Multiple sequence alignment - TraesCS2A01G487900

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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 TraesCS2A01G487900 chr2A 100.000 5206 0 0 1 5206 722523800 722518595 0.000000e+00 9614.0
1 TraesCS2A01G487900 chr2A 89.474 190 7 5 4914 5096 32974335 32974152 1.460000e-55 228.0
2 TraesCS2A01G487900 chr2A 94.737 57 1 1 3421 3475 722520337 722520281 2.580000e-13 87.9
3 TraesCS2A01G487900 chr2A 94.737 57 1 1 3464 3520 722520380 722520326 2.580000e-13 87.9
4 TraesCS2A01G487900 chr2D 93.941 1832 83 14 1661 3475 587700162 587698342 0.000000e+00 2743.0
5 TraesCS2A01G487900 chr2D 89.715 1721 101 39 3464 5160 587698396 587696728 0.000000e+00 2128.0
6 TraesCS2A01G487900 chr2D 90.919 958 49 12 716 1657 587701221 587700286 0.000000e+00 1253.0
7 TraesCS2A01G487900 chr2D 89.865 592 38 13 1 590 587701935 587701364 0.000000e+00 741.0
8 TraesCS2A01G487900 chr2B 91.062 1723 94 26 3464 5160 710282457 710280769 0.000000e+00 2274.0
9 TraesCS2A01G487900 chr2B 90.203 1725 111 30 782 2480 710285207 710283515 0.000000e+00 2196.0
10 TraesCS2A01G487900 chr2B 93.545 1007 41 11 2482 3475 710283398 710282403 0.000000e+00 1478.0
11 TraesCS2A01G487900 chr2B 90.909 594 36 10 1 590 710285991 710285412 0.000000e+00 782.0
12 TraesCS2A01G487900 chr4D 87.673 868 63 16 4311 5152 344372799 344373648 0.000000e+00 970.0
13 TraesCS2A01G487900 chr3A 85.505 683 50 16 4495 5152 195451515 195452173 0.000000e+00 667.0
14 TraesCS2A01G487900 chr3A 92.135 178 14 0 4311 4488 195447429 195447606 8.650000e-63 252.0
15 TraesCS2A01G487900 chr7B 82.963 405 58 8 1785 2187 611719043 611718648 6.410000e-94 355.0
16 TraesCS2A01G487900 chr7A 80.941 404 66 9 1785 2187 647295810 647295417 5.060000e-80 309.0
17 TraesCS2A01G487900 chr7D 78.322 429 61 15 1785 2187 562121393 562120971 1.120000e-61 248.0
18 TraesCS2A01G487900 chr1D 92.667 150 11 0 4311 4460 2480514 2480365 3.160000e-52 217.0


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 TraesCS2A01G487900 chr2A 722518595 722523800 5205 True 3263.266667 9614 96.491333 1 5206 3 chr2A.!!$R2 5205
1 TraesCS2A01G487900 chr2D 587696728 587701935 5207 True 1716.250000 2743 91.110000 1 5160 4 chr2D.!!$R1 5159
2 TraesCS2A01G487900 chr2B 710280769 710285991 5222 True 1682.500000 2274 91.429750 1 5160 4 chr2B.!!$R1 5159
3 TraesCS2A01G487900 chr4D 344372799 344373648 849 False 970.000000 970 87.673000 4311 5152 1 chr4D.!!$F1 841
4 TraesCS2A01G487900 chr3A 195447429 195452173 4744 False 459.500000 667 88.820000 4311 5152 2 chr3A.!!$F1 841

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
872 939 0.034337 GGACCAGTTACACCTGCGAA 59.966 55.0 0.00 0.00 0.00 4.70 F
1554 1652 0.174617 GGACTCTGGAGGCTTCGAAG 59.825 60.0 21.02 21.02 36.46 3.79 F
1918 2136 0.527817 GGTTCGGTGATAGCAGTCCG 60.528 60.0 3.78 3.78 43.65 4.79 F
2288 2508 0.537143 CTGCCTACAACCCTTGTGCA 60.537 55.0 0.00 0.00 45.03 4.57 F
3402 3775 0.620556 ACTGTGACCACCATCCATCC 59.379 55.0 0.00 0.00 0.00 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2269 2488 0.537143 TGCACAAGGGTTGTAGGCAG 60.537 55.000 1.78 0.00 43.23 4.85 R
2421 2663 2.838202 AGTATGAACGTGGGATCTTGGT 59.162 45.455 0.00 0.00 0.00 3.67 R
3682 4058 2.421073 TGATGCTAAATCTGTGCAGCAC 59.579 45.455 19.37 19.37 46.01 4.40 R
3933 4313 0.452184 GAGAGGATCGAACTGACGCA 59.548 55.000 0.00 0.00 42.67 5.24 R
4900 9232 0.036483 TAGGTGCGCATGCTCTGAAA 60.036 50.000 15.91 0.00 43.34 2.69 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
27 28 0.964358 ACATTGAGCTGGAAGGCAGC 60.964 55.000 0.00 0.00 45.38 5.25
108 109 1.663739 CACTCCGTCGAAGAACCCA 59.336 57.895 0.00 0.00 39.69 4.51
112 113 2.342279 CGTCGAAGAACCCAGCCA 59.658 61.111 0.00 0.00 39.69 4.75
358 362 1.831580 ATTCTGTTCTCCCTTGCTGC 58.168 50.000 0.00 0.00 0.00 5.25
408 412 9.913310 TGTATTTTGGTTCTATGGATTGTGATA 57.087 29.630 0.00 0.00 0.00 2.15
465 470 2.479566 TTCTTGCTGTCATCCCAGTC 57.520 50.000 0.00 0.00 34.84 3.51
472 477 4.093743 TGCTGTCATCCCAGTCTAGTTAA 58.906 43.478 0.00 0.00 34.84 2.01
476 481 4.398358 TGTCATCCCAGTCTAGTTAAGTCG 59.602 45.833 0.00 0.00 0.00 4.18
492 497 4.983671 AAGTCGCCTTTTGAGTTTTCTT 57.016 36.364 0.00 0.00 0.00 2.52
493 498 4.983671 AGTCGCCTTTTGAGTTTTCTTT 57.016 36.364 0.00 0.00 0.00 2.52
494 499 4.921547 AGTCGCCTTTTGAGTTTTCTTTC 58.078 39.130 0.00 0.00 0.00 2.62
495 500 4.640647 AGTCGCCTTTTGAGTTTTCTTTCT 59.359 37.500 0.00 0.00 0.00 2.52
496 501 4.970611 GTCGCCTTTTGAGTTTTCTTTCTC 59.029 41.667 0.00 0.00 0.00 2.87
497 502 4.036380 TCGCCTTTTGAGTTTTCTTTCTCC 59.964 41.667 0.00 0.00 0.00 3.71
