.833 0.00 0.00 0.00 4.70
547 548 4.258543 TCCGATCCAAATTACTTTTCGCT 58.741 39.130 0.00 0.00 0.00 4.93
548 549 4.331717 TCCGATCCAAATTACTTTTCGCTC 59.668 41.667 0.00 0.00 0.00 5.03
549 550 4.263800 CGATCCAAATTACTTTTCGCTCG 58.736 43.478 0.00 0.00 0.00 5.03
550 551 4.032445 CGATCCAAATTACTTTTCGCTCGA 59.968 41.667 0.00 0.00 0.00 4.04
551 552 5.445407 CGATCCAAATTACTTTTCGCTCGAA 60.445 40.000 0.02 0.02 0.00 3.71
552 553 5.873179 TCCAAATTACTTTTCGCTCGAAT 57.127 34.783 5.50 0.00 33.79 3.34
553 554 5.627172 TCCAAATTACTTTTCGCTCGAATG 58.373 37.500 5.50 5.06 33.79 2.67
554 555 4.793216 CCAAATTACTTTTCGCTCGAATGG 59.207 41.667 5.50 4.41 33.79 3.16
555 556 5.391523 CCAAATTACTTTTCGCTCGAATGGA 60.392 40.000 5.50 0.00 33.79 3.41
556 557 6.258160 CAAATTACTTTTCGCTCGAATGGAT 58.742 36.000 5.50 0.00 33.79 3.41
557 558 4.857871 TTACTTTTCGCTCGAATGGATG 57.142 40.909 5.50 0.00 33.79 3.51
558 559 2.699954 ACTTTTCGCTCGAATGGATGT 58.300 42.857 5.50 0.00 33.79 3.06
559 560 3.857052 ACTTTTCGCTCGAATGGATGTA 58.143 40.909 5.50 0.00 33.79 2.29
560 561 4.442706 ACTTTTCGCTCGAATGGATGTAT 58.557 39.130 5.50 0.00 33.79 2.29
561 562 4.508124 ACTTTTCGCTCGAATGGATGTATC 59.492 41.667 5.50 0.00 33.79 2.24
562 563 4.322080 TTTCGCTCGAATGGATGTATCT 57.678 40.909 5.50 0.00 33.79 1.98
563 564 5.447624 TTTCGCTCGAATGGATGTATCTA 57.552 39.130 5.50 0.00 33.79 1.98
564 565 4.686839 TCGCTCGAATGGATGTATCTAG 57.313 45.455 0.00 0.00 0.00 2.43
565 566 3.119814 TCGCTCGAATGGATGTATCTAGC 60.120 47.826 0.00 0.00 0.00 3.42
566 567 3.516615 GCTCGAATGGATGTATCTAGCC 58.483 50.000 0.00 0.00 0.00 3.93
567 568 3.194542 GCTCGAATGGATGTATCTAGCCT 59.805 47.826 0.00 0.00 0.00 4.58
568 569 4.742417 CTCGAATGGATGTATCTAGCCTG 58.258 47.826 0.00 0.00 0.00 4.85
569 570 4.407365 TCGAATGGATGTATCTAGCCTGA 58.593 43.478 0.00 0.00 0.00 3.86
570 571 4.832823 TCGAATGGATGTATCTAGCCTGAA 59.167 41.667 0.00 0.00 0.00 3.02
571 572 5.304357 TCGAATGGATGTATCTAGCCTGAAA 59.696 40.000 0.00 0.00 0.00 2.69
572 573 6.014242 TCGAATGGATGTATCTAGCCTGAAAT 60.014 38.462 0.00 0.00 0.00 2.17
573 574 7.178451 TCGAATGGATGTATCTAGCCTGAAATA 59.822 37.037 0.00 0.00 0.00 1.40
574 575 7.984050 CGAATGGATGTATCTAGCCTGAAATAT 59.016 37.037 0.00 0.00 0.00 1.28
575 576 9.107177 GAATGGATGTATCTAGCCTGAAATATG 57.893 37.037 0.00 0.00 0.00 1.78
576 577 7.559335 TGGATGTATCTAGCCTGAAATATGT 57.441 36.000 0.00 0.00 0.00 2.29
577 578 7.615403 TGGATGTATCTAGCCTGAAATATGTC 58.385 38.462 0.00 0.00 0.00 3.06
578 579 7.455953 TGGATGTATCTAGCCTGAAATATGTCT 59.544 37.037 0.00 0.00 0.00 3.41
579 580 8.972127 GGATGTATCTAGCCTGAAATATGTCTA 58.028 37.037 0.00 0.00 0.00 2.59
582 583 9.588096 TGTATCTAGCCTGAAATATGTCTAAGA 57.412 33.333 0.00 0.00 0.00 2.10
587 588 9.814899 CTAGCCTGAAATATGTCTAAGATATGG 57.185 37.037 0.00 0.00 0.00 2.74
588 589 8.441311 AGCCTGAAATATGTCTAAGATATGGA 57.559 34.615 0.00 0.00 0.00 3.41
589 590 9.055689 AGCCTGAAATATGTCTAAGATATGGAT 57.944 33.333 0.00 0.00 0.00 3.41
590 591 9.323985 GCCTGAAATATGTCTAAGATATGGATC 57.676 37.037 0.00 0.00 0.00 3.36
591 592 9.526713 CCTGAAATATGTCTAAGATATGGATCG 57.473 37.037 0.00 0.00 37.15 3.69
592 593 9.526713 CTGAAATATGTCTAAGATATGGATCGG 57.473 37.037 0.00 0.00 37.15 4.18
593 594 8.478066 TGAAATATGTCTAAGATATGGATCGGG 58.522 37.037 0.00 0.00 37.15 5.14
594 595 6.985653 ATATGTCTAAGATATGGATCGGGG 57.014 41.667 0.00 0.00 37.15 5.73
595 596 3.441101 TGTCTAAGATATGGATCGGGGG 58.559 50.000 0.00 0.00 37.15 5.40
645 646 1.017387 GGTGGAGGTCATGCGATTTC 58.983 55.000 0.00 0.00 0.00 2.17
650 651 2.096496 GGAGGTCATGCGATTTCTTGTG 59.904 50.000 0.00 0.00 0.00 3.33
