Multiple sequence alignment - TraesCS6A01G347800

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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 TraesCS6A01G347800 chr6A 100.000 8154 0 0 1 8154 580195445 580203598 0.000000e+00 15058.0
1 TraesCS6A01G347800 chr6D 92.157 3570 163 53 14 3527 433928858 433932366 0.000000e+00 4933.0
2 TraesCS6A01G347800 chr6D 94.615 1857 58 12 6305 8154 433935502 433937323 0.000000e+00 2837.0
3 TraesCS6A01G347800 chr6D 93.606 1001 53 8 4575 5570 433933422 433934416 0.000000e+00 1483.0
4 TraesCS6A01G347800 chr6D 94.194 689 35 4 3870 4557 433932752 433933436 0.000000e+00 1046.0
5 TraesCS6A01G347800 chr6D 93.846 325 10 2 3548 3871 433932360 433932675 1.590000e-131 481.0
6 TraesCS6A01G347800 chr6D 88.462 364 24 6 5573 5926 433934523 433934878 2.720000e-114 424.0
7 TraesCS6A01G347800 chr6D 88.596 342 31 6 5974 6308 433934875 433935215 7.620000e-110 409.0
8 TraesCS6A01G347800 chr6D 79.630 108 16 5 7692 7795 433936822 433936927 1.140000e-08 73.1
9 TraesCS6A01G347800 chr6B 92.049 3119 123 45 817 3871 656273574 656276631 0.000000e+00 4270.0
10 TraesCS6A01G347800 chr6B 92.135 1335 71 18 6306 7629 656279567 656280878 0.000000e+00 1853.0
11 TraesCS6A01G347800 chr6B 95.536 896 24 4 5203 6091 656278165 656279051 0.000000e+00 1419.0
12 TraesCS6A01G347800 chr6B 95.349 645 25 5 4573 5215 656277338 656277979 0.000000e+00 1020.0
13 TraesCS6A01G347800 chr6B 93.976 498 21 4 3874 4363 656276720 656277216 0.000000e+00 745.0
14 TraesCS6A01G347800 chr6B 89.445 559 45 7 4675 5231 679380005 679380551 0.000000e+00 693.0
15 TraesCS6A01G347800 chr6B 90.331 393 27 4 7765 8154 656280933 656281317 9.440000e-139 505.0
16 TraesCS6A01G347800 chr6B 93.684 190 12 0 6130 6319 656279048 656279237 1.340000e-72 285.0
17 TraesCS6A01G347800 chr6B 92.593 189 11 2 608 796 656273131 656273316 1.350000e-67 268.0
18 TraesCS6A01G347800 chr6B 86.400 125 17 0 8030 8154 655765435 655765311 3.970000e-28 137.0
19 TraesCS6A01G347800 chr2B 90.126 557 41 7 4677 5231 184676622 184677166 0.000000e+00 712.0
20 TraesCS6A01G347800 chr2B 89.624 559 44 7 4675 5231 26144976 26144430 0.000000e+00 699.0
21 TraesCS6A01G347800 chr2B 81.614 446 61 10 1 439 383616374 383615943 4.680000e-92 350.0
22 TraesCS6A01G347800 chr7B 90.126 557 39 8 4677 5231 42788239 42788781 0.000000e+00 710.0
23 TraesCS6A01G347800 chr7B 89.946 557 41 8 4677 5231 747439089 747438546 0.000000e+00 704.0
24 TraesCS6A01G347800 chr3B 88.612 562 47 9 4675 5231 467058141 467057592 0.000000e+00 667.0
25 TraesCS6A01G347800 chr3B 94.118 51 3 0 7778 7828 422472216 422472166 2.440000e-10 78.7
26 TraesCS6A01G347800 chr4D 82.805 442 57 11 4 439 445089123 445088695 2.150000e-100 377.0
27 TraesCS6A01G347800 chr4D 95.833 48 2 0 7776 7823 301533960 301533913 2.440000e-10 78.7
28 TraesCS6A01G347800 chr4D 90.909 55 5 0 7776 7830 99524771 99524825 3.160000e-09 75.0
29 TraesCS6A01G347800 chr4A 82.921 445 51 14 1 439 689651029 689651454 2.150000e-100 377.0
30 TraesCS6A01G347800 chr1B 82.511 446 58 10 1 439 178726273 178725841 2.780000e-99 374.0
31 TraesCS6A01G347800 chr1B 95.745 47 2 0 7777 7823 145721585 145721539 8.780000e-10 76.8
32 TraesCS6A01G347800 chr3A 82.500 440 56 14 2 434 45772878 45773303 4.650000e-97 366.0
33 TraesCS6A01G347800 chr5D 82.262 451 52 20 3 443 373777946 373777514 1.670000e-96 364.0
34 TraesCS6A01G347800 chr1D 81.081 481 64 15 1 473 37415812 37415351 7.780000e-95 359.0
35 TraesCS6A01G347800 chr1D 82.103 447 55 17 1 439 487775914 487775485 7.780000e-95 359.0
36 TraesCS6A01G347800 chr4B 88.031 259 19 5 4977 5235 69452660 69452906 6.190000e-76 296.0
37 TraesCS6A01G347800 chr7D 90.667 75 5 2 404 477 208214613 208214686 1.870000e-16 99.0