498 503 4.036852 CGCCTTTTGAGTTTTCTTTCTCCT 59.963 41.667 0.00 0.00 0.00 3.69
499 504 5.450550 CGCCTTTTGAGTTTTCTTTCTCCTT 60.451 40.000 0.00 0.00 0.00 3.36
500 505 5.750547 GCCTTTTGAGTTTTCTTTCTCCTTG 59.249 40.000 0.00 0.00 0.00 3.61
504 509 3.312421 TGAGTTTTCTTTCTCCTTGTGCG 59.688 43.478 0.00 0.00 0.00 5.34
515 521 2.482721 CTCCTTGTGCGTTTTATTCGGT 59.517 45.455 0.00 0.00 0.00 4.69
516 522 2.879646 TCCTTGTGCGTTTTATTCGGTT 59.120 40.909 0.00 0.00 0.00 4.44
517 523 3.058777 TCCTTGTGCGTTTTATTCGGTTC 60.059 43.478 0.00 0.00 0.00 3.62
519 525 4.152759 CCTTGTGCGTTTTATTCGGTTCTA 59.847 41.667 0.00 0.00 0.00 2.10
525 531 4.493708 GCGTTTTATTCGGTTCTAGCTTCC 60.494 45.833 0.00 0.00 0.00 3.46
526 532 4.259690 CGTTTTATTCGGTTCTAGCTTCCG 60.260 45.833 11.80 11.80 44.76 4.30
527 533 2.503920 TATTCGGTTCTAGCTTCCGC 57.496 50.000 12.77 0.00 43.35 5.54
529 535 2.552585 TTCGGTTCTAGCTTCCGCGG 62.553 60.000 22.12 22.12 43.35 6.46
530 536 2.577593 GGTTCTAGCTTCCGCGGT 59.422 61.111 27.15 8.36 42.32 5.68
532 538 1.518792 GTTCTAGCTTCCGCGGTCC 60.519 63.158 27.15 14.42 42.32 4.46
533 539 1.980232 TTCTAGCTTCCGCGGTCCA 60.980 57.895 27.15 9.72 42.32 4.02
534 540 1.327690 TTCTAGCTTCCGCGGTCCAT 61.328 55.000 27.15 12.77 42.32 3.41
535 541 1.144057 CTAGCTTCCGCGGTCCATT 59.856 57.895 27.15 10.88 42.32 3.16
536 542 1.153449 TAGCTTCCGCGGTCCATTG 60.153 57.895 27.15 10.81 42.32 2.82
537 543 4.179579 GCTTCCGCGGTCCATTGC 62.180 66.667 27.15 16.56 0.00 3.56
538 544 2.436646 CTTCCGCGGTCCATTGCT 60.437 61.111 27.15 0.00 0.00 3.91
549 555 2.423538 GGTCCATTGCTGTGGTGATTAC 59.576 50.000 7.64 0.00 40.27 1.89
564 570 2.084546 GATTACCCAGCTGTGTTGACC 58.915 52.381 13.81 0.00 0.00 4.02
565 571 0.840617 TTACCCAGCTGTGTTGACCA 59.159 50.000 13.81 0.00 0.00 4.02
585 591 1.691976 ACAGACGGGTCACTGATTTCA 59.308 47.619 0.00 0.00 37.54 2.69
590 596 1.800586 CGGGTCACTGATTTCACTGTG 59.199 52.381 0.17 0.17 39.75 3.66
591 597 1.537202 GGGTCACTGATTTCACTGTGC 59.463 52.381 2.12 0.00 38.79 4.57
592 598 2.498167 GGTCACTGATTTCACTGTGCT 58.502 47.619 2.12 0.00 38.79 4.40
593 599 2.481952 GGTCACTGATTTCACTGTGCTC 59.518 50.000 2.12 0.78 38.79 4.26
595 601 3.812053 GTCACTGATTTCACTGTGCTCTT 59.188 43.478 2.12 0.00 38.79 2.85
596 602 4.991056 GTCACTGATTTCACTGTGCTCTTA 59.009 41.667 2.12 0.00 38.79 2.10
597 603 5.641209 GTCACTGATTTCACTGTGCTCTTAT 59.359 40.000 2.12 0.00 38.79 1.73
598 604 5.640783 TCACTGATTTCACTGTGCTCTTATG 59.359 40.000 2.12 0.00 38.79 1.90
599 605 5.640783 CACTGATTTCACTGTGCTCTTATGA 59.359 40.000 2.12 0.00 34.24 2.15
601 607 6.315642 ACTGATTTCACTGTGCTCTTATGATG 59.684 38.462 2.12 0.00 0.00 3.07
602 608 4.952262 TTTCACTGTGCTCTTATGATGC 57.048 40.909 2.12 0.00 0.00 3.91
603 609 2.910199 TCACTGTGCTCTTATGATGCC 58.090 47.619 2.12 0.00 0.00 4.40
606 612 1.602851 CTGTGCTCTTATGATGCCTGC 59.397 52.381 0.00 0.00 0.00 4.85
607 613 1.065272 TGTGCTCTTATGATGCCTGCA 60.065 47.619 0.00 0.00 0.00 4.41
608 614 2.228059 GTGCTCTTATGATGCCTGCAT 58.772 47.619 3.90 3.90 39.69 3.96
610 616 3.067742 GTGCTCTTATGATGCCTGCATTT 59.932 43.478 6.02 0.37 36.70 2.32
611 617 3.067601 TGCTCTTATGATGCCTGCATTTG 59.932 43.478 6.02 0.00 36.70 2.32
612 618 3.639538 CTCTTATGATGCCTGCATTTGC 58.360 45.455 6.02 0.00 36.70 3.68
645 706 5.290386 ACGTACTTCCTTGTTCTTCTCAAG 58.710 41.667 0.00 0.00 41.06 3.02
646 707 5.068723 ACGTACTTCCTTGTTCTTCTCAAGA 59.931 40.000 7.16 0.00 43.17 3.02
686 749 8.330466 TCGAGAAAAATAGCAAAATCTACCAA 57.670 30.769 0.00 0.00 0.00 3.67
687 750 8.956426 TCGAGAAAAATAGCAAAATCTACCAAT 58.044 29.630 0.00 0.00 0.00 3.16
735 798 9.559732 TTCGTCCATCATAAGATATGTTTTCAT 57.440 29.630 0.00 0.00 43.60 2.57
736 799 8.992073 TCGTCCATCATAAGATATGTTTTCATG 58.008 33.333 0.00 0.00 41.09 3.07
770 833 8.954950 ATTTGGTCACTATTGTAGATCTTGAG 57.045 34.615 0.00 0.00 0.00 3.02
772 835 7.340122 TGGTCACTATTGTAGATCTTGAGAG 57.660 40.000 0.00 0.00 0.00 3.20
774 837 8.053355 TGGTCACTATTGTAGATCTTGAGAGTA 58.947 37.037 0.00 0.00 0.00 2.59
775 838 9.073475 GGTCACTATTGTAGATCTTGAGAGTAT 57.927 37.037 0.00 0.00 0.00 2.12
830 897 7.230466 AGTTTGACTTTTGAAGTAGTGTACG 57.770 36.000 0.00 0.00 43.03 3.67
855 922 1.423161 TGGTGTCAATGACATGTGGGA 59.577 47.619 19.72 0.00 44.63 4.37
868 935 0.762418 TGTGGGACCAGTTACACCTG 59.238 55.000 0.00 0.00 33.07 4.00
872 939 0.034337 GGACCAGTTACACCTGCGAA 59.966 55.000 0.00 0.00 0.00 4.70
953 1021 1.064946 CCACGACATCTCGAGCTCC 59.935 63.158 7.81 0.00 43.06 4.70
1259 1352 0.543277 TCCTCGCAGAATGAATGGCT 59.457 50.000 0.00 0.00 39.69 4.75
1287 1380 4.373116 CCGTACTGCCGTGCTGGT 62.373 66.667 7.46 4.76 41.21 4.00