651 652 3.002791 GAGGTCATGCGATTTCTTGTGA 58.997 45.455 0.00 0.00 0.00 3.58
652 653 3.614092 AGGTCATGCGATTTCTTGTGAT 58.386 40.909 0.00 0.00 0.00 3.06
653 654 3.376234 AGGTCATGCGATTTCTTGTGATG 59.624 43.478 0.00 0.00 0.00 3.07
654 655 3.127548 GGTCATGCGATTTCTTGTGATGT 59.872 43.478 0.00 0.00 0.00 3.06
655 656 4.332543 GGTCATGCGATTTCTTGTGATGTA 59.667 41.667 0.00 0.00 0.00 2.29
657 658 6.202762 GGTCATGCGATTTCTTGTGATGTATA 59.797 38.462 0.00 0.00 0.00 1.47
658 659 7.065894 GTCATGCGATTTCTTGTGATGTATAC 58.934 38.462 0.00 0.00 0.00 1.47
659 660 6.986231 TCATGCGATTTCTTGTGATGTATACT 59.014 34.615 4.17 0.00 0.00 2.12
660 661 8.141268 TCATGCGATTTCTTGTGATGTATACTA 58.859 33.333 4.17 0.00 0.00 1.82
661 662 8.929746 CATGCGATTTCTTGTGATGTATACTAT 58.070 33.333 4.17 0.00 0.00 2.12
662 663 8.298030 TGCGATTTCTTGTGATGTATACTATG 57.702 34.615 4.17 0.00 0.00 2.23
663 664 7.384932 TGCGATTTCTTGTGATGTATACTATGG 59.615 37.037 4.17 0.00 0.00 2.74
664 665 7.148573 GCGATTTCTTGTGATGTATACTATGGG 60.149 40.741 4.17 0.00 0.00 4.00
665 666 8.088365 CGATTTCTTGTGATGTATACTATGGGA 58.912 37.037 4.17 0.00 0.00 4.37
676 687 7.381789 TGTATACTATGGGATGCAAACCTTA 57.618 36.000 10.88 8.11 0.00 2.69
701 712 4.786575 GTCAGTTTGAAGTCAACGTTGTTC 59.213 41.667 26.47 22.47 35.28 3.18
707 718 6.912203 TTGAAGTCAACGTTGTTCTGAATA 57.088 33.333 26.47 3.00 0.00 1.75
708 719 7.490962 TTGAAGTCAACGTTGTTCTGAATAT 57.509 32.000 26.47 11.34 0.00 1.28
742 753 8.803201 TGCGTTGATCAAATTATTGTTTGTAA 57.197 26.923 10.35 0.00 39.50 2.41
804 816 7.497595 TCTGCTTATGAATTATTGGTAGTCGT 58.502 34.615 0.00 0.00 0.00 4.34
865 881 1.065636 TGCATCTCTTTCAGGCCTCAG 60.066 52.381 0.00 0.00 0.00 3.35
885 901 1.186200 CATCAGTCCAGTTCTCCGGA 58.814 55.000 2.93 2.93 0.00 5.14
937 953 1.959042 CCAATTGCAGAGCCGAGTAT 58.041 50.000 0.00 0.00 0.00 2.12
980 1000 3.119459 GCTAAAAGCCTAAAACCTCCTGC 60.119 47.826 0.00 0.00 34.48 4.85
988 1008 0.037447 AAAACCTCCTGCCTGAGAGC 59.963 55.000 1.37 0.00 34.11 4.09
991 1011 1.221293 CCTCCTGCCTGAGAGCAAG 59.779 63.158 1.37 0.00 43.52 4.01
992 1012 1.449956 CTCCTGCCTGAGAGCAAGC 60.450 63.158 0.00 0.00 43.52 4.01
1078 1098 3.854669 CGGCGCATTCCTCCTCCT 61.855 66.667 10.83 0.00 0.00 3.69
1081 1101 1.522580 GCGCATTCCTCCTCCTGTC 60.523 63.158 0.30 0.00 0.00 3.51
1183 1203 3.964875 GCTGCCGGTGGTTGTGTG 61.965 66.667 1.90 0.00 0.00 3.82
1371 1423 0.883833 CGTCTACAGTACCACCGGTT 59.116 55.000 2.97 0.00 37.09 4.44
1393 1445 2.291741 GTGCAAACCTCCTCTGAAGTTG 59.708 50.000 0.00 0.00 0.00 3.16
1458 1510 2.127271 TGAATTCGGCATCCATGTGT 57.873 45.000 0.04 0.00 0.00 3.72
1459 1511 1.744522 TGAATTCGGCATCCATGTGTG 59.255 47.619 0.04 0.00 0.00 3.82
1460 1512 1.745087 GAATTCGGCATCCATGTGTGT 59.255 47.619 0.00 0.00 0.00 3.72
1461 1513 2.708216 ATTCGGCATCCATGTGTGTA 57.292 45.000 0.00 0.00 0.00 2.90
1547 1599 3.387374 TGAAGATCAGGGAGCAGAAGATC 59.613 47.826 0.00 0.00 36.29 2.75
1655 1707 4.362470 AAAGGTTGGTGGTAGGACTAAC 57.638 45.455 0.00 0.00 36.77 2.34
1682 1740 6.370718 ACCATTTCTAGTGTTGGTTAATCGTC 59.629 38.462 7.22 0.00 39.41 4.20
1864 1922 2.560981 TCGTTGGATCTGACTGTTGCTA 59.439 45.455 0.00 0.00 0.00 3.49
1941 1999 4.696479 AGTTGCCATAGAAGGACCATAG 57.304 45.455 0.00 0.00 0.00 2.23
1960 2018 5.608449 CATAGCATGGAGTGATTCTTCAGA 58.392 41.667 0.00 0.00 34.81 3.27
2020 2078 5.347635 GTGCATCAAACACAGTTACGAGATA 59.652 40.000 0.00 0.00 37.96 1.98
2087 2147 8.328146 CAACTCATACAATACCATCGTTTGTAG 58.672 37.037 0.00 0.00 38.72 2.74
2095 2155 7.491372 ACAATACCATCGTTTGTAGTATGTCAG 59.509 37.037 0.00 0.00 32.09 3.51
2216 2276 8.192774 ACAATGTCATTCAATAAGTATGCTTGG 58.807 33.333 6.28 0.00 36.22 3.61