38 TraesCS6A01G347800 chr3D 97.872 47 1 0 7777 7823 571136232 571136278 1.890000e-11 82.4
39 TraesCS6A01G347800 chr5B 92.308 52 3 1 7777 7828 327750320 327750370 1.140000e-08 73.1
40 TraesCS6A01G347800 chr5B 93.750 48 2 1 7694 7741 617829987 617829941 4.080000e-08 71.3
41 TraesCS6A01G347800 chr1A 93.750 48 3 0 7694 7741 588015384 588015337 1.140000e-08 73.1
42 TraesCS6A01G347800 chr1A 97.500 40 1 0 7777 7816 540110138 540110177 1.470000e-07 69.4
43 TraesCS6A01G347800 chr2D 89.583 48 5 0 417 464 45563455 45563502 2.460000e-05 62.1


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6A01G347800 chr6A 580195445 580203598 8153 False 15058.0000 15058 100.000000 1 8154 1 chr6A.!!$F1 8153
1 TraesCS6A01G347800 chr6D 433928858 433937323 8465 False 1460.7625 4933 90.638250 14 8154 8 chr6D.!!$F1 8140
2 TraesCS6A01G347800 chr6B 656273131 656281317 8186 False 1295.6250 4270 93.206625 608 8154 8 chr6B.!!$F2 7546
3 TraesCS6A01G347800 chr6B 679380005 679380551 546 False 693.0000 693 89.445000 4675 5231 1 chr6B.!!$F1 556
4 TraesCS6A01G347800 chr2B 184676622 184677166 544 False 712.0000 712 90.126000 4677 5231 1 chr2B.!!$F1 554
5 TraesCS6A01G347800 chr2B 26144430 26144976 546 True 699.0000 699 89.624000 4675 5231 1 chr2B.!!$R1 556
6 TraesCS6A01G347800 chr7B 42788239 42788781 542 False 710.0000 710 90.126000 4677 5231 1 chr7B.!!$F1 554
7 TraesCS6A01G347800 chr7B 747438546 747439089 543 True 704.0000 704 89.946000 4677 5231 1 chr7B.!!$R1 554
8 TraesCS6A01G347800 chr3B 467057592 467058141 549 True 667.0000 667 88.612000 4675 5231 1 chr3B.!!$R2 556

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
478 479 0.394352 GGGTTGCGATTGGAGATGGT 60.394 55.000 0.00 0.00 0.00 3.55 F
479 480 1.017387 GGTTGCGATTGGAGATGGTC 58.983 55.000 0.00 0.00 0.00 4.02 F
786 792 1.134280 CCAGTCCACCTAATCAGCCTG 60.134 57.143 0.00 0.00 0.00 4.85 F
1717 1968 0.526524 GCGTCTTGTGATCCGAGGAG 60.527 60.000 0.00 0.00 0.00 3.69 F
2175 2450 0.952984 GAAGACAGGTGCAGAGCCAC 60.953 60.000 0.00 0.00 35.00 5.01 F
3105 3402 1.291877 GGCCGATATGCGATGACACC 61.292 60.000 0.00 0.00 44.57 4.16 F
4197 4615 0.595588 TGTGTAATTTGGTGCAGGCG 59.404 50.000 0.00 0.00 0.00 5.52 F
5126 5551 2.803030 AAGCTGGATGTGATTCTGCT 57.197 45.000 0.00 0.00 0.00 4.24 F
6519 7721 0.801251 GTTGGTAGCTGAGCTTGCTG 59.199 55.000 14.14 0.81 41.32 4.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1711 1962 0.684479 TCACACCATCCTCCTCCTCG 60.684 60.000 0.00 0.00 0.00 4.63 R
1715 1966 1.153549 GCGTCACACCATCCTCCTC 60.154 63.158 0.00 0.00 0.00 3.71 R
2082 2346 1.341209 TCACTACTGTCACCTGCACAG 59.659 52.381 0.02 0.02 45.86 3.66 R
3044 3341 1.453155 CAAGGTCATTTCCTGTCCCG 58.547 55.000 0.00 0.00 37.93 5.14 R
3968 4380 1.134128 TGCAGAGTCAAAGAGTGGCAA 60.134 47.619 0.00 0.00 32.63 4.52 R
5049 5474 0.251341 ATGGGAGAACTTGGGTGCAC 60.251 55.000 8.80 8.80 0.00 4.57 R
5312 5935 2.188817 GGAGTACAGAACCATCCCTGT 58.811 52.381 0.00 0.00 44.81 4.00 R
6883 8093 0.531657 TCAATGCAAAATCAGGGCGG 59.468 50.000 0.00 0.00 0.00 6.13 R
8072 9293 0.835543 CAGAGGATAGAGGGGGCAGG 60.836 65.000 0.00 0.00 0.00 4.85 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 2.026879 GGCAGAGGACGAGATCGC 59.973 66.667 1.39 0.00 44.43 4.58
33 34 0.869454 GCAGAGGACGAGATCGCAAG 60.869 60.000 1.39 0.00 44.43 4.01
39 40 2.737252 AGGACGAGATCGCAAGTTTTTC 59.263 45.455 1.39 0.00 44.43 2.29
40 41 2.737252 GGACGAGATCGCAAGTTTTTCT 59.263 45.455 1.39 0.00 44.43 2.52
41 42 3.186613 GGACGAGATCGCAAGTTTTTCTT 59.813 43.478 1.39 0.00 44.43 2.52
42 43 4.387083 GACGAGATCGCAAGTTTTTCTTC 58.613 43.478 1.39 0.00 44.43 2.87
48 49 4.552166 TCGCAAGTTTTTCTTCCTCTTG 57.448 40.909 0.00 0.00 38.60 3.02
53 54 5.517904 CAAGTTTTTCTTCCTCTTGCTCAG 58.482 41.667 0.00 0.00 33.63 3.35
117 118 4.286297 ACACATTATATGTAGCCCGCAT 57.714 40.909 0.00 0.00 42.70 4.73