1335 1430 2.180017 GTGCAGCTGCCGATTTGG 59.820 61.111 34.64 0.00 41.18 3.28
1375 1472 2.676121 CCAATTGTGCCCAGCGGA 60.676 61.111 4.43 0.00 0.00 5.54
1377 1474 1.213537 CAATTGTGCCCAGCGGAAG 59.786 57.895 0.00 0.00 0.00 3.46
1381 1478 3.050275 GTGCCCAGCGGAAGTCAC 61.050 66.667 0.00 0.00 0.00 3.67
1390 1488 0.380378 GCGGAAGTCACTTTTGCACA 59.620 50.000 9.43 0.00 0.00 4.57
1454 1552 2.487934 CCCACCGAATCATGAGCTTAG 58.512 52.381 0.09 0.00 0.00 2.18
1554 1652 0.174617 GGACTCTGGAGGCTTCGAAG 59.825 60.000 21.02 21.02 36.46 3.79
1674 1892 1.206072 GCGCTGCAGTTCTCAACAG 59.794 57.895 16.64 0.00 0.00 3.16
1699 1917 8.253113 AGGCAAACTATCATCAAAATAAGTTGG 58.747 33.333 0.00 0.00 0.00 3.77
1807 2025 8.160765 TCCCATCATTTCTGACTAAAACAGTTA 58.839 33.333 0.00 0.00 37.72 2.24
1809 2027 9.778993 CCATCATTTCTGACTAAAACAGTTATG 57.221 33.333 0.00 0.00 37.72 1.90
1918 2136 0.527817 GGTTCGGTGATAGCAGTCCG 60.528 60.000 3.78 3.78 43.65 4.79
2048 2267 7.550551 TCTCATGAGAATGAGTTACATGGTTTC 59.449 37.037 23.17 0.00 46.09 2.78
2151 2370 2.789893 CGAGTATGCTCTTTTCGTAGGC 59.210 50.000 9.26 0.00 39.53 3.93
2268 2487 6.270064 ACGGTAATTTCAAAAGTTGTGGAAG 58.730 36.000 0.00 0.00 0.00 3.46
2269 2488 5.174943 CGGTAATTTCAAAAGTTGTGGAAGC 59.825 40.000 0.00 0.00 0.00 3.86
2288 2508 0.537143 CTGCCTACAACCCTTGTGCA 60.537 55.000 0.00 0.00 45.03 4.57
2421 2663 5.102953 AGCTCTTGTAATGTGGCAAGATA 57.897 39.130 7.33 0.00 46.52 1.98
2530 2887 5.132502 TGAGTTCTGTTGTTCCATTCATGT 58.867 37.500 0.00 0.00 0.00 3.21
2543 2900 4.929211 TCCATTCATGTCTCACAGTTTACG 59.071 41.667 0.00 0.00 0.00 3.18
2816 3175 9.384764 AGGCTTGATTTATAGACTTCTTGTTAC 57.615 33.333 0.00 0.00 0.00 2.50
2864 3223 6.367983 AGGACATACTGCCAATTCATACAAT 58.632 36.000 0.00 0.00 0.00 2.71
2923 3283 8.504005 GTTAGAAAACTGCTACTTGCTTCAATA 58.496 33.333 0.00 0.00 43.37 1.90
2992 3352 2.106566 TGCTGCCTTTTGTTTCTTCCA 58.893 42.857 0.00 0.00 0.00 3.53
3053 3413 5.985530 CACAGTATTCATGACATCACGGTAT 59.014 40.000 0.00 0.00 0.00 2.73
3350 3712 5.895636 AAGCGAACACCAAAATCATATCA 57.104 34.783 0.00 0.00 0.00 2.15
3402 3775 0.620556 ACTGTGACCACCATCCATCC 59.379 55.000 0.00 0.00 0.00 3.51
3455 3828 9.219603 CTGTATGAACTAACAGAAAAGATGGAA 57.780 33.333 0.00 0.00 44.79 3.53
3456 3829 9.739276 TGTATGAACTAACAGAAAAGATGGAAT 57.261 29.630 0.00 0.00 0.00 3.01
3475 3848 9.771534 GATGGAATCAGTACTTTTATAGCTTCT 57.228 33.333 0.00 0.00 44.70 2.85
3476 3849 8.948631 TGGAATCAGTACTTTTATAGCTTCTG 57.051 34.615 0.00 0.00 0.00 3.02
3477 3850 8.540388 TGGAATCAGTACTTTTATAGCTTCTGT 58.460 33.333 0.00 0.00 0.00 3.41
3498 3871 8.777865 TCTGTATGAACTAACAGAAAAGATGG 57.222 34.615 2.82 0.00 46.82 3.51
3499 3872 8.593679 TCTGTATGAACTAACAGAAAAGATGGA 58.406 33.333 2.82 0.00 46.82 3.41
3540 3913 2.671396 CCACGCTTGAGTTGTACCATAC 59.329 50.000 0.00 0.00 0.00 2.39
3541 3914 3.322369 CACGCTTGAGTTGTACCATACA 58.678 45.455 0.00 0.00 36.79 2.29
3542 3915 3.367932 CACGCTTGAGTTGTACCATACAG 59.632 47.826 0.00 0.00 40.24 2.74
3543 3916 3.006537 ACGCTTGAGTTGTACCATACAGT 59.993 43.478 0.00 0.00 40.24 3.55
3544 3917 4.219070 ACGCTTGAGTTGTACCATACAGTA 59.781 41.667 0.00 0.00 40.24 2.74
3572 3948 6.873605 TCTTAAGTGTCACATGTTGGACATAG 59.126 38.462 18.72 14.08 44.94 2.23
3636 4012 9.347934 CCTGATTCTATACTTAGCTCATAAACG 57.652 37.037 0.00 0.00 0.00 3.60
3648 4024 6.435430 AGCTCATAAACGCATAAATGTCAA 57.565 33.333 0.00 0.00 0.00 3.18
3682 4058 5.417811 AGCTGATGACATACTGAGTTTGAG 58.582 41.667 10.00 0.00 0.00 3.02
3758 4134 1.853963 ATCCGCTGAAGTACCAGTCT 58.146 50.000 1.78 0.00 36.57 3.24
3933 4313 6.808321 TCTAATCAGCCTACCAATACAGTT 57.192 37.500 0.00 0.00 0.00 3.16
3980 4360 9.591792 TCTAGACAAGTCAATCTAATCATGTTG 57.408 33.333 2.72 0.00 0.00 3.33
4178 4558 0.798776 CAATGGAGAACACGCCAGAC 59.201 55.000 0.00 0.00 36.97 3.51
4205 4585 9.547753 GTAGTGATTCCTGAATATCAAAGCTAA 57.452 33.333 0.00 0.00 32.94 3.09
4214 4594 7.147846 CCTGAATATCAAAGCTAATGTTTGGGT 60.148 37.037 0.00 0.00 35.88 4.51
4260 4640 6.944234 ACTTTTTCGGAGATGTCTTTTCTT 57.056 33.333 0.00 0.00 35.04 2.52
4298 4678 4.923281 AGGTTTTCGCATACATGAAAAAGC 59.077 37.500 16.47 16.47 43.42 3.51
4316 4696 1.945394 AGCAGTGCATATGTTAGCAGC 59.055 47.619 19.20 2.19 42.14 5.25
4333 4713 2.554032 GCAGCCACTTGAGTGTGTAAAT 59.446 45.455 10.03 0.00 44.21 1.40
4382 4764 3.892588 AGTAGTTACTGCTATCCTGGAGC 59.107 47.826 0.06 1.33 40.53 4.70
4409 4791 0.037419 TACTTGCGCACTCAGATGCA 60.037 50.000 11.12 0.00 46.47 3.96
4412 4794 0.448990 TTGCGCACTCAGATGCAATC 59.551 50.000 11.12 0.00 46.47 2.67