2335 2395 4.629200 CCGAGGAGAAGTTCTCAAAAGATG 59.371 45.833 29.36 13.79 45.12 2.90
2490 2552 3.381045 ACACACTGACAACACATACTCG 58.619 45.455 0.00 0.00 0.00 4.18
2514 2576 1.000171 CTTTTCACCTTGCTGGCCTTC 60.000 52.381 3.32 0.00 40.22 3.46
2515 2577 0.106268 TTTCACCTTGCTGGCCTTCA 60.106 50.000 3.32 0.00 40.22 3.02
2624 2686 1.891150 TCTCTACCGTTTCCTGGACAC 59.109 52.381 2.83 2.83 0.00 3.67
2786 2870 7.065803 TGCACTCTAGTAATTTAAGGTTGCATC 59.934 37.037 0.00 0.00 0.00 3.91
2946 3031 3.552684 GCAACTTTACAATGCTGGCTTCA 60.553 43.478 0.00 0.00 37.12 3.02
2950 3035 5.857268 ACTTTACAATGCTGGCTTCAAAAT 58.143 33.333 0.00 0.00 0.00 1.82
3012 3097 3.396611 GGAGGTAGGAGTAGGAGTCATCT 59.603 52.174 0.00 0.00 0.00 2.90
3258 3354 3.628032 TCCTGTGAGATACAAGCTACGAG 59.372 47.826 0.00 0.00 39.20 4.18
3278 3374 1.534729 CTTGCCACCAACCTAAGACC 58.465 55.000 0.00 0.00 0.00 3.85
3802 3940 1.037493 ACTGCACGAGGACACAGTTA 58.963 50.000 0.00 0.00 40.35 2.24
3815 3954 1.066143 CACAGTTAGGCCGTTCCTCAT 60.066 52.381 0.00 0.00 43.20 2.90
3829 3968 4.645535 GTTCCTCATGCCTGCTATGATAA 58.354 43.478 0.00 2.39 34.33 1.75
3835 3974 2.549926 TGCCTGCTATGATAACACACG 58.450 47.619 0.00 0.00 0.00 4.49
3897 4072 2.957491 AGAGCCTCATTTCTGACTCG 57.043 50.000 0.00 0.00 32.46 4.18
3969 4144 7.596621 GGAATTCTCCTGTTGAAAATTCTGTTC 59.403 37.037 5.23 0.00 38.88 3.18
4037 7818 8.806429 TGTGTGGATATAAATCTCATTGTGTT 57.194 30.769 0.00 0.00 32.29 3.32
4038 7819 9.898152 TGTGTGGATATAAATCTCATTGTGTTA 57.102 29.630 0.00 0.00 32.29 2.41
4045 7826 7.865706 ATAAATCTCATTGTGTTAGTGACCC 57.134 36.000 0.00 0.00 0.00 4.46
4046 7827 5.505181 AATCTCATTGTGTTAGTGACCCT 57.495 39.130 0.00 0.00 0.00 4.34
4047 7828 4.271696 TCTCATTGTGTTAGTGACCCTG 57.728 45.455 0.00 0.00 0.00 4.45
4048 7829 2.744202 CTCATTGTGTTAGTGACCCTGC 59.256 50.000 0.00 0.00 0.00 4.85
4049 7830 1.812571 CATTGTGTTAGTGACCCTGCC 59.187 52.381 0.00 0.00 0.00 4.85
4050 7831 0.109723 TTGTGTTAGTGACCCTGCCC 59.890 55.000 0.00 0.00 0.00 5.36
4051 7832 1.057275 TGTGTTAGTGACCCTGCCCA 61.057 55.000 0.00 0.00 0.00 5.36
4052 7833 0.109723 GTGTTAGTGACCCTGCCCAA 59.890 55.000 0.00 0.00 0.00 4.12
4053 7834 0.400213 TGTTAGTGACCCTGCCCAAG 59.600 55.000 0.00 0.00 0.00 3.61
4054 7835 0.690762 GTTAGTGACCCTGCCCAAGA 59.309 55.000 0.00 0.00 0.00 3.02
4055 7836 1.073284 GTTAGTGACCCTGCCCAAGAA 59.927 52.381 0.00 0.00 0.00 2.52
4056 7837 0.984230 TAGTGACCCTGCCCAAGAAG 59.016 55.000 0.00 0.00 0.00 2.85
4057 7838 1.303643 GTGACCCTGCCCAAGAAGG 60.304 63.158 0.00 0.00 37.03 3.46
4065 7846 4.023137 CCCAAGAAGGCCCACATG 57.977 61.111 0.00 0.00 35.39 3.21
4066 7847 2.353610 CCCAAGAAGGCCCACATGC 61.354 63.158 0.00 0.00 35.39 4.06
4074 7855 2.903855 GCCCACATGCCAGGATCG 60.904 66.667 0.00 0.00 0.00 3.69
4075 7856 2.591753 CCCACATGCCAGGATCGT 59.408 61.111 0.00 0.00 0.00 3.73
4076 7857 1.524621 CCCACATGCCAGGATCGTC 60.525 63.158 0.00 0.00 0.00 4.20
4077 7858 1.221566 CCACATGCCAGGATCGTCA 59.778 57.895 0.00 0.00 0.00 4.35
4078 7859 0.392863 CCACATGCCAGGATCGTCAA 60.393 55.000 0.00 0.00 0.00 3.18
4079 7860 1.012086 CACATGCCAGGATCGTCAAG 58.988 55.000 0.00 0.00 0.00 3.02
4080 7861 0.904649 ACATGCCAGGATCGTCAAGA 59.095 50.000 0.00 0.00 0.00 3.02
4081 7862 1.293924 CATGCCAGGATCGTCAAGAC 58.706 55.000 0.00 0.00 0.00 3.01
4082 7863 0.904649 ATGCCAGGATCGTCAAGACA 59.095 50.000 0.00 0.00 0.00 3.41
4083 7864 0.247460 TGCCAGGATCGTCAAGACAG 59.753 55.000 0.00 0.00 0.00 3.51
4084 7865 1.086634 GCCAGGATCGTCAAGACAGC 61.087 60.000 0.00 0.00 0.00 4.40
4085 7866 0.460987 CCAGGATCGTCAAGACAGCC 60.461 60.000 0.72 0.69 0.00 4.85