156 157 3.071023 CCATATAGGGACAACCATCACGT 59.929 47.826 0.00 0.00 43.89 4.49
167 168 1.082561 CATCACGTGCACACACTGC 60.083 57.895 18.64 0.00 45.10 4.40
182 183 3.316029 CACACTGCTGGATGAAACTGAAA 59.684 43.478 0.00 0.00 0.00 2.69
211 212 0.537188 GTGTGGGACGACATGATCCT 59.463 55.000 0.00 0.00 35.15 3.24
230 231 5.336150 TCCTTTCATGCAAAACTTGTTGA 57.664 34.783 0.00 0.00 0.00 3.18
259 260 6.441924 TCCAGGATCTAGTTGAATTTGAGACT 59.558 38.462 0.00 0.00 0.00 3.24
287 288 2.044123 ACTAGGCCTAACTTGCATGC 57.956 50.000 14.85 11.82 0.00 4.06
296 297 4.083110 GCCTAACTTGCATGCTATGTATGG 60.083 45.833 20.33 17.75 0.00 2.74
297 298 5.308014 CCTAACTTGCATGCTATGTATGGA 58.692 41.667 20.33 0.00 0.00 3.41
298 299 5.942236 CCTAACTTGCATGCTATGTATGGAT 59.058 40.000 20.33 2.55 0.00 3.41
299 300 5.700722 AACTTGCATGCTATGTATGGATG 57.299 39.130 20.33 0.00 36.53 3.51
300 301 4.077108 ACTTGCATGCTATGTATGGATGG 58.923 43.478 20.33 0.00 34.51 3.51
311 312 5.717078 ATGTATGGATGGATGATTTGTGC 57.283 39.130 0.00 0.00 0.00 4.57
325 326 6.618287 TGATTTGTGCTATTTTCTATCCGG 57.382 37.500 0.00 0.00 0.00 5.14
341 342 7.539034 TCTATCCGGACTTTGATGAATATCA 57.461 36.000 6.12 0.00 41.44 2.15
354 355 6.287525 TGATGAATATCAGTCGGTTTGCATA 58.712 36.000 0.00 0.00 38.37 3.14
372 373 5.623335 TGCATAAATTTCGTTCGGTTAGTG 58.377 37.500 0.00 0.00 0.00 2.74
380 381 3.132160 TCGTTCGGTTAGTGAAAATGCA 58.868 40.909 0.00 0.00 0.00 3.96
385 386 5.295431 TCGGTTAGTGAAAATGCAGATTG 57.705 39.130 0.00 0.00 0.00 2.67
395 396 7.277098 AGTGAAAATGCAGATTGAAATGTATGC 59.723 33.333 0.00 0.00 0.00 3.14
400 401 3.250762 GCAGATTGAAATGTATGCGGCTA 59.749 43.478 0.00 0.00 0.00 3.93
430 431 1.745320 GCGTCCTCCCATATCCGTGT 61.745 60.000 0.00 0.00 0.00 4.49
437 438 1.396607 CCCATATCCGTGTCCGTGGA 61.397 60.000 0.00 0.00 38.95 4.02
455 456 1.330829 GGACGGATGCGGAAGAAAATC 59.669 52.381 12.44 0.00 0.00 2.17
474 475 2.435938 GCGGGTTGCGATTGGAGA 60.436 61.111 0.00 0.00 0.00 3.71
475 476 1.819632 GCGGGTTGCGATTGGAGAT 60.820 57.895 0.00 0.00 0.00 2.75
476 477 2.016961 CGGGTTGCGATTGGAGATG 58.983 57.895 0.00 0.00 0.00 2.90
477 478 1.439353 CGGGTTGCGATTGGAGATGG 61.439 60.000 0.00 0.00 0.00 3.51
478 479 0.394352 GGGTTGCGATTGGAGATGGT 60.394 55.000 0.00 0.00 0.00 3.55
479 480 1.017387 GGTTGCGATTGGAGATGGTC 58.983 55.000 0.00 0.00 0.00 4.02
562 568 5.410132 GCCCTCTAGAAAGAGTTTTGACTTC 59.590 44.000 0.00 0.00 46.80 3.01
566 572 8.093927 CCTCTAGAAAGAGTTTTGACTTCAGAT 58.906 37.037 0.00 0.00 46.80 2.90
593 599 6.496144 TCTGTGGAGCACTACTATCTACTA 57.504 41.667 0.00 0.00 35.11 1.82
595 601 6.099990 TCTGTGGAGCACTACTATCTACTACT 59.900 42.308 0.00 0.00 35.11 2.57
596 602 6.289834 TGTGGAGCACTACTATCTACTACTC 58.710 44.000 0.00 0.00 35.11 2.59
597 603 5.702209 GTGGAGCACTACTATCTACTACTCC 59.298 48.000 0.00 0.00 41.24 3.85
598 604 5.607592 TGGAGCACTACTATCTACTACTCCT 59.392 44.000 0.00 0.00 41.40 3.69
599 605 6.786461 TGGAGCACTACTATCTACTACTCCTA 59.214 42.308 0.00 0.00 41.40 2.94
600 606 7.099120 GGAGCACTACTATCTACTACTCCTAC 58.901 46.154 0.00 0.00 38.49 3.18
601 607 7.038799 GGAGCACTACTATCTACTACTCCTACT 60.039 44.444 0.00 0.00 38.49 2.57
602 608 7.899973 AGCACTACTATCTACTACTCCTACTC 58.100 42.308 0.00 0.00 0.00 2.59
603 609 7.038799 AGCACTACTATCTACTACTCCTACTCC 60.039 44.444 0.00 0.00 0.00 3.85
604 610 7.315142 CACTACTATCTACTACTCCTACTCCG 58.685 46.154 0.00 0.00 0.00 4.63
611 617 4.946478 ACTACTCCTACTCCGTATACGT 57.054 45.455 22.87 8.21 37.74 3.57
613 619 5.053145 ACTACTCCTACTCCGTATACGTTG 58.947 45.833 22.87 16.64 37.74 4.10
645 651 2.125952 GAAAACGCCAGCCATGCC 60.126 61.111 0.00 0.00 0.00 4.40
685 691 4.156182 CGCGTCAAGAAAAGTAAATTCCC 58.844 43.478 0.00 0.00 0.00 3.97
686 692 4.083484 CGCGTCAAGAAAAGTAAATTCCCT 60.083 41.667 0.00 0.00 0.00 4.20
688 694 5.048991 GCGTCAAGAAAAGTAAATTCCCTCA 60.049 40.000 0.00 0.00 0.00 3.86