4440 4822 2.224606 AGATATGCGAAATGGGCAGTG 58.775 47.619 0.00 0.00 44.71 3.66
4459 4841 6.128526 GGCAGTGAATAACTCTGAACTGTAAC 60.129 42.308 0.00 0.00 41.05 2.50
4517 8805 1.442520 CGGCGCAAATGACACCAAG 60.443 57.895 10.83 0.00 0.00 3.61
4519 8807 1.659794 GCGCAAATGACACCAAGGT 59.340 52.632 0.30 0.00 0.00 3.50
4520 8808 0.878416 GCGCAAATGACACCAAGGTA 59.122 50.000 0.30 0.00 0.00 3.08
4521 8809 1.268352 GCGCAAATGACACCAAGGTAA 59.732 47.619 0.30 0.00 0.00 2.85
4522 8810 2.287909 GCGCAAATGACACCAAGGTAAA 60.288 45.455 0.30 0.00 0.00 2.01
4535 8823 5.236478 CACCAAGGTAAATTAGCTCGGTATG 59.764 44.000 13.71 4.55 41.36 2.39
4547 8835 5.220710 AGCTCGGTATGCTATCTCAAATT 57.779 39.130 0.00 0.00 39.21 1.82
4583 8871 5.826208 CAGGAAGATGAAATGTGGATCATGA 59.174 40.000 0.00 0.00 36.45 3.07
4597 8901 3.434167 GGATCATGAGGCCATTGTACTGT 60.434 47.826 5.01 0.00 0.00 3.55
4610 8914 3.420300 TGTACTGTAATTTTGGGCCGA 57.580 42.857 0.00 0.00 0.00 5.54
4633 8937 6.292973 CGATGATCTACGGCCATAGTATCTAC 60.293 46.154 5.63 5.79 0.00 2.59
4643 8947 5.485708 GGCCATAGTATCTACAATCTTCCCT 59.514 44.000 0.00 0.00 0.00 4.20
4645 8949 6.876257 GCCATAGTATCTACAATCTTCCCTTG 59.124 42.308 0.00 0.00 0.00 3.61
4646 8950 7.473511 GCCATAGTATCTACAATCTTCCCTTGT 60.474 40.741 0.00 0.00 39.93 3.16
4648 8952 9.482627 CATAGTATCTACAATCTTCCCTTGTTC 57.517 37.037 0.00 0.00 37.89 3.18
4649 8953 6.574350 AGTATCTACAATCTTCCCTTGTTCG 58.426 40.000 0.00 0.00 37.89 3.95
4650 8954 5.677319 ATCTACAATCTTCCCTTGTTCGA 57.323 39.130 0.00 0.00 37.89 3.71
4667 8979 5.185454 TGTTCGATTGCATCAGGAGTAATT 58.815 37.500 0.00 0.00 0.00 1.40
4672 8984 6.646653 TCGATTGCATCAGGAGTAATTATCAC 59.353 38.462 0.00 0.00 0.00 3.06
4700 9012 0.036010 CCGTCATTCCTCACAGGCTT 60.036 55.000 0.00 0.00 34.61 4.35
4710 9022 3.710722 ACAGGCTTGAGGAGGGCG 61.711 66.667 1.40 0.00 0.00 6.13
4736 9048 6.398918 TCTACCTGAACTGAAGAATGCTTAC 58.601 40.000 0.00 0.00 33.61 2.34
4789 9101 1.635844 TATCGTGTGGACATTGCGAC 58.364 50.000 0.00 0.00 34.36 5.19
4805 9117 2.125673 ACCATCCTGTACGTGCGC 60.126 61.111 0.00 0.00 0.00 6.09
4857 9189 2.125753 CTCCTGACAGGCTGACGC 60.126 66.667 23.66 10.49 34.61 5.19
4858 9190 2.601666 TCCTGACAGGCTGACGCT 60.602 61.111 23.66 0.00 34.61 5.07
4859 9191 2.433838 CCTGACAGGCTGACGCTG 60.434 66.667 23.66 12.97 36.09 5.18
4860 9192 3.117171 CTGACAGGCTGACGCTGC 61.117 66.667 23.66 3.61 36.09 5.25
4861 9193 3.871248 CTGACAGGCTGACGCTGCA 62.871 63.158 23.66 7.95 36.09 4.41
4862 9194 2.666190 GACAGGCTGACGCTGCAA 60.666 61.111 23.66 0.00 36.09 4.08
4863 9195 2.203195 ACAGGCTGACGCTGCAAA 60.203 55.556 23.66 0.00 36.09 3.68
4864 9196 2.180131 GACAGGCTGACGCTGCAAAG 62.180 60.000 23.66 0.00 36.09 2.77
4865 9197 1.962822 CAGGCTGACGCTGCAAAGA 60.963 57.895 9.42 0.00 36.09 2.52
4884 9216 3.883669 AGAATTCTGCCATGTCTTCCTC 58.116 45.455 7.30 0.00 0.00 3.71
4900 9232 2.739943 TCCTCCATCGTCAGTTCAGAT 58.260 47.619 0.00 0.00 0.00 2.90
4910 9242 3.931468 CGTCAGTTCAGATTTCAGAGCAT 59.069 43.478 0.00 0.00 0.00 3.79
4911 9243 4.201695 CGTCAGTTCAGATTTCAGAGCATG 60.202 45.833 0.00 0.00 0.00 4.06
4927 9259 1.685765 ATGCGCACCTACCTCTCCA 60.686 57.895 14.90 0.00 0.00 3.86
4958 9298 2.763448 CTCCCTCTAGTTCACCCAGAAG 59.237 54.545 0.00 0.00 36.78 2.85
4962 9302 4.323104 CCCTCTAGTTCACCCAGAAGAAAG 60.323 50.000 0.00 0.00 36.78 2.62
4964 9304 5.188751 CCTCTAGTTCACCCAGAAGAAAGAT 59.811 44.000 0.00 0.00 36.78 2.40
4965 9305 6.381420 CCTCTAGTTCACCCAGAAGAAAGATA 59.619 42.308 0.00 0.00 36.78 1.98
4973 9313 5.006386 ACCCAGAAGAAAGATACAAGCAAG 58.994 41.667 0.00 0.00 0.00 4.01
4979 9319 5.505181 AGAAAGATACAAGCAAGGAAGGA 57.495 39.130 0.00 0.00 0.00 3.36
5038 9378 5.271598 ACTAATCTGCCATTTCCATTCCAA 58.728 37.500 0.00 0.00 0.00 3.53
5152 9495 0.536006 GCCGAAATGGGGGATCTCTG 60.536 60.000 0.00 0.00 38.63 3.35
5154 9497 1.212935 CCGAAATGGGGGATCTCTGTT 59.787 52.381 0.00 0.00 0.00 3.16
5155 9498 2.438021 CCGAAATGGGGGATCTCTGTTA 59.562 50.000 0.00 0.00 0.00 2.41
5156 9499 3.118038 CCGAAATGGGGGATCTCTGTTAA 60.118 47.826 0.00 0.00 0.00 2.01
5157 9500 3.877508 CGAAATGGGGGATCTCTGTTAAC 59.122 47.826 0.00 0.00 0.00 2.01
5158 9501 3.953542 AATGGGGGATCTCTGTTAACC 57.046 47.619 2.48 0.00 0.00 2.85
5159 9502 1.200519 TGGGGGATCTCTGTTAACCG 58.799 55.000 2.48 0.00 0.00 4.44
5160 9503 1.201424 GGGGGATCTCTGTTAACCGT 58.799 55.000 2.48 0.00 0.00 4.83
5161 9504 1.138464 GGGGGATCTCTGTTAACCGTC 59.862 57.143 2.48 0.00 0.00 4.79
5162 9505 1.829222 GGGGATCTCTGTTAACCGTCA 59.171 52.381 2.48 0.00 0.00 4.35
5163 9506 2.418334 GGGGATCTCTGTTAACCGTCAC 60.418 54.545 2.48 0.00 0.00 3.67