4086 7867 0.247460 CAGGATCGTCAAGACAGCCA 59.753 55.000 0.72 0.00 0.00 4.75
4087 7868 0.534412 AGGATCGTCAAGACAGCCAG 59.466 55.000 0.72 0.00 0.00 4.85
4088 7869 1.086634 GGATCGTCAAGACAGCCAGC 61.087 60.000 0.72 0.00 0.00 4.85
4089 7870 1.416813 GATCGTCAAGACAGCCAGCG 61.417 60.000 0.72 0.00 0.00 5.18
4090 7871 3.782244 CGTCAAGACAGCCAGCGC 61.782 66.667 0.00 0.00 0.00 5.92
4146 7927 1.595093 GAATGGGTGAACAAGGCCGG 61.595 60.000 0.00 0.00 0.00 6.13
4166 7947 2.490217 CGACCCGGAGCACTACTG 59.510 66.667 0.73 0.00 0.00 2.74
4179 7960 1.153549 CTACTGAAGCCAGCGACCC 60.154 63.158 0.00 0.00 44.16 4.46
4180 7961 2.579684 CTACTGAAGCCAGCGACCCC 62.580 65.000 0.00 0.00 44.16 4.95
4238 8022 3.771160 CGGCGGCTACCAACTCCT 61.771 66.667 7.61 0.00 0.00 3.69
4239 8023 2.125106 GGCGGCTACCAACTCCTG 60.125 66.667 0.00 0.00 0.00 3.86
4240 8024 2.656069 GGCGGCTACCAACTCCTGA 61.656 63.158 0.00 0.00 0.00 3.86
4241 8025 1.522569 GCGGCTACCAACTCCTGAT 59.477 57.895 0.00 0.00 0.00 2.90
4267 8055 1.486211 CCCTTTCTTCCTCCTCGCTA 58.514 55.000 0.00 0.00 0.00 4.26
4285 8078 3.887916 CTAGAACCCTAGCTACCTCCT 57.112 52.381 0.00 0.00 36.32 3.69
4286 8079 2.463047 AGAACCCTAGCTACCTCCTG 57.537 55.000 0.00 0.00 0.00 3.86
4289 8082 2.162264 ACCCTAGCTACCTCCTGAAC 57.838 55.000 0.00 0.00 0.00 3.18
4293 8086 2.428890 CCTAGCTACCTCCTGAACTGTG 59.571 54.545 0.00 0.00 0.00 3.66
4306 8099 5.482526 TCCTGAACTGTGTAATTGCTACCTA 59.517 40.000 0.00 0.00 0.00 3.08
4311 8104 9.073475 TGAACTGTGTAATTGCTACCTAAATTT 57.927 29.630 0.00 0.00 0.00 1.82
4340 8133 4.299586 TGAGTGAGATTGCCACCAAATA 57.700 40.909 0.00 0.00 35.23 1.40
4341 8134 4.009675 TGAGTGAGATTGCCACCAAATAC 58.990 43.478 0.00 0.00 35.23 1.89
4350 8143 3.343617 TGCCACCAAATACTTGAGCTAC 58.656 45.455 0.00 0.00 34.14 3.58
4393 8186 4.248842 CAGTCGCCACCACCACCA 62.249 66.667 0.00 0.00 0.00 4.17
4398 8191 2.440599 GCCACCACCACCATTCCT 59.559 61.111 0.00 0.00 0.00 3.36
4399 8192 1.688811 GCCACCACCACCATTCCTA 59.311 57.895 0.00 0.00 0.00 2.94
4405 8198 0.179084 CACCACCATTCCTATCGCGT 60.179 55.000 5.77 0.00 0.00 6.01
4407 8200 0.880278 CCACCATTCCTATCGCGTGG 60.880 60.000 5.77 7.11 35.24 4.94
4429 8222 2.508891 GGCGCAGTTCATCGAGACG 61.509 63.158 10.83 0.00 0.00 4.18
4457 8250 3.244105 GTCACGCACGACTGCAAT 58.756 55.556 0.00 0.00 44.50 3.56
4483 8276 1.451207 CATGGATCCCGCGGTCAAA 60.451 57.895 26.12 8.56 0.00 2.69
4501 8294 3.139077 CAAAACCTACCTCGACAAGCTT 58.861 45.455 0.00 0.00 0.00 3.74
4525 8318 1.039233 CCATGATGGAGGCCAACACC 61.039 60.000 5.27 3.18 39.04 4.16
4526 8319 1.077501 ATGATGGAGGCCAACACCG 60.078 57.895 5.01 0.00 39.04 4.94
4597 8390 2.951745 GATCTGGAGCGACGCGTG 60.952 66.667 20.70 10.73 0.00 5.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.311110 GCAGGGATCGCCGGGATA 61.311 66.667 2.18 0.00 34.82 2.59
15 16 0.670162 GAAGAGCAAAAGCAGTGGCA 59.330 50.000 0.00 0.00 44.61 4.92
54 55 1.293924 CACAAGTCCTGATGCGGATC 58.706 55.000 10.37 10.37 35.11 3.36
78 79 4.800993 GCATACACAGATAGTCAGACACAC 59.199 45.833 2.66 0.00 0.00 3.82
126 127 3.764237 AACCAGCGACCTAAAAGAAGA 57.236 42.857 0.00 0.00 0.00 2.87
129 130 2.292292 GCAAAACCAGCGACCTAAAAGA 59.708 45.455 0.00 0.00 0.00 2.52
130 131 2.661594 GCAAAACCAGCGACCTAAAAG 58.338 47.619 0.00 0.00 0.00 2.27
357 358 4.717877 TCCATGCCGATCTGATGTTAATT 58.282 39.130 0.00 0.00 0.00 1.40
367 368 1.824230 GATAGCTCTCCATGCCGATCT 59.176 52.381 0.00 0.00 0.00 2.75
406 407 1.073763 AGATGCACCAACTGGCAACTA 59.926 47.619 0.00 0.00 44.20 2.24
411 412 2.223340 CGAAATAGATGCACCAACTGGC 60.223 50.000 0.00 0.00 39.32 4.85