714 720 5.693104 TGTAACGAAAAGACGTAAATGCTCT 59.307 36.000 0.00 0.00 45.83 4.09
715 721 4.905412 ACGAAAAGACGTAAATGCTCTC 57.095 40.909 0.00 0.00 44.72 3.20
786 792 1.134280 CCAGTCCACCTAATCAGCCTG 60.134 57.143 0.00 0.00 0.00 4.85
800 836 2.833121 CCTGCCCCCGCATTAACC 60.833 66.667 0.00 0.00 46.11 2.85
827 863 6.144845 ACTTTATTCCCTGCCTGCATATAT 57.855 37.500 0.00 0.00 0.00 0.86
828 864 5.948162 ACTTTATTCCCTGCCTGCATATATG 59.052 40.000 8.45 8.45 0.00 1.78
911 1153 2.738743 TCTTTCCCCAATTCATCCAGC 58.261 47.619 0.00 0.00 0.00 4.85
912 1154 2.312741 TCTTTCCCCAATTCATCCAGCT 59.687 45.455 0.00 0.00 0.00 4.24
913 1155 2.442236 TTCCCCAATTCATCCAGCTC 57.558 50.000 0.00 0.00 0.00 4.09
955 1198 2.540265 GCTGCCTAGCTGTGATACAT 57.460 50.000 0.00 0.00 46.57 2.29
956 1199 3.667497 GCTGCCTAGCTGTGATACATA 57.333 47.619 0.00 0.00 46.57 2.29
957 1200 3.321497 GCTGCCTAGCTGTGATACATAC 58.679 50.000 0.00 0.00 46.57 2.39
958 1201 3.006323 GCTGCCTAGCTGTGATACATACT 59.994 47.826 0.00 0.00 46.57 2.12
959 1202 4.804108 CTGCCTAGCTGTGATACATACTC 58.196 47.826 0.00 0.00 0.00 2.59
960 1203 3.574396 TGCCTAGCTGTGATACATACTCC 59.426 47.826 0.00 0.00 0.00 3.85
961 1204 3.829601 GCCTAGCTGTGATACATACTCCT 59.170 47.826 0.00 0.00 0.00 3.69
1446 1692 1.452108 CGTGCTCCCTCCCAATTCC 60.452 63.158 0.00 0.00 0.00 3.01
1478 1725 2.680913 CCTCGCCTTGCTTTCGTGG 61.681 63.158 0.00 0.00 0.00 4.94
1512 1759 2.159476 TGCTACTACTTGTTACTCCGCG 60.159 50.000 0.00 0.00 0.00 6.46
1571 1821 6.605119 CAGGGAATTGGTTTAGAGATACCAT 58.395 40.000 0.00 0.00 43.56 3.55
1574 1824 8.218488 AGGGAATTGGTTTAGAGATACCATTAC 58.782 37.037 0.00 0.00 43.56 1.89
1575 1825 8.218488 GGGAATTGGTTTAGAGATACCATTACT 58.782 37.037 0.00 0.00 43.56 2.24
1576 1826 9.274206 GGAATTGGTTTAGAGATACCATTACTC 57.726 37.037 0.00 0.00 43.56 2.59
1577 1827 8.888579 AATTGGTTTAGAGATACCATTACTCG 57.111 34.615 0.00 0.00 43.56 4.18
1578 1828 7.414222 TTGGTTTAGAGATACCATTACTCGT 57.586 36.000 0.00 0.00 43.56 4.18
1579 1829 8.523915 TTGGTTTAGAGATACCATTACTCGTA 57.476 34.615 0.00 0.00 43.56 3.43
1580 1830 7.934457 TGGTTTAGAGATACCATTACTCGTAC 58.066 38.462 0.00 0.00 39.44 3.67
1617 1867 3.143728 GGTAATACACCCCATTTAGGCG 58.856 50.000 0.00 0.00 42.07 5.52
1625 1875 2.668144 CCCATTTAGGCGGGGATTAA 57.332 50.000 0.00 0.00 45.08 1.40
1711 1962 2.167861 GCTCCGCGTCTTGTGATCC 61.168 63.158 4.92 0.00 0.00 3.36
1715 1966 1.874019 CGCGTCTTGTGATCCGAGG 60.874 63.158 0.00 0.00 0.00 4.63
1716 1967 1.511305 GCGTCTTGTGATCCGAGGA 59.489 57.895 0.00 0.00 0.00 3.71
1717 1968 0.526524 GCGTCTTGTGATCCGAGGAG 60.527 60.000 0.00 0.00 0.00 3.69
1735 1986 2.509336 GAGGATGGTGTGACGCGG 60.509 66.667 12.47 0.00 0.00 6.46
1769 2020 5.078411 AGTTGCCTAGTATGTGTTGAGAG 57.922 43.478 0.00 0.00 0.00 3.20
1781 2032 1.827344 TGTTGAGAGGATCGTCATGCT 59.173 47.619 17.19 0.00 42.67 3.79
1973 2237 4.864916 AATAAACGTATGCTGCTGTGAG 57.135 40.909 0.00 0.00 0.00 3.51
1998 2262 1.273606 CCATCAGACCGTGTCTCACTT 59.726 52.381 3.87 0.00 41.37 3.16
2081 2345 2.456443 GGGGAAGGAGGGAGGATGC 61.456 68.421 0.00 0.00 0.00 3.91
2138 2407 9.757227 AATGAGACTGTCTATAATTTGTAGCTC 57.243 33.333 10.86 0.00 0.00 4.09
2175 2450 0.952984 GAAGACAGGTGCAGAGCCAC 60.953 60.000 0.00 0.00 35.00 5.01
2237 2528 2.100989 CTGGCTTCTACCCGAGTTAGT 58.899 52.381 0.00 0.00 0.00 2.24
2328 2619 6.688073 AAAAGGGTCAGAACTGATAGAAGA 57.312 37.500 7.77 0.00 42.18 2.87
2431 2723 5.749596 TGTTATTGTGGTTGTCAAGACAG 57.250 39.130 2.87 0.00 42.94 3.51
2549 2844 3.535280 TTTGCTTGTTCTGGAAAACCC 57.465 42.857 0.00 0.00 0.00 4.11
2606 2903 5.977489 TGTTCAGGTCTTCGATCTTTCTA 57.023 39.130 0.00 0.00 0.00 2.10
2632 2929 3.882888 TGAAGCCTTCTGATTTTGTTCGT 59.117 39.130 5.96 0.00 0.00 3.85
3056 3353 3.082619 TCCACTCGGGACAGGAAAT 57.917 52.632 0.00 0.00 42.15 2.17