5164 9507 2.418334 GGGATCTCTGTTAACCGTCACC 60.418 54.545 2.48 0.27 0.00 4.02
5165 9508 2.232941 GGATCTCTGTTAACCGTCACCA 59.767 50.000 2.48 0.00 0.00 4.17
5166 9509 3.118738 GGATCTCTGTTAACCGTCACCAT 60.119 47.826 2.48 0.00 0.00 3.55
5167 9510 3.587797 TCTCTGTTAACCGTCACCATC 57.412 47.619 2.48 0.00 0.00 3.51
5168 9511 2.232941 TCTCTGTTAACCGTCACCATCC 59.767 50.000 2.48 0.00 0.00 3.51
5169 9512 2.233922 CTCTGTTAACCGTCACCATCCT 59.766 50.000 2.48 0.00 0.00 3.24
5170 9513 3.433343 TCTGTTAACCGTCACCATCCTA 58.567 45.455 2.48 0.00 0.00 2.94
5171 9514 4.028131 TCTGTTAACCGTCACCATCCTAT 58.972 43.478 2.48 0.00 0.00 2.57
5172 9515 4.119862 CTGTTAACCGTCACCATCCTATG 58.880 47.826 2.48 0.00 0.00 2.23
5173 9516 2.870411 GTTAACCGTCACCATCCTATGC 59.130 50.000 0.00 0.00 0.00 3.14
5174 9517 0.908910 AACCGTCACCATCCTATGCA 59.091 50.000 0.00 0.00 0.00 3.96
5175 9518 0.465705 ACCGTCACCATCCTATGCAG 59.534 55.000 0.00 0.00 0.00 4.41
5176 9519 0.882042 CCGTCACCATCCTATGCAGC 60.882 60.000 0.00 0.00 0.00 5.25
5177 9520 0.179076 CGTCACCATCCTATGCAGCA 60.179 55.000 0.00 0.00 0.00 4.41
5178 9521 1.743431 CGTCACCATCCTATGCAGCAA 60.743 52.381 0.00 0.00 0.00 3.91
5179 9522 1.672881 GTCACCATCCTATGCAGCAAC 59.327 52.381 0.00 0.00 0.00 4.17
5180 9523 1.281577 TCACCATCCTATGCAGCAACA 59.718 47.619 0.00 0.00 0.00 3.33
5181 9524 1.674441 CACCATCCTATGCAGCAACAG 59.326 52.381 0.00 0.00 0.00 3.16
5182 9525 0.666913 CCATCCTATGCAGCAACAGC 59.333 55.000 0.00 0.00 0.00 4.40
5183 9526 0.306840 CATCCTATGCAGCAACAGCG 59.693 55.000 0.00 0.00 33.85 5.18
5184 9527 0.816825 ATCCTATGCAGCAACAGCGG 60.817 55.000 0.00 0.00 33.85 5.52
5185 9528 2.475466 CCTATGCAGCAACAGCGGG 61.475 63.158 0.00 0.00 33.85 6.13
5186 9529 2.438254 TATGCAGCAACAGCGGGG 60.438 61.111 0.00 0.00 33.85 5.73
5187 9530 3.993614 TATGCAGCAACAGCGGGGG 62.994 63.158 0.00 0.00 33.85 5.40
5201 9544 3.681473 GGGGGCAAAAGTTCTCGG 58.319 61.111 0.00 0.00 0.00 4.63
5202 9545 1.074248 GGGGGCAAAAGTTCTCGGA 59.926 57.895 0.00 0.00 0.00 4.55
5203 9546 1.241990 GGGGGCAAAAGTTCTCGGAC 61.242 60.000 0.00 0.00 0.00 4.79
5204 9547 0.250770 GGGGCAAAAGTTCTCGGACT 60.251 55.000 0.00 0.00 0.00 3.85
5205 9548 1.605753 GGGCAAAAGTTCTCGGACTT 58.394 50.000 0.00 0.00 41.44 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 2.352960 GGCTTGCTTTATCTGGTCGAAG 59.647 50.000 0.00 0.00 0.00 3.79
93 94 2.654877 GCTGGGTTCTTCGACGGA 59.345 61.111 0.00 0.00 0.00 4.69
304 308 1.205655 CACAAGAAGGAGCGAGGATCA 59.794 52.381 0.00 0.00 33.17 2.92
358 362 1.346068 GGCCTAATCACCTAGAGCCAG 59.654 57.143 0.00 0.00 36.25 4.85
436 441 4.882671 TGACAGCAAGAAAGTTCTGAAC 57.117 40.909 12.54 12.54 37.65 3.18
472 477 5.220873 GAGAAAGAAAACTCAAAAGGCGACT 60.221 40.000 0.00 0.00 36.20 4.18
476 481 5.521906 AGGAGAAAGAAAACTCAAAAGGC 57.478 39.130 0.00 0.00 35.17 4.35
492 497 3.187637 CCGAATAAAACGCACAAGGAGAA 59.812 43.478 0.00 0.00 0.00 2.87
493 498 2.739913 CCGAATAAAACGCACAAGGAGA 59.260 45.455 0.00 0.00 0.00 3.71
494 499 2.482721 ACCGAATAAAACGCACAAGGAG 59.517 45.455 0.00 0.00 0.00 3.69
495 500 2.496111 ACCGAATAAAACGCACAAGGA 58.504 42.857 0.00 0.00 0.00 3.36
496 501 2.981400 ACCGAATAAAACGCACAAGG 57.019 45.000 0.00 0.00 0.00 3.61
497 502 4.141855 AGAACCGAATAAAACGCACAAG 57.858 40.909 0.00 0.00 0.00 3.16
498 503 4.377635 GCTAGAACCGAATAAAACGCACAA 60.378 41.667 0.00 0.00 0.00 3.33
499 504 3.123959 GCTAGAACCGAATAAAACGCACA 59.876 43.478 0.00 0.00 0.00 4.57
500 505 3.370061 AGCTAGAACCGAATAAAACGCAC 59.630 43.478 0.00 0.00 0.00 5.34
525 531 3.803082 CCACAGCAATGGACCGCG 61.803 66.667 0.00 0.00 43.02 6.46
526 532 2.672996 ACCACAGCAATGGACCGC 60.673 61.111 12.88 0.00 43.02 5.68
527 533 0.677731 ATCACCACAGCAATGGACCG 60.678 55.000 12.88 1.93 43.02 4.79
529 535 2.423538 GGTAATCACCACAGCAATGGAC 59.576 50.000 12.88 0.67 45.04 4.02
530 536 2.722094 GGTAATCACCACAGCAATGGA 58.278 47.619 12.88 0.00 45.04 3.41
564 570 2.069273 GAAATCAGTGACCCGTCTGTG 58.931 52.381 0.00 0.00 33.89 3.66
565 571 1.691976 TGAAATCAGTGACCCGTCTGT 59.308 47.619 0.00 0.00 33.89 3.41
585 591 2.915349 CAGGCATCATAAGAGCACAGT 58.085 47.619 0.00 0.00 0.00 3.55
590 596 3.639538 CAAATGCAGGCATCATAAGAGC 58.360 45.455 7.29 0.00 35.31 4.09
591 597 3.639538 GCAAATGCAGGCATCATAAGAG 58.360 45.455 7.29 0.00 41.59 2.85
592 598 3.720949 GCAAATGCAGGCATCATAAGA 57.279 42.857 7.29 0.00 41.59 2.10
601 607 5.989293 CGTATTACGTTTGCAAATGCAGGC 61.989 45.833 27.36 14.66 43.85 4.85
602 608 3.541916 CGTATTACGTTTGCAAATGCAGG 59.458 43.478 27.36 13.75 43.85 4.85
603 609 4.720415 CGTATTACGTTTGCAAATGCAG 57.280 40.909 27.36 15.79 43.85 4.41