449 450 2.498481 TCTCCATAAGTTACACCCACGG 59.502 50.000 0.00 0.00 0.00 4.94
481 482 7.890127 AGTCCATCCAAAATAATCTTCAAGACA 59.110 33.333 0.00 0.00 0.00 3.41
506 507 2.092914 GGAGGGAGTAACATGGTGGAAG 60.093 54.545 0.00 0.00 0.00 3.46
510 511 1.191535 TCGGAGGGAGTAACATGGTG 58.808 55.000 0.00 0.00 0.00 4.17
511 512 2.040178 GATCGGAGGGAGTAACATGGT 58.960 52.381 0.00 0.00 0.00 3.55
513 514 2.039418 TGGATCGGAGGGAGTAACATG 58.961 52.381 0.00 0.00 0.00 3.21
514 515 2.471815 TGGATCGGAGGGAGTAACAT 57.528 50.000 0.00 0.00 0.00 2.71
515 516 2.241281 TTGGATCGGAGGGAGTAACA 57.759 50.000 0.00 0.00 0.00 2.41
516 517 3.840124 ATTTGGATCGGAGGGAGTAAC 57.160 47.619 0.00 0.00 0.00 2.50
517 518 4.966805 AGTAATTTGGATCGGAGGGAGTAA 59.033 41.667 0.00 0.00 0.00 2.24
518 519 4.553678 AGTAATTTGGATCGGAGGGAGTA 58.446 43.478 0.00 0.00 0.00 2.59
519 520 3.385115 AGTAATTTGGATCGGAGGGAGT 58.615 45.455 0.00 0.00 0.00 3.85
520 521 4.423625 AAGTAATTTGGATCGGAGGGAG 57.576 45.455 0.00 0.00 0.00 4.30
521 522 4.855298 AAAGTAATTTGGATCGGAGGGA 57.145 40.909 0.00 0.00 0.00 4.20
522 523 4.035208 CGAAAAGTAATTTGGATCGGAGGG 59.965 45.833 1.38 0.00 0.00 4.30
523 524 4.495844 GCGAAAAGTAATTTGGATCGGAGG 60.496 45.833 9.45 0.00 0.00 4.30
524 525 4.332819 AGCGAAAAGTAATTTGGATCGGAG 59.667 41.667 9.45 0.00 0.00 4.63
525 526 4.258543 AGCGAAAAGTAATTTGGATCGGA 58.741 39.130 9.45 0.00 0.00 4.55
526 527 4.588278 GAGCGAAAAGTAATTTGGATCGG 58.412 43.478 9.45 0.00 33.52 4.18
528 529 5.464965 TCGAGCGAAAAGTAATTTGGATC 57.535 39.130 0.00 0.00 38.36 3.36
529 530 5.873179 TTCGAGCGAAAAGTAATTTGGAT 57.127 34.783 2.42 0.00 0.00 3.41
530 531 5.391523 CCATTCGAGCGAAAAGTAATTTGGA 60.392 40.000 9.52 0.00 37.69 3.53
531 532 4.793216 CCATTCGAGCGAAAAGTAATTTGG 59.207 41.667 9.52 6.36 37.69 3.28
532 533 5.627172 TCCATTCGAGCGAAAAGTAATTTG 58.373 37.500 9.52 1.09 37.69 2.32
533 534 5.873179 TCCATTCGAGCGAAAAGTAATTT 57.127 34.783 9.52 0.00 37.69 1.82
534 535 5.354234 ACATCCATTCGAGCGAAAAGTAATT 59.646 36.000 9.52 0.00 37.69 1.40
535 536 4.876107 ACATCCATTCGAGCGAAAAGTAAT 59.124 37.500 9.52 0.00 37.69 1.89
536 537 4.250464 ACATCCATTCGAGCGAAAAGTAA 58.750 39.130 9.52 0.00 37.69 2.24
537 538 3.857052 ACATCCATTCGAGCGAAAAGTA 58.143 40.909 9.52 0.00 37.69 2.24
538 539 2.699954 ACATCCATTCGAGCGAAAAGT 58.300 42.857 9.52 2.01 37.69 2.66
539 540 4.747108 AGATACATCCATTCGAGCGAAAAG 59.253 41.667 9.52 5.58 37.69 2.27
540 541 4.693283 AGATACATCCATTCGAGCGAAAA 58.307 39.130 9.52 0.00 37.69 2.29
541 542 4.322080 AGATACATCCATTCGAGCGAAA 57.678 40.909 9.52 0.00 37.69 3.46
542 543 4.616143 GCTAGATACATCCATTCGAGCGAA 60.616 45.833 7.84 7.84 38.59 4.70
543 544 3.119814 GCTAGATACATCCATTCGAGCGA 60.120 47.826 0.00 0.00 30.43 4.93
544 545 3.175152 GCTAGATACATCCATTCGAGCG 58.825 50.000 0.00 0.00 30.43 5.03
545 546 3.194542 AGGCTAGATACATCCATTCGAGC 59.805 47.826 0.00 0.00 37.38 5.03
546 547 4.460731 TCAGGCTAGATACATCCATTCGAG 59.539 45.833 0.00 0.00 0.00 4.04
547 548 4.407365 TCAGGCTAGATACATCCATTCGA 58.593 43.478 0.00 0.00 0.00 3.71
548 549 4.790765 TCAGGCTAGATACATCCATTCG 57.209 45.455 0.00 0.00 0.00 3.34
549 550 9.107177 CATATTTCAGGCTAGATACATCCATTC 57.893 37.037 0.00 0.00 0.00 2.67
550 551 8.609483 ACATATTTCAGGCTAGATACATCCATT 58.391 33.333 0.00 0.00 0.00 3.16
551 552 8.155620 ACATATTTCAGGCTAGATACATCCAT 57.844 34.615 0.00 0.00 0.00 3.41
552 553 7.455953 AGACATATTTCAGGCTAGATACATCCA 59.544 37.037 0.00 0.00 0.00 3.41
553 554 7.846066 AGACATATTTCAGGCTAGATACATCC 58.154 38.462 0.00 0.00 0.00 3.51
556 557 9.588096 TCTTAGACATATTTCAGGCTAGATACA 57.412 33.333 0.00 0.00 0.00 2.29
561 562 9.814899 CCATATCTTAGACATATTTCAGGCTAG 57.185 37.037 0.00 0.00 0.00 3.42