3105 3402 1.291877 GGCCGATATGCGATGACACC 61.292 60.000 0.00 0.00 44.57 4.16
3129 3426 7.868922 ACCGTTCTGTTTAAGTTCTTTGTTTTT 59.131 29.630 0.00 0.00 0.00 1.94
3258 3555 4.687901 TCTTGACAGGTGAGAATGTGAA 57.312 40.909 0.00 0.00 0.00 3.18
3403 3724 5.782893 TGGTGGAAAGAAAATCGTCAATT 57.217 34.783 0.00 0.00 0.00 2.32
3491 3816 6.013812 AGAGGCTCAACTCTAGATGTTTCTTT 60.014 38.462 18.26 0.00 45.62 2.52
3536 3861 7.864379 TCTTCATCTGTTTTTGCTCTGAAAATC 59.136 33.333 0.00 0.00 0.00 2.17
3546 3871 4.765273 TGCTCTGAAAATCGCTACCAATA 58.235 39.130 0.00 0.00 0.00 1.90
3703 4028 8.814038 ATTACAGCCTGAAATAGAAAACAGAT 57.186 30.769 0.00 0.00 32.90 2.90
3871 4196 3.862267 CGAAAGCGAGTCTTGAGATGAAT 59.138 43.478 0.00 0.00 40.82 2.57
3910 4322 3.624777 AGTTGCATACAGGATTCCCTTG 58.375 45.455 0.00 0.00 42.02 3.61
3920 4332 3.711704 CAGGATTCCCTTGCTTACCTAGA 59.288 47.826 0.00 0.00 42.02 2.43
3968 4380 7.661040 AGTTTTGCATAGTAACTTTGAATGCT 58.339 30.769 7.08 0.00 42.63 3.79
4102 4520 3.059884 TGTCGATTGTCAACTCTGCTTC 58.940 45.455 0.00 0.00 0.00 3.86
4107 4525 5.239306 TCGATTGTCAACTCTGCTTCAAAAT 59.761 36.000 0.00 0.00 0.00 1.82
4110 4528 7.752239 CGATTGTCAACTCTGCTTCAAAATTAT 59.248 33.333 0.00 0.00 0.00 1.28
4112 4530 8.578308 TTGTCAACTCTGCTTCAAAATTATTG 57.422 30.769 0.00 0.00 0.00 1.90
4114 4532 6.642131 GTCAACTCTGCTTCAAAATTATTGCA 59.358 34.615 0.00 0.00 0.00 4.08
4197 4615 0.595588 TGTGTAATTTGGTGCAGGCG 59.404 50.000 0.00 0.00 0.00 5.52
4227 4645 4.879545 AGTGAGTTAACCGAAAAAGCTTCA 59.120 37.500 0.00 0.00 0.00 3.02
4280 4698 8.403236 CCTTAGCATTGGTATTACTTTGTTACC 58.597 37.037 0.00 0.00 36.68 2.85
4301 4719 9.939802 GTTACCTCATCTACTTTCTTTCCTTAA 57.060 33.333 0.00 0.00 0.00 1.85
4310 4728 9.367444 TCTACTTTCTTTCCTTAAGCTAATTCG 57.633 33.333 0.00 0.00 33.66 3.34
4315 4733 8.851541 TTCTTTCCTTAAGCTAATTCGGTTAA 57.148 30.769 12.19 12.19 36.02 2.01
4425 4844 3.514309 TCTCCAGTTCCTAGGTGTTTAGC 59.486 47.826 9.08 0.00 0.00 3.09
4478 4898 8.109705 ACCTTAATTTGAAATTTTGAATGGCC 57.890 30.769 8.60 0.00 0.00 5.36
4480 4900 7.094848 CCTTAATTTGAAATTTTGAATGGCCGT 60.095 33.333 8.60 0.00 0.00 5.68
4498 4918 5.773176 TGGCCGTATATTCTTCAGTATCTGA 59.227 40.000 0.00 0.00 38.87 3.27
4543 4963 7.715265 AATCTAAAACTACACACACTGTCTG 57.285 36.000 0.00 0.00 33.91 3.51
4544 4964 6.459670 TCTAAAACTACACACACTGTCTGA 57.540 37.500 0.00 0.00 33.91 3.27
4545 4965 7.050970 TCTAAAACTACACACACTGTCTGAT 57.949 36.000 0.00 0.00 33.91 2.90
4546 4966 8.173542 TCTAAAACTACACACACTGTCTGATA 57.826 34.615 0.00 0.00 33.91 2.15
4547 4967 8.635328 TCTAAAACTACACACACTGTCTGATAA 58.365 33.333 0.00 0.00 33.91 1.75
4548 4968 9.424319 CTAAAACTACACACACTGTCTGATAAT 57.576 33.333 0.00 0.00 33.91 1.28
4550 4970 9.944376 AAAACTACACACACTGTCTGATAATAT 57.056 29.630 0.00 0.00 33.91 1.28
4556 4976 9.944376 ACACACACTGTCTGATAATATAAAGTT 57.056 29.630 0.00 0.00 0.00 2.66
4609 5029 7.186021 AGTTGTAAGACTACAATTGAAACCG 57.814 36.000 13.59 0.00 46.91 4.44
4686 5106 7.916914 TCTTTATTACAGTTTGTTAGAGCCC 57.083 36.000 0.00 0.00 0.00 5.19
4931 5352 6.248433 TGAATTCTTTTGGTGAGGAGCTTAT 58.752 36.000 7.05 0.00 0.00 1.73
4994 5419 7.726033 AGTTGTCTTCTATCAGTAGGATGTT 57.274 36.000 0.00 0.00 36.72 2.71
4995 5420 8.140112 AGTTGTCTTCTATCAGTAGGATGTTT 57.860 34.615 0.00 0.00 36.72 2.83
5008 5433 6.823689 CAGTAGGATGTTTTAAGTATGGCAGT 59.176 38.462 0.00 0.00 0.00 4.40
5049 5474 4.466567 TGCACACATACAAAAGAACTCG 57.533 40.909 0.00 0.00 0.00 4.18
5126 5551 2.803030 AAGCTGGATGTGATTCTGCT 57.197 45.000 0.00 0.00 0.00 4.24
5240 5863 8.486210 ACCTCAGAATTCTATGTTATGCTGTTA 58.514 33.333 7.86 0.00 30.72 2.41
5246 5869 7.912056 ATTCTATGTTATGCTGTTATGCGAT 57.088 32.000 0.00 0.00 35.36 4.58
5312 5935 4.622260 TTATGCTGGATATAGCTGCACA 57.378 40.909 10.34 0.00 44.01 4.57