617 623 8.025445 TGAGAAGAACAAGGAAGTACGTATTAC 58.975 37.037 0.00 0.00 0.00 1.89
618 624 8.114331 TGAGAAGAACAAGGAAGTACGTATTA 57.886 34.615 0.00 0.00 0.00 0.98
619 625 6.989659 TGAGAAGAACAAGGAAGTACGTATT 58.010 36.000 0.00 0.00 0.00 1.89
623 629 5.529791 TCTTGAGAAGAACAAGGAAGTACG 58.470 41.667 0.00 0.00 43.11 3.67
624 630 7.971183 AATCTTGAGAAGAACAAGGAAGTAC 57.029 36.000 0.00 0.00 43.11 2.73
625 631 8.210946 TCAAATCTTGAGAAGAACAAGGAAGTA 58.789 33.333 0.00 0.00 43.11 2.24
626 632 7.056635 TCAAATCTTGAGAAGAACAAGGAAGT 58.943 34.615 0.00 0.00 43.11 3.01
627 633 7.502120 TCAAATCTTGAGAAGAACAAGGAAG 57.498 36.000 0.00 0.00 43.11 3.46
628 634 7.720957 TGATCAAATCTTGAGAAGAACAAGGAA 59.279 33.333 0.00 0.00 43.98 3.36
629 635 7.226441 TGATCAAATCTTGAGAAGAACAAGGA 58.774 34.615 0.00 0.00 43.98 3.36
630 636 7.444629 TGATCAAATCTTGAGAAGAACAAGG 57.555 36.000 0.00 0.00 43.98 3.61
631 637 9.909644 AATTGATCAAATCTTGAGAAGAACAAG 57.090 29.630 13.09 0.00 43.98 3.16
706 769 9.784531 AAAACATATCTTATGATGGACGAATCT 57.215 29.630 1.45 0.00 34.32 2.40
708 771 9.559732 TGAAAACATATCTTATGATGGACGAAT 57.440 29.630 1.45 0.00 34.32 3.34
709 772 8.956533 TGAAAACATATCTTATGATGGACGAA 57.043 30.769 1.45 0.00 34.32 3.85
710 773 8.992073 CATGAAAACATATCTTATGATGGACGA 58.008 33.333 1.45 0.00 34.32 4.20
711 774 8.777413 ACATGAAAACATATCTTATGATGGACG 58.223 33.333 0.00 0.00 34.32 4.79
830 897 1.200716 CATGTCATTGACACCACTGGC 59.799 52.381 21.19 0.00 45.65 4.85
855 922 0.034896 CCTTCGCAGGTGTAACTGGT 59.965 55.000 0.00 0.00 38.90 4.00
868 935 2.167487 AGGAGAGAGAAATGACCTTCGC 59.833 50.000 0.00 0.00 0.00 4.70
872 939 4.843516 AGAACAAGGAGAGAGAAATGACCT 59.156 41.667 0.00 0.00 0.00 3.85
953 1021 2.520741 GCCGAGGGGAGGAGAGAG 60.521 72.222 0.00 0.00 34.06 3.20
1259 1352 4.764771 AGTACGGGGCAGGCCGTA 62.765 66.667 6.98 9.09 42.72 4.02
1283 1376 2.543861 CGATTCGTATGGACCAGACCAG 60.544 54.545 13.58 0.86 43.49 4.00
1284 1377 1.407618 CGATTCGTATGGACCAGACCA 59.592 52.381 13.58 0.00 44.41 4.02
1285 1378 1.407979 ACGATTCGTATGGACCAGACC 59.592 52.381 13.58 0.00 38.73 3.85
1286 1379 2.865343 ACGATTCGTATGGACCAGAC 57.135 50.000 10.53 9.31 38.73 3.51
1327 1422 6.984474 TGAGAAACTACTAATAGCCAAATCGG 59.016 38.462 0.00 0.00 38.11 4.18
1335 1430 8.888579 TGGCTTATTGAGAAACTACTAATAGC 57.111 34.615 0.00 0.00 30.75 2.97
1339 1434 9.515226 ACAATTGGCTTATTGAGAAACTACTAA 57.485 29.630 10.83 0.00 38.56 2.24
1340 1435 8.946085 CACAATTGGCTTATTGAGAAACTACTA 58.054 33.333 10.83 0.00 38.56 1.82
1341 1436 7.575720 GCACAATTGGCTTATTGAGAAACTACT 60.576 37.037 10.83 0.00 38.56 2.57
1342 1437 6.528072 GCACAATTGGCTTATTGAGAAACTAC 59.472 38.462 10.83 0.00 38.56 2.73
1343 1438 6.350110 GGCACAATTGGCTTATTGAGAAACTA 60.350 38.462 10.83 0.00 44.99 2.24
1375 1472 3.731867 CGAAAGCTGTGCAAAAGTGACTT 60.732 43.478 0.00 0.00 0.00 3.01
1377 1474 2.111756 CGAAAGCTGTGCAAAAGTGAC 58.888 47.619 0.00 0.00 0.00 3.67
1381 1478 4.043750 TCAAATCGAAAGCTGTGCAAAAG 58.956 39.130 0.00 0.00 0.00 2.27
1390 1488 3.997021 ACTCGTCAATCAAATCGAAAGCT 59.003 39.130 0.00 0.00 32.12 3.74
1454 1552 2.404215 ACATGCAGACACGAACACTAC 58.596 47.619 0.00 0.00 0.00 2.73
1562 1660 2.992689 TCCGTGGTCTTGCCGCTA 60.993 61.111 0.00 0.00 45.36 4.26
1674 1892 8.250332 TCCAACTTATTTTGATGATAGTTTGCC 58.750 33.333 0.00 0.00 0.00 4.52
1699 1917 6.674694 AACTGAACATCATGTTAGCATCTC 57.325 37.500 2.04 0.00 41.28 2.75
1807 2025 4.764823 ACCAACGAAATGTCCATACAACAT 59.235 37.500 0.00 0.00 39.58 2.71
1809 2027 4.379082 GGACCAACGAAATGTCCATACAAC 60.379 45.833 11.40 0.00 46.29 3.32
1810 2028 3.754323 GGACCAACGAAATGTCCATACAA 59.246 43.478 11.40 0.00 46.29 2.41
1824 2042 5.621197 TGATTAATGAACAAGGACCAACG 57.379 39.130 0.00 0.00 0.00 4.10
1918 2136 1.551883 AGCTTGGATGCAAATGTTCCC 59.448 47.619 0.00 0.00 34.99 3.97
2055 2274 5.527951 TGCAACACACCATGAAAAGATAAC 58.472 37.500 0.00 0.00 0.00 1.89
2151 2370 1.007336 GCGACACTTGTAGGTGACCG 61.007 60.000 0.00 5.50 40.13 4.79
2268 2487 1.866853 GCACAAGGGTTGTAGGCAGC 61.867 60.000 0.00 0.00 43.23 5.25
2269 2488 0.537143 TGCACAAGGGTTGTAGGCAG 60.537 55.000 1.78 0.00 43.23 4.85
2421 2663 2.838202 AGTATGAACGTGGGATCTTGGT 59.162 45.455 0.00 0.00 0.00 3.67
2530 2887 2.922740 AAAGGCCGTAAACTGTGAGA 57.077 45.000 0.00 0.00 0.00 3.27
2543 2900 3.874392 ATCTGCATACACAAAAAGGCC 57.126 42.857 0.00 0.00 0.00 5.19
2816 3175 7.756722 CCTAATAAAACTGGAAAAGTGATGCAG 59.243 37.037 0.00 0.00 39.81 4.41
2911 3271 8.796475 AGTGATTACAAATGTATTGAAGCAAGT 58.204 29.630 0.00 0.00 0.00 3.16
2992 3352 6.232581 TGTCATGGTTGGAAGTCAAATTTT 57.767 33.333 0.00 0.00 37.08 1.82