562 563 9.547279 TCCATATCTTAGACATATTTCAGGCTA 57.453 33.333 0.00 0.00 0.00 3.93
563 564 8.441311 TCCATATCTTAGACATATTTCAGGCT 57.559 34.615 0.00 0.00 0.00 4.58
564 565 9.323985 GATCCATATCTTAGACATATTTCAGGC 57.676 37.037 0.00 0.00 0.00 4.85
565 566 9.526713 CGATCCATATCTTAGACATATTTCAGG 57.473 37.037 0.00 0.00 0.00 3.86
566 567 9.526713 CCGATCCATATCTTAGACATATTTCAG 57.473 37.037 0.00 0.00 0.00 3.02
567 568 8.478066 CCCGATCCATATCTTAGACATATTTCA 58.522 37.037 0.00 0.00 0.00 2.69
568 569 7.928706 CCCCGATCCATATCTTAGACATATTTC 59.071 40.741 0.00 0.00 0.00 2.17
569 570 7.147479 CCCCCGATCCATATCTTAGACATATTT 60.147 40.741 0.00 0.00 0.00 1.40
570 571 6.327626 CCCCCGATCCATATCTTAGACATATT 59.672 42.308 0.00 0.00 0.00 1.28
571 572 5.841237 CCCCCGATCCATATCTTAGACATAT 59.159 44.000 0.00 0.00 0.00 1.78
572 573 5.208890 CCCCCGATCCATATCTTAGACATA 58.791 45.833 0.00 0.00 0.00 2.29
573 574 4.033709 CCCCCGATCCATATCTTAGACAT 58.966 47.826 0.00 0.00 0.00 3.06
574 575 3.441101 CCCCCGATCCATATCTTAGACA 58.559 50.000 0.00 0.00 0.00 3.41
592 593 7.733955 ACTTCTATCCTAATTTACTACTCCCCC 59.266 40.741 0.00 0.00 0.00 5.40
593 594 8.586744 CACTTCTATCCTAATTTACTACTCCCC 58.413 40.741 0.00 0.00 0.00 4.81
594 595 8.089597 GCACTTCTATCCTAATTTACTACTCCC 58.910 40.741 0.00 0.00 0.00 4.30
595 596 8.089597 GGCACTTCTATCCTAATTTACTACTCC 58.910 40.741 0.00 0.00 0.00 3.85
596 597 8.639761 TGGCACTTCTATCCTAATTTACTACTC 58.360 37.037 0.00 0.00 0.00 2.59
597 598 8.422566 GTGGCACTTCTATCCTAATTTACTACT 58.577 37.037 11.13 0.00 0.00 2.57
598 599 8.422566 AGTGGCACTTCTATCCTAATTTACTAC 58.577 37.037 15.88 0.00 0.00 2.73
645 646 6.466812 TGCATCCCATAGTATACATCACAAG 58.533 40.000 5.50 0.00 0.00 3.16
650 651 6.476378 AGGTTTGCATCCCATAGTATACATC 58.524 40.000 5.50 0.00 0.00 3.06
651 652 6.454223 AGGTTTGCATCCCATAGTATACAT 57.546 37.500 5.50 0.00 0.00 2.29
652 653 5.904984 AGGTTTGCATCCCATAGTATACA 57.095 39.130 5.50 0.00 0.00 2.29
653 654 7.883311 ACATAAGGTTTGCATCCCATAGTATAC 59.117 37.037 5.09 0.00 0.00 1.47
654 655 7.984475 ACATAAGGTTTGCATCCCATAGTATA 58.016 34.615 5.09 0.00 0.00 1.47
655 656 6.852404 ACATAAGGTTTGCATCCCATAGTAT 58.148 36.000 5.09 0.00 0.00 2.12
657 658 5.129368 ACATAAGGTTTGCATCCCATAGT 57.871 39.130 5.09 0.00 0.00 2.12
658 659 5.132502 TGACATAAGGTTTGCATCCCATAG 58.867 41.667 5.09 0.00 0.00 2.23
659 660 5.122707 TGACATAAGGTTTGCATCCCATA 57.877 39.130 5.09 0.00 0.00 2.74
660 661 3.956199 CTGACATAAGGTTTGCATCCCAT 59.044 43.478 5.09 0.00 0.00 4.00
661 662 3.245229 ACTGACATAAGGTTTGCATCCCA 60.245 43.478 5.09 0.00 0.00 4.37
662 663 3.356290 ACTGACATAAGGTTTGCATCCC 58.644 45.455 5.04 0.00 0.00 3.85
663 664 5.048083 TCAAACTGACATAAGGTTTGCATCC 60.048 40.000 11.31 0.00 45.15 3.51
664 665 6.012658 TCAAACTGACATAAGGTTTGCATC 57.987 37.500 11.31 0.00 45.15 3.91
665 666 6.040842 ACTTCAAACTGACATAAGGTTTGCAT 59.959 34.615 11.31 0.57 45.15 3.96
676 687 4.394920 ACAACGTTGACTTCAAACTGACAT 59.605 37.500 33.66 3.12 37.63 3.06
701 712 8.715088 TGATCAACGCAGATGAATTATATTCAG 58.285 33.333 7.98 0.00 43.92 3.02
778 790 8.150945 ACGACTACCAATAATTCATAAGCAGAT 58.849 33.333 0.00 0.00 0.00 2.90
780 792 7.715265 ACGACTACCAATAATTCATAAGCAG 57.285 36.000 0.00 0.00 0.00 4.24
797 809 1.749634 ACATCCTGGTGCTACGACTAC 59.250 52.381 0.00 0.00 0.00 2.73
804 816 1.339055 GCACTGAACATCCTGGTGCTA 60.339 52.381 8.79 0.00 46.39 3.49
865 881 0.460987 CCGGAGAACTGGACTGATGC 60.461 60.000 0.00 0.00 44.87 3.91
885 901 1.645402 AACTGCAGACCTTGTGGGGT 61.645 55.000 23.35 0.00 43.07 4.95
911 927 1.252904 GCTCTGCAATTGGCCAAGGA 61.253 55.000 24.94 11.53 43.89 3.36