5389 6013 6.418057 TGCCTTTCCATGTACTTTGAAATT 57.582 33.333 8.03 0.00 0.00 1.82
5467 6093 6.924111 ACACAATCATGGTTTGAGGTTAATC 58.076 36.000 13.93 0.00 37.89 1.75
5494 6122 3.936372 TTCGACCCACAGAACTTCTAG 57.064 47.619 0.00 0.00 0.00 2.43
5511 6139 8.910351 AACTTCTAGAAAATAGCAGTTGTTCT 57.090 30.769 6.63 0.00 31.65 3.01
5548 6176 6.817765 TTCTTGGTTAACACATGAGGATTC 57.182 37.500 8.10 0.00 0.00 2.52
5649 6381 9.685828 TTAGTGTTCATAAATAAACTGCAAACC 57.314 29.630 0.00 0.00 0.00 3.27
5650 6382 7.951591 AGTGTTCATAAATAAACTGCAAACCT 58.048 30.769 0.00 0.00 0.00 3.50
5651 6383 7.867403 AGTGTTCATAAATAAACTGCAAACCTG 59.133 33.333 0.00 0.00 0.00 4.00
5935 6677 4.097892 GTGACCATTGCTATTAGTTTGGGG 59.902 45.833 11.10 0.00 0.00 4.96
5945 6687 7.863722 TGCTATTAGTTTGGGGATTAGTGTTA 58.136 34.615 0.00 0.00 0.00 2.41
5970 6712 4.724074 AATCAACACTGGGCAATGTATG 57.276 40.909 0.00 0.00 0.00 2.39
5986 6728 4.972751 TGTATGGCCTATGCAGATAACA 57.027 40.909 3.32 0.00 40.13 2.41
6093 6836 8.882415 TGTGGGTTCGTAATTATCTAGATTTC 57.118 34.615 11.25 0.00 0.00 2.17
6094 6837 7.929785 TGTGGGTTCGTAATTATCTAGATTTCC 59.070 37.037 11.25 0.00 0.00 3.13
6203 6951 2.283460 AGCAGCCTGCCCTTTTCC 60.283 61.111 14.25 0.00 46.52 3.13
6217 6965 2.447443 CTTTTCCTGGGCCTTACCTTC 58.553 52.381 4.53 0.00 39.10 3.46
6232 6980 6.372381 GCCTTACCTTCAACCGTAGAAAAATA 59.628 38.462 0.00 0.00 0.00 1.40
6519 7721 0.801251 GTTGGTAGCTGAGCTTGCTG 59.199 55.000 14.14 0.81 41.32 4.41
6546 7748 4.024302 CGCATTGCATGTATCATCAGTTCT 60.024 41.667 9.69 0.00 0.00 3.01
6547 7749 5.505159 CGCATTGCATGTATCATCAGTTCTT 60.505 40.000 9.69 0.00 0.00 2.52
6585 7787 6.070938 AGGATATGGGGTTTATAGCTAACGTC 60.071 42.308 0.00 0.00 0.00 4.34
6603 7805 1.068541 GTCGAAGTTGCCAAATGGGAC 60.069 52.381 0.90 0.00 40.01 4.46
6635 7837 5.352293 CAGCAAGTGAGCATTACATGTTCTA 59.648 40.000 2.30 0.00 40.62 2.10
6647 7849 4.391405 ACATGTTCTATCATCGCTGACA 57.609 40.909 0.00 0.00 33.22 3.58
6744 7954 6.426980 TGTTCTATGCAAATGATGTGTCTC 57.573 37.500 0.00 0.00 0.00 3.36
6884 8094 2.482326 GCACATTGCTCAGGTACCC 58.518 57.895 8.74 0.00 40.96 3.69
6906 8116 4.431809 CGCCCTGATTTTGCATTGATTTA 58.568 39.130 0.00 0.00 0.00 1.40
6955 8165 9.832445 TGGGTATCATTTCTTCAGTAACTTATC 57.168 33.333 0.00 0.00 0.00 1.75
6983 8193 8.149647 TGAACTTCTGTCCAAAAATATTGCATT 58.850 29.630 0.00 0.00 0.00 3.56
7054 8264 5.334414 GGATCGAGCATATGTTCAAATGGAC 60.334 44.000 18.24 3.75 0.00 4.02
7120 8330 4.839668 TGTGGAAATAAACAAGGTTCCG 57.160 40.909 0.00 0.00 42.10 4.30
7156 8366 5.366482 TGATAAACGGGGATTCATGAGAA 57.634 39.130 0.00 0.00 38.31 2.87
7230 8440 1.742761 CCGACATCAGTTGCATCCTT 58.257 50.000 0.00 0.00 0.00 3.36
7348 8558 0.675837 GAGATGGCTCAGTTGCAGCA 60.676 55.000 2.55 0.00 40.96 4.41
7375 8585 4.757594 TGATGCAATGTTTATTGGCCTTC 58.242 39.130 3.32 0.00 43.12 3.46
7593 8804 6.577103 TGCTTTGTGTTCAATCCAACAATTA 58.423 32.000 0.00 0.00 38.01 1.40
7637 8848 4.487714 TGTCTGATGTCAAATACTCCCC 57.512 45.455 0.00 0.00 0.00 4.81
7659 8870 5.047519 CCCTCGTCCTAAAGTTCTTGTCTTA 60.048 44.000 0.00 0.00 0.00 2.10
7660 8871 6.094061 CCTCGTCCTAAAGTTCTTGTCTTAG 58.906 44.000 0.00 0.00 0.00 2.18
7661 8872 6.294620 CCTCGTCCTAAAGTTCTTGTCTTAGT 60.295 42.308 0.00 0.00 0.00 2.24
7662 8873 6.444633 TCGTCCTAAAGTTCTTGTCTTAGTG 58.555 40.000 0.00 0.00 0.00 2.74
7663 8874 6.040166 TCGTCCTAAAGTTCTTGTCTTAGTGT 59.960 38.462 0.00 0.00 0.00 3.55
7664 8875 6.700520 CGTCCTAAAGTTCTTGTCTTAGTGTT 59.299 38.462 0.00 0.00 0.00 3.32
7665 8876 7.306632 CGTCCTAAAGTTCTTGTCTTAGTGTTG 60.307 40.741 0.00 0.00 0.00 3.33
7673 8884 8.085296 AGTTCTTGTCTTAGTGTTGTCTAGATG 58.915 37.037 0.00 0.00 0.00 2.90
7709 8920 6.071334 TGGTCATGTTCTTAGAGTTGTCTAGG 60.071 42.308 0.00 0.00 36.61 3.02
7713 8926 9.916360 TCATGTTCTTAGAGTTGTCTAGGTATA 57.084 33.333 0.00 0.00 36.61 1.47