3053 3413 6.547880 GGACAACATGGATAGAGAGAACTAGA 59.452 42.308 0.00 0.00 0.00 2.43
3193 3555 8.712363 CGGAACTAATCAATCCATGTAACATAG 58.288 37.037 0.00 0.00 32.58 2.23
3194 3556 8.208224 ACGGAACTAATCAATCCATGTAACATA 58.792 33.333 0.00 0.00 32.58 2.29
3195 3557 7.054124 ACGGAACTAATCAATCCATGTAACAT 58.946 34.615 0.00 0.00 32.58 2.71
3239 3601 5.510690 CGCTGGTACATCCCATCTGTAATTA 60.511 44.000 0.00 0.00 38.20 1.40
3240 3602 4.718961 GCTGGTACATCCCATCTGTAATT 58.281 43.478 0.00 0.00 38.20 1.40
3473 3846 8.593679 TCCATCTTTTCTGTTAGTTCATACAGA 58.406 33.333 0.00 0.00 46.57 3.41
3474 3847 8.777865 TCCATCTTTTCTGTTAGTTCATACAG 57.222 34.615 0.00 0.00 42.41 2.74
3475 3848 9.739276 ATTCCATCTTTTCTGTTAGTTCATACA 57.261 29.630 0.00 0.00 0.00 2.29
3477 3850 9.958180 TGATTCCATCTTTTCTGTTAGTTCATA 57.042 29.630 0.00 0.00 0.00 2.15
3478 3851 8.868522 TGATTCCATCTTTTCTGTTAGTTCAT 57.131 30.769 0.00 0.00 0.00 2.57
3479 3852 7.939039 ACTGATTCCATCTTTTCTGTTAGTTCA 59.061 33.333 0.00 0.00 0.00 3.18
3480 3853 8.329203 ACTGATTCCATCTTTTCTGTTAGTTC 57.671 34.615 0.00 0.00 0.00 3.01
3481 3854 9.220767 GTACTGATTCCATCTTTTCTGTTAGTT 57.779 33.333 0.00 0.00 0.00 2.24
3482 3855 8.598041 AGTACTGATTCCATCTTTTCTGTTAGT 58.402 33.333 0.00 0.00 0.00 2.24
3483 3856 9.442047 AAGTACTGATTCCATCTTTTCTGTTAG 57.558 33.333 0.00 0.00 0.00 2.34
3484 3857 9.793259 AAAGTACTGATTCCATCTTTTCTGTTA 57.207 29.630 0.00 0.00 0.00 2.41
3485 3858 8.697507 AAAGTACTGATTCCATCTTTTCTGTT 57.302 30.769 0.00 0.00 0.00 3.16
3486 3859 8.697507 AAAAGTACTGATTCCATCTTTTCTGT 57.302 30.769 0.00 0.00 32.19 3.41
3493 3866 9.771534 GAAGCTATAAAAGTACTGATTCCATCT 57.228 33.333 0.00 0.00 0.00 2.90
3494 3867 8.994170 GGAAGCTATAAAAGTACTGATTCCATC 58.006 37.037 16.54 1.83 34.10 3.51
3495 3868 8.494433 TGGAAGCTATAAAAGTACTGATTCCAT 58.506 33.333 18.98 4.14 37.98 3.41
3496 3869 7.769044 GTGGAAGCTATAAAAGTACTGATTCCA 59.231 37.037 18.98 18.98 39.95 3.53
3497 3870 7.042658 CGTGGAAGCTATAAAAGTACTGATTCC 60.043 40.741 15.23 15.23 34.43 3.01
3498 3871 7.516943 GCGTGGAAGCTATAAAAGTACTGATTC 60.517 40.741 0.00 0.00 0.00 2.52
3499 3872 6.258068 GCGTGGAAGCTATAAAAGTACTGATT 59.742 38.462 0.00 0.00 0.00 2.57
3540 3913 7.360353 CCAACATGTGACACTTAAGACATACTG 60.360 40.741 10.09 8.48 0.00 2.74
3541 3914 6.650807 CCAACATGTGACACTTAAGACATACT 59.349 38.462 10.09 0.00 0.00 2.12
3542 3915 6.649141 TCCAACATGTGACACTTAAGACATAC 59.351 38.462 10.09 3.89 0.00 2.39
3543 3916 6.649141 GTCCAACATGTGACACTTAAGACATA 59.351 38.462 10.09 5.39 0.00 2.29
3544 3917 5.470098 GTCCAACATGTGACACTTAAGACAT 59.530 40.000 10.09 5.60 0.00 3.06
3572 3948 5.855740 AGAACTAGGCATAGTCCAGTAAC 57.144 43.478 12.09 0.00 41.54 2.50
3682 4058 2.421073 TGATGCTAAATCTGTGCAGCAC 59.579 45.455 19.37 19.37 46.01 4.40
3720 4096 5.221126 GCGGATTAAGAGCCTTCATTTCAAT 60.221 40.000 0.00 0.00 0.00 2.57
3758 4134 7.712639 GCTCAACATTCTCAAGAAGATACCATA 59.287 37.037 0.00 0.00 37.48 2.74
3933 4313 0.452184 GAGAGGATCGAACTGACGCA 59.548 55.000 0.00 0.00 42.67 5.24
3980 4360 5.376854 ACCATTCATTCTGTACTTTGTGC 57.623 39.130 0.00 0.00 0.00 4.57
4031 4411 9.626045 CTTTTCAATCCTTCCAAAATACTGTAC 57.374 33.333 0.00 0.00 0.00 2.90
4051 4431 3.318839 CCATGAGAAGTTGTGGCTTTTCA 59.681 43.478 0.00 2.38 41.62 2.69
4124 4504 1.873591 CCTTCCAGTTTTGTCAGGACG 59.126 52.381 0.00 0.00 0.00 4.79
4178 4558 6.703607 AGCTTTGATATTCAGGAATCACTACG 59.296 38.462 0.00 0.00 31.99 3.51
4190 4570 7.716799 ACCCAAACATTAGCTTTGATATTCA 57.283 32.000 0.00 0.00 31.32 2.57
4205 4585 2.355412 GCTCCGGTTAGTACCCAAACAT 60.355 50.000 0.00 0.00 41.75 2.71
4214 4594 3.022557 ACCATAGTGCTCCGGTTAGTA 57.977 47.619 0.00 0.00 0.00 1.82
4260 4640 4.702831 GAAAACCTGGAAAATGGCAAGAA 58.297 39.130 0.00 0.00 0.00 2.52
4298 4678 2.032550 GTGGCTGCTAACATATGCACTG 59.967 50.000 1.58 0.00 35.20 3.66
4333 4713 2.034124 AGCAGCAAAAAGGAGCTTGAA 58.966 42.857 0.00 0.00 39.50 2.69
4409 4791 9.480053 CCCATTTCGCATATCTAATTTTTGATT 57.520 29.630 0.00 0.00 0.00 2.57
4412 4794 6.700960 TGCCCATTTCGCATATCTAATTTTTG 59.299 34.615 0.00 0.00 0.00 2.44
4517 8805 6.631962 AGATAGCATACCGAGCTAATTTACC 58.368 40.000 0.00 0.00 46.55 2.85
4519 8807 7.462571 TGAGATAGCATACCGAGCTAATTTA 57.537 36.000 0.00 0.00 46.55 1.40
4520 8808 6.346477 TGAGATAGCATACCGAGCTAATTT 57.654 37.500 0.00 0.00 46.55 1.82
4521 8809 5.984695 TGAGATAGCATACCGAGCTAATT 57.015 39.130 0.00 0.00 46.55 1.40
4522 8810 5.984695 TTGAGATAGCATACCGAGCTAAT 57.015 39.130 0.00 0.00 46.55 1.73
4535 8823 5.975939 GCTGGATGTTTGAATTTGAGATAGC 59.024 40.000 0.00 0.00 0.00 2.97
4547 8835 3.009363 TCATCTTCCTGCTGGATGTTTGA 59.991 43.478 20.44 19.80 42.81 2.69