937 953 2.632996 CCGTAGCTTTATCCCCATCTCA 59.367 50.000 0.00 0.00 0.00 3.27
980 1000 1.901591 TTTCTTGGCTTGCTCTCAGG 58.098 50.000 0.00 0.00 0.00 3.86
992 1012 0.680618 TGGTGCTGCCATTTTCTTGG 59.319 50.000 0.00 0.00 43.61 3.61
1008 1028 3.386237 GCGAGGCTGAGAGGTGGT 61.386 66.667 0.00 0.00 0.00 4.16
1371 1423 1.490490 ACTTCAGAGGAGGTTTGCACA 59.510 47.619 0.00 0.00 27.15 4.57
1393 1445 1.594862 CCGTGATTCCGAGATGAAAGC 59.405 52.381 0.00 0.00 0.00 3.51
1435 1487 2.159393 ACATGGATGCCGAATTCAAACG 60.159 45.455 6.22 0.00 0.00 3.60
1682 1740 2.096496 GGACAGGAAAATGTGAGCATCG 59.904 50.000 0.00 0.00 38.61 3.84
1864 1922 1.694150 TGCCTTCAAGACAGTAGTGCT 59.306 47.619 0.00 0.00 0.00 4.40
1941 1999 6.202570 GTCTATTCTGAAGAATCACTCCATGC 59.797 42.308 8.80 0.00 43.17 4.06
2020 2078 6.883744 TGTTGAAAGAAAAGGCCTGTTTTAT 58.116 32.000 10.28 0.00 29.58 1.40
2087 2147 5.230942 GTGGTACCATATGAGCTGACATAC 58.769 45.833 19.72 0.00 35.91 2.39
2216 2276 3.738982 AGGCCCAAGTTTTAACAAATGC 58.261 40.909 0.00 0.00 0.00 3.56
2335 2395 5.362143 TCTGGCATACTAGGATGATATCTGC 59.638 44.000 19.72 2.24 0.00 4.26
2490 2552 1.269723 GCCAGCAAGGTGAAAAGGTAC 59.730 52.381 0.03 0.00 40.61 3.34
2514 2576 8.512956 GGATGATGAGATGATTTAACTTCCATG 58.487 37.037 0.00 0.00 0.00 3.66
2515 2577 8.446394 AGGATGATGAGATGATTTAACTTCCAT 58.554 33.333 0.00 0.00 0.00 3.41
2580 2642 4.221703 CCTTTCTAGTCACATGGTGAGTCT 59.778 45.833 9.79 2.89 41.73 3.24
2616 2678 4.155733 TATGCGCCGGTGTCCAGG 62.156 66.667 17.91 0.00 0.00 4.45
2624 2686 0.179094 TAAGAAGTGGTATGCGCCGG 60.179 55.000 4.18 0.00 0.00 6.13
2786 2870 0.464373 AGCACCAATACGATGGGCAG 60.464 55.000 15.83 7.02 45.18 4.85
2946 3031 7.953493 TCCTCCTTGTACCCAGAATAAAATTTT 59.047 33.333 8.75 8.75 0.00 1.82
2950 3035 6.652205 ATCCTCCTTGTACCCAGAATAAAA 57.348 37.500 0.00 0.00 0.00 1.52
3089 3177 1.247567 TACCAGCAAGCTTGAAAGGC 58.752 50.000 30.39 14.10 0.00 4.35
3258 3354 0.881796 GTCTTAGGTTGGTGGCAAGC 59.118 55.000 0.00 0.00 0.00 4.01
3386 3482 5.520288 CCTAGTGGATGTCATTTCACTAACG 59.480 44.000 20.63 14.29 40.69 3.18
3557 3695 5.640189 AAGATCTTTCCATTGCAGACAAG 57.360 39.130 0.88 0.00 39.69 3.16
3745 3883 2.332063 AGATGAACGCCCGAAATGAT 57.668 45.000 0.00 0.00 0.00 2.45
3746 3884 1.737236 CAAGATGAACGCCCGAAATGA 59.263 47.619 0.00 0.00 0.00 2.57
3815 3954 2.549926 CGTGTGTTATCATAGCAGGCA 58.450 47.619 0.00 0.00 0.00 4.75
3829 3968 0.391597 AACATTCCGTCTCCGTGTGT 59.608 50.000 0.00 0.00 0.00 3.72
3897 4072 4.034510 CGGCCTGAACTTCTGTAATTCATC 59.965 45.833 0.00 0.00 32.16 2.92
4037 7818 0.984230 CTTCTTGGGCAGGGTCACTA 59.016 55.000 0.00 0.00 0.00 2.74
4038 7819 1.763770 CTTCTTGGGCAGGGTCACT 59.236 57.895 0.00 0.00 0.00 3.41
4039 7820 1.303643 CCTTCTTGGGCAGGGTCAC 60.304 63.158 0.00 0.00 0.00 3.67
4040 7821 3.170362 CCTTCTTGGGCAGGGTCA 58.830 61.111 0.00 0.00 0.00 4.02
4048 7829 2.353610 GCATGTGGGCCTTCTTGGG 61.354 63.158 4.53 0.00 36.00 4.12
4049 7830 3.291611 GCATGTGGGCCTTCTTGG 58.708 61.111 4.53 0.00 39.35 3.61
4057 7838 2.903855 CGATCCTGGCATGTGGGC 60.904 66.667 0.00 0.00 43.73 5.36
4058 7839 1.524621 GACGATCCTGGCATGTGGG 60.525 63.158 0.00 0.00 0.00 4.61
4059 7840 0.392863 TTGACGATCCTGGCATGTGG 60.393 55.000 0.00 0.00 0.00 4.17
4060 7841 1.012086 CTTGACGATCCTGGCATGTG 58.988 55.000 0.00 0.00 0.00 3.21
4061 7842 0.904649 TCTTGACGATCCTGGCATGT 59.095 50.000 0.00 0.00 0.00 3.21
4062 7843 1.293924 GTCTTGACGATCCTGGCATG 58.706 55.000 0.00 0.00 0.00 4.06
4063 7844 0.904649 TGTCTTGACGATCCTGGCAT 59.095 50.000 0.00 0.00 0.00 4.40
4064 7845 0.247460 CTGTCTTGACGATCCTGGCA 59.753 55.000 0.00 0.00 0.00 4.92