7826 9044 6.610075 TTTAGGACGGAGGTAATACAAACT 57.390 37.500 0.00 0.00 0.00 2.66
7964 9182 3.369546 AACGATTTTCTGGCCAAAGTG 57.630 42.857 7.01 0.00 0.00 3.16
7996 9214 6.041069 GTGCCACAAGACTAGAACTCCTATAT 59.959 42.308 0.00 0.00 0.00 0.86
8035 9256 3.238108 TGCTTCTACTCTTACTGCAGC 57.762 47.619 15.27 0.00 0.00 5.25
8036 9257 2.093973 TGCTTCTACTCTTACTGCAGCC 60.094 50.000 15.27 0.00 0.00 4.85
8065 9286 2.365293 GTTTGACCTTGCCATTTCCACT 59.635 45.455 0.00 0.00 0.00 4.00
8072 9293 0.322816 TGCCATTTCCACTGAGGCTC 60.323 55.000 7.79 7.79 45.42 4.70
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 3.815569 GATCTCGTCCTCTGCCGCG 62.816 68.421 0.00 0.00 0.00 6.46
11 12 2.026879 GATCTCGTCCTCTGCCGC 59.973 66.667 0.00 0.00 0.00 6.53
12 13 2.329690 CGATCTCGTCCTCTGCCG 59.670 66.667 0.00 0.00 34.11 5.69
30 31 5.505173 TGAGCAAGAGGAAGAAAAACTTG 57.495 39.130 0.00 0.00 39.13 3.16
33 34 3.567585 AGCTGAGCAAGAGGAAGAAAAAC 59.432 43.478 7.39 0.00 0.00 2.43
39 40 3.122297 CGATAAGCTGAGCAAGAGGAAG 58.878 50.000 7.39 0.00 0.00 3.46
40 41 2.760650 TCGATAAGCTGAGCAAGAGGAA 59.239 45.455 7.39 0.00 0.00 3.36
41 42 2.379005 TCGATAAGCTGAGCAAGAGGA 58.621 47.619 7.39 0.00 0.00 3.71
42 43 2.879002 TCGATAAGCTGAGCAAGAGG 57.121 50.000 7.39 0.00 0.00 3.69
48 49 5.859521 ATGAATCAATCGATAAGCTGAGC 57.140 39.130 0.00 0.00 0.00 4.26
51 52 7.187244 AGTGAATGAATCAATCGATAAGCTG 57.813 36.000 0.00 0.00 40.50 4.24
81 82 9.330063 CATATAATGTGTAGACCAACATTGAGT 57.670 33.333 10.47 1.47 34.95 3.41
82 83 9.330063 ACATATAATGTGTAGACCAACATTGAG 57.670 33.333 10.47 2.20 43.01 3.02
139 140 0.036765 GCACGTGATGGTTGTCCCTA 60.037 55.000 22.23 0.00 0.00 3.53
145 146 0.316937 GTGTGTGCACGTGATGGTTG 60.317 55.000 22.23 0.00 35.75 3.77
146 147 2.021722 GTGTGTGCACGTGATGGTT 58.978 52.632 22.23 0.00 35.75 3.67
147 148 3.731136 GTGTGTGCACGTGATGGT 58.269 55.556 22.23 0.00 35.75 3.55
167 168 4.904241 ACTCTCCTTTCAGTTTCATCCAG 58.096 43.478 0.00 0.00 0.00 3.86
182 183 1.005569 TCGTCCCACACATACTCTCCT 59.994 52.381 0.00 0.00 0.00 3.69
211 212 6.036953 GGATGTTCAACAAGTTTTGCATGAAA 59.963 34.615 0.00 0.00 39.74 2.69
218 219 5.261209 TCCTGGATGTTCAACAAGTTTTG 57.739 39.130 0.00 0.00 0.00 2.44
230 231 7.405292 TCAAATTCAACTAGATCCTGGATGTT 58.595 34.615 15.25 9.40 0.00 2.71
259 260 5.302360 CAAGTTAGGCCTAGTACAACAACA 58.698 41.667 13.36 0.00 0.00 3.33
287 288 6.657966 AGCACAAATCATCCATCCATACATAG 59.342 38.462 0.00 0.00 0.00 2.23
296 297 9.837525 GATAGAAAATAGCACAAATCATCCATC 57.162 33.333 0.00 0.00 0.00 3.51
297 298 8.800332 GGATAGAAAATAGCACAAATCATCCAT 58.200 33.333 0.00 0.00 0.00 3.41
298 299 7.041167 CGGATAGAAAATAGCACAAATCATCCA 60.041 37.037 0.00 0.00 0.00 3.41
299 300 7.301054 CGGATAGAAAATAGCACAAATCATCC 58.699 38.462 0.00 0.00 0.00 3.51
300 301 7.173218 TCCGGATAGAAAATAGCACAAATCATC 59.827 37.037 0.00 0.00 0.00 2.92
311 312 8.662781 TTCATCAAAGTCCGGATAGAAAATAG 57.337 34.615 7.81 0.00 0.00 1.73
325 326 6.910536 AACCGACTGATATTCATCAAAGTC 57.089 37.500 0.00 0.00 40.66 3.01
341 342 4.759516 ACGAAATTTATGCAAACCGACT 57.240 36.364 0.00 0.00 0.00 4.18
354 355 6.143278 GCATTTTCACTAACCGAACGAAATTT 59.857 34.615 0.00 0.00 0.00 1.82
372 373 6.291955 CCGCATACATTTCAATCTGCATTTTC 60.292 38.462 0.00 0.00 0.00 2.29
380 381 4.960938 TCTAGCCGCATACATTTCAATCT 58.039 39.130 0.00 0.00 0.00 2.40
385 386 3.248602 CCAACTCTAGCCGCATACATTTC 59.751 47.826 0.00 0.00 0.00 2.17
395 396 1.592669 CGCCATCCAACTCTAGCCG 60.593 63.158 0.00 0.00 0.00 5.52
419 420 0.249322 GTCCACGGACACGGATATGG 60.249 60.000 11.43 0.00 46.48 2.74
422 423 3.189921 CGTCCACGGACACGGATA 58.810 61.111 16.23 0.00 44.77 2.59
437 438 2.009774 CAGATTTTCTTCCGCATCCGT 58.990 47.619 0.00 0.00 0.00 4.69
447 448 0.240945 CGCAACCCGCAGATTTTCTT 59.759 50.000 0.00 0.00 42.60 2.52
455 456 2.745884 TCCAATCGCAACCCGCAG 60.746 61.111 0.00 0.00 42.60 5.18