4583 8871 4.466015 CCCAAAATTACAGTACAATGGCCT 59.534 41.667 3.32 0.00 0.00 5.19
4597 8901 4.062293 CGTAGATCATCGGCCCAAAATTA 58.938 43.478 0.00 0.00 0.00 1.40
4610 8914 6.424032 TGTAGATACTATGGCCGTAGATCAT 58.576 40.000 34.04 23.03 0.00 2.45
4625 8929 6.380274 TCGAACAAGGGAAGATTGTAGATACT 59.620 38.462 0.00 0.00 39.91 2.12
4633 8937 3.191162 TGCAATCGAACAAGGGAAGATTG 59.809 43.478 10.92 10.92 46.32 2.67
4649 8953 7.443575 ACTGTGATAATTACTCCTGATGCAATC 59.556 37.037 0.00 0.00 45.83 2.67
4650 8954 7.285566 ACTGTGATAATTACTCCTGATGCAAT 58.714 34.615 0.00 0.00 0.00 3.56
4667 8979 5.538813 AGGAATGACGGCTTATACTGTGATA 59.461 40.000 0.00 0.00 0.00 2.15
4672 8984 4.051922 GTGAGGAATGACGGCTTATACTG 58.948 47.826 0.00 0.00 0.00 2.74
4700 9012 0.970937 CAGGTAGAACGCCCTCCTCA 60.971 60.000 0.00 0.00 0.00 3.86
4710 9022 6.874134 TAAGCATTCTTCAGTTCAGGTAGAAC 59.126 38.462 0.00 0.00 43.48 3.01
4732 9044 3.258622 ACTGTTTCTCCCGAGGAAGTAAG 59.741 47.826 0.00 0.00 0.00 2.34
4736 9048 1.896465 AGACTGTTTCTCCCGAGGAAG 59.104 52.381 0.00 0.00 0.00 3.46
4789 9101 3.254654 CGCGCACGTACAGGATGG 61.255 66.667 8.75 0.00 35.45 3.51
4805 9117 1.959899 CTAACAGACCTTGCGCTGCG 61.960 60.000 19.17 19.17 35.57 5.18
4818 9136 2.301870 TGGTTAGGTGCAGGACTAACAG 59.698 50.000 25.12 0.00 46.73 3.16
4857 9189 3.192844 AGACATGGCAGAATTCTTTGCAG 59.807 43.478 18.25 11.26 42.02 4.41
4858 9190 3.159472 AGACATGGCAGAATTCTTTGCA 58.841 40.909 18.25 7.73 42.02 4.08
4859 9191 3.863142 AGACATGGCAGAATTCTTTGC 57.137 42.857 4.86 8.20 39.56 3.68
4860 9192 4.461781 AGGAAGACATGGCAGAATTCTTTG 59.538 41.667 4.86 4.28 0.00 2.77
4861 9193 4.670765 AGGAAGACATGGCAGAATTCTTT 58.329 39.130 4.86 0.00 0.00 2.52
4862 9194 4.268359 GAGGAAGACATGGCAGAATTCTT 58.732 43.478 4.86 0.00 0.00 2.52
4863 9195 3.371380 GGAGGAAGACATGGCAGAATTCT 60.371 47.826 0.00 0.88 0.00 2.40
4864 9196 2.948315 GGAGGAAGACATGGCAGAATTC 59.052 50.000 0.00 0.00 0.00 2.17
4865 9197 2.309755 TGGAGGAAGACATGGCAGAATT 59.690 45.455 0.00 0.00 0.00 2.17
4884 9216 4.498241 TCTGAAATCTGAACTGACGATGG 58.502 43.478 0.00 0.00 0.00 3.51
4900 9232 0.036483 TAGGTGCGCATGCTCTGAAA 60.036 50.000 15.91 0.00 43.34 2.69
4910 9242 1.676678 GATGGAGAGGTAGGTGCGCA 61.677 60.000 5.66 5.66 0.00 6.09
4911 9243 1.068250 GATGGAGAGGTAGGTGCGC 59.932 63.158 0.00 0.00 0.00 6.09
4927 9259 6.240176 GGTGAACTAGAGGGAGATAGAGAGAT 60.240 46.154 0.00 0.00 0.00 2.75
4958 9298 5.067023 CCATCCTTCCTTGCTTGTATCTTTC 59.933 44.000 0.00 0.00 0.00 2.62
4962 9302 4.156455 TCCATCCTTCCTTGCTTGTATC 57.844 45.455 0.00 0.00 0.00 2.24
4964 9304 4.018506 TGATTCCATCCTTCCTTGCTTGTA 60.019 41.667 0.00 0.00 0.00 2.41
4965 9305 2.978156 TTCCATCCTTCCTTGCTTGT 57.022 45.000 0.00 0.00 0.00 3.16
4973 9313 2.555199 CGTGTCTGATTCCATCCTTCC 58.445 52.381 0.00 0.00 0.00 3.46
4979 9319 1.402968 GCATTGCGTGTCTGATTCCAT 59.597 47.619 0.00 0.00 0.00 3.41
4993 9333 1.001745 GGTTGTTTCGACGGCATTGC 61.002 55.000 0.00 0.00 0.00 3.56
5152 9495 2.870411 GCATAGGATGGTGACGGTTAAC 59.130 50.000 0.00 0.00 0.00 2.01
5154 9497 2.102420 CTGCATAGGATGGTGACGGTTA 59.898 50.000 0.00 0.00 0.00 2.85
5155 9498 0.908910 TGCATAGGATGGTGACGGTT 59.091 50.000 0.00 0.00 0.00 4.44
5156 9499 0.465705 CTGCATAGGATGGTGACGGT 59.534 55.000 0.00 0.00 0.00 4.83
5157 9500 0.882042 GCTGCATAGGATGGTGACGG 60.882 60.000 0.00 0.00 0.00 4.79
5158 9501 0.179076 TGCTGCATAGGATGGTGACG 60.179 55.000 0.00 0.00 0.00 4.35
5159 9502 1.672881 GTTGCTGCATAGGATGGTGAC 59.327 52.381 1.84 0.00 0.00 3.67
5160 9503 1.281577 TGTTGCTGCATAGGATGGTGA 59.718 47.619 1.84 0.00 0.00 4.02
5161 9504 1.674441 CTGTTGCTGCATAGGATGGTG 59.326 52.381 1.84 0.00 0.00 4.17
5162 9505 2.020694 GCTGTTGCTGCATAGGATGGT 61.021 52.381 1.84 0.00 36.03 3.55
5163 9506 0.666913 GCTGTTGCTGCATAGGATGG 59.333 55.000 1.84 0.00 36.03 3.51
5164 9507 0.306840 CGCTGTTGCTGCATAGGATG 59.693 55.000 1.84 0.00 36.97 3.51
5165 9508 0.816825 CCGCTGTTGCTGCATAGGAT 60.817 55.000 1.84 0.00 36.97 3.24
5166 9509 1.450134 CCGCTGTTGCTGCATAGGA 60.450 57.895 1.84 0.00 36.97 2.94
5167 9510 2.475466 CCCGCTGTTGCTGCATAGG 61.475 63.158 1.84 2.91 36.97 2.57
5168 9511 2.475466 CCCCGCTGTTGCTGCATAG 61.475 63.158 1.84 6.61 36.97 2.23
5169 9512 2.438254 CCCCGCTGTTGCTGCATA 60.438 61.111 1.84 0.00 36.97 3.14
5184 9527 1.074248 TCCGAGAACTTTTGCCCCC 59.926 57.895 0.00 0.00 0.00 5.40
5185 9528 0.250770 AGTCCGAGAACTTTTGCCCC 60.251 55.000 0.00 0.00 0.00 5.80
5186 9529 1.605753 AAGTCCGAGAACTTTTGCCC 58.394 50.000 0.00 0.00 36.02 5.36


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

AutoCloner maintained by Alex Coulton.