4065 7846 1.086634 GCTGTCTTGACGATCCTGGC 61.087 60.000 0.00 0.00 0.00 4.85
4066 7847 0.460987 GGCTGTCTTGACGATCCTGG 60.461 60.000 0.00 0.00 0.00 4.45
4067 7848 0.247460 TGGCTGTCTTGACGATCCTG 59.753 55.000 0.00 0.00 0.00 3.86
4068 7849 0.534412 CTGGCTGTCTTGACGATCCT 59.466 55.000 0.00 0.00 0.00 3.24
4069 7850 1.086634 GCTGGCTGTCTTGACGATCC 61.087 60.000 0.00 0.00 0.00 3.36
4070 7851 1.416813 CGCTGGCTGTCTTGACGATC 61.417 60.000 0.00 0.00 0.00 3.69
4071 7852 1.446792 CGCTGGCTGTCTTGACGAT 60.447 57.895 0.00 0.00 0.00 3.73
4072 7853 2.049156 CGCTGGCTGTCTTGACGA 60.049 61.111 0.00 0.00 0.00 4.20
4073 7854 3.782244 GCGCTGGCTGTCTTGACG 61.782 66.667 0.00 0.00 35.83 4.35
4074 7855 3.426568 GGCGCTGGCTGTCTTGAC 61.427 66.667 7.64 0.00 39.81 3.18
4099 7880 0.602638 TGTAGCGTGGGTTGCTCTTG 60.603 55.000 0.00 0.00 42.85 3.02
4103 7884 2.032071 GGTGTAGCGTGGGTTGCT 59.968 61.111 0.00 0.00 46.29 3.91
4104 7885 3.419759 CGGTGTAGCGTGGGTTGC 61.420 66.667 0.00 0.00 0.00 4.17
4159 7940 0.737715 GGTCGCTGGCTTCAGTAGTG 60.738 60.000 0.00 0.00 40.51 2.74
4161 7942 1.153549 GGGTCGCTGGCTTCAGTAG 60.154 63.158 0.00 0.00 40.51 2.57
4166 7947 4.475135 GAGGGGGTCGCTGGCTTC 62.475 72.222 0.00 0.00 0.00 3.86
4195 7977 3.910914 TTTGCCGTGATCCACCGGG 62.911 63.158 6.32 0.00 32.04 5.73
4198 7980 2.686816 CCGTTTGCCGTGATCCACC 61.687 63.158 0.00 0.00 33.66 4.61
4223 8007 0.530870 GATCAGGAGTTGGTAGCCGC 60.531 60.000 0.00 0.00 0.00 6.53
4238 8022 1.768870 GGAAGAAAGGGGATCGGATCA 59.231 52.381 18.99 0.00 0.00 2.92
4239 8023 2.037902 GAGGAAGAAAGGGGATCGGATC 59.962 54.545 9.54 9.54 0.00 3.36
4240 8024 2.050918 GAGGAAGAAAGGGGATCGGAT 58.949 52.381 0.00 0.00 0.00 4.18
4241 8025 1.497161 GAGGAAGAAAGGGGATCGGA 58.503 55.000 0.00 0.00 0.00 4.55
4267 8055 1.930914 TCAGGAGGTAGCTAGGGTTCT 59.069 52.381 0.00 0.00 0.00 3.01
4277 8065 4.631813 GCAATTACACAGTTCAGGAGGTAG 59.368 45.833 0.00 0.00 0.00 3.18
4281 8074 4.631813 GGTAGCAATTACACAGTTCAGGAG 59.368 45.833 0.00 0.00 33.73 3.69
4282 8075 4.286032 AGGTAGCAATTACACAGTTCAGGA 59.714 41.667 0.00 0.00 33.73 3.86
4285 8078 8.630054 AATTTAGGTAGCAATTACACAGTTCA 57.370 30.769 0.00 0.00 33.73 3.18
4286 8079 9.341899 CAAATTTAGGTAGCAATTACACAGTTC 57.658 33.333 0.00 0.00 33.73 3.01
4306 8099 8.844244 GGCAATCTCACTCATAGATACAAATTT 58.156 33.333 0.00 0.00 33.32 1.82
4311 8104 5.221521 GGTGGCAATCTCACTCATAGATACA 60.222 44.000 0.00 0.00 33.32 2.29
4330 8123 2.683362 GGTAGCTCAAGTATTTGGTGGC 59.317 50.000 0.00 1.65 34.97 5.01
4340 8133 2.826725 GGACACACTAGGTAGCTCAAGT 59.173 50.000 0.00 0.00 0.00 3.16
4341 8134 2.166664 GGGACACACTAGGTAGCTCAAG 59.833 54.545 0.00 0.00 0.00 3.02
4350 8143 3.133003 CCAGATGTAAGGGACACACTAGG 59.867 52.174 0.00 0.00 42.17 3.02
4393 8186 0.389391 CCAGACCACGCGATAGGAAT 59.611 55.000 15.93 3.14 0.00 3.01
4405 8198 1.375908 GATGAACTGCGCCAGACCA 60.376 57.895 4.18 6.66 35.18 4.02
4407 8200 1.416813 CTCGATGAACTGCGCCAGAC 61.417 60.000 4.18 3.80 35.18 3.51
4447 8240 0.534877 TGTGCTCCAATTGCAGTCGT 60.535 50.000 0.00 0.00 41.41 4.34
4457 8250 1.224315 CGGGATCCATGTGCTCCAA 59.776 57.895 15.23 0.00 0.00 3.53
4474 8267 2.452767 GAGGTAGGTTTTGACCGCG 58.547 57.895 0.00 0.00 40.91 6.46
4483 8276 2.233186 GGTAAGCTTGTCGAGGTAGGTT 59.767 50.000 9.86 9.74 34.30 3.50
4628 8421 4.069232 CCGGGTCGCTCTTGCTGA 62.069 66.667 0.00 0.00 36.97 4.26
4645 8438 1.298041 CCGTTGGTGTCGTTGTTGC 60.298 57.895 0.00 0.00 0.00 4.17
4648 8441 3.266376 CGCCGTTGGTGTCGTTGT 61.266 61.111 0.00 0.00 0.00 3.32


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

AutoCloner maintained by Alex Coulton.