460 461 1.017387 GACCATCTCCAATCGCAACC 58.983 55.000 0.00 0.00 0.00 3.77
466 467 2.103094 TGACATCGGACCATCTCCAATC 59.897 50.000 0.00 0.00 39.39 2.67
467 468 2.118679 TGACATCGGACCATCTCCAAT 58.881 47.619 0.00 0.00 39.39 3.16
469 470 0.824109 GTGACATCGGACCATCTCCA 59.176 55.000 0.00 0.00 39.39 3.86
471 472 2.898729 ATGTGACATCGGACCATCTC 57.101 50.000 0.00 0.00 0.00 2.75
472 473 4.963318 AATATGTGACATCGGACCATCT 57.037 40.909 0.00 0.00 0.00 2.90
473 474 4.452455 GGAAATATGTGACATCGGACCATC 59.548 45.833 0.00 0.00 0.00 3.51
474 475 4.141505 TGGAAATATGTGACATCGGACCAT 60.142 41.667 0.00 0.00 0.00 3.55
475 476 3.198853 TGGAAATATGTGACATCGGACCA 59.801 43.478 0.00 5.90 0.00 4.02
476 477 3.804036 TGGAAATATGTGACATCGGACC 58.196 45.455 0.00 3.26 0.00 4.46
477 478 4.634004 TGTTGGAAATATGTGACATCGGAC 59.366 41.667 0.00 0.00 0.00 4.79
478 479 4.837972 TGTTGGAAATATGTGACATCGGA 58.162 39.130 0.00 0.00 0.00 4.55
479 480 5.756195 ATGTTGGAAATATGTGACATCGG 57.244 39.130 0.00 0.00 0.00 4.18
480 481 7.919690 ACTAATGTTGGAAATATGTGACATCG 58.080 34.615 0.00 0.00 0.00 3.84
522 523 5.567138 AGAGGGCTTTGATGTTTATTTCG 57.433 39.130 0.00 0.00 0.00 3.46
526 531 7.633789 TCTTTCTAGAGGGCTTTGATGTTTAT 58.366 34.615 0.00 0.00 0.00 1.40
600 606 6.753279 TGAATTTTCCTACAACGTATACGGAG 59.247 38.462 27.62 20.80 44.95 4.63
601 607 6.629128 TGAATTTTCCTACAACGTATACGGA 58.371 36.000 27.62 12.21 44.95 4.69
602 608 6.890663 TGAATTTTCCTACAACGTATACGG 57.109 37.500 27.62 14.20 44.95 4.02
611 617 5.456173 GCGTTTTCGTTGAATTTTCCTACAA 59.544 36.000 0.00 0.00 46.03 2.41
613 619 4.380678 GGCGTTTTCGTTGAATTTTCCTAC 59.619 41.667 0.00 0.00 46.03 3.18
645 651 2.480555 GTGAAAGGGACGCGCATG 59.519 61.111 5.73 0.00 0.00 4.06
685 691 6.500775 TTTACGTCTTTTCGTTACAGTGAG 57.499 37.500 0.00 0.00 43.80 3.51
686 692 6.562640 GCATTTACGTCTTTTCGTTACAGTGA 60.563 38.462 0.00 0.00 43.80 3.41
688 694 5.464389 AGCATTTACGTCTTTTCGTTACAGT 59.536 36.000 0.00 0.00 43.80 3.55
786 792 0.390603 GTTTTGGTTAATGCGGGGGC 60.391 55.000 0.00 0.00 0.00 5.80
800 836 3.006752 TGCAGGCAGGGAATAAAGTTTTG 59.993 43.478 0.00 0.00 0.00 2.44
827 863 4.560743 TTGCTGACGGGTGCTGCA 62.561 61.111 0.00 0.00 38.23 4.41
828 864 4.030452 GTTGCTGACGGGTGCTGC 62.030 66.667 0.00 0.00 0.00 5.25
911 1153 2.484287 AATTGGCACCGGTGGAGGAG 62.484 60.000 34.58 10.02 34.73 3.69
912 1154 2.478335 GAATTGGCACCGGTGGAGGA 62.478 60.000 34.58 6.45 34.73 3.71
913 1155 2.035626 AATTGGCACCGGTGGAGG 59.964 61.111 34.58 11.25 37.30 4.30
954 1197 3.370209 GGAAAAGGCAACGGTAGGAGTAT 60.370 47.826 0.00 0.00 46.39 2.12
955 1198 2.027837 GGAAAAGGCAACGGTAGGAGTA 60.028 50.000 0.00 0.00 46.39 2.59
956 1199 1.271217 GGAAAAGGCAACGGTAGGAGT 60.271 52.381 0.00 0.00 46.39 3.85
957 1200 1.003233 AGGAAAAGGCAACGGTAGGAG 59.997 52.381 0.00 0.00 46.39 3.69
958 1201 1.061546 AGGAAAAGGCAACGGTAGGA 58.938 50.000 0.00 0.00 46.39 2.94
959 1202 1.905637 AAGGAAAAGGCAACGGTAGG 58.094 50.000 0.00 0.00 46.39 3.18
960 1203 2.228103 GGAAAGGAAAAGGCAACGGTAG 59.772 50.000 0.00 0.00 46.39 3.18
961 1204 2.232399 GGAAAGGAAAAGGCAACGGTA 58.768 47.619 0.00 0.00 46.39 4.02
1095 1341 1.062685 CGACTCCCAGATCGACACG 59.937 63.158 0.00 0.00 40.86 4.49
1312 1558 3.849953 GAACACGACCATCGGCGC 61.850 66.667 0.00 0.00 45.59 6.53
1466 1713 4.404654 GGCCGCCACGAAAGCAAG 62.405 66.667 3.91 0.00 0.00 4.01
1492 1739 2.448219 CGCGGAGTAACAAGTAGTAGC 58.552 52.381 0.00 0.00 0.00 3.58
1512 1759 3.424962 CGAACGGAGAAGAAAAATCTGCC 60.425 47.826 0.00 0.00 32.20 4.85
1571 1821 7.250445 TCGCACTAAATCATAGTACGAGTAA 57.750 36.000 6.80 0.00 38.11 2.24
1575 1825 4.577693 ACCTCGCACTAAATCATAGTACGA 59.422 41.667 9.74 9.74 39.96 3.43
1576 1826 4.856664 ACCTCGCACTAAATCATAGTACG 58.143 43.478 2.61 2.61 36.09 3.67
1577 1827 9.339492 GTATTACCTCGCACTAAATCATAGTAC 57.661 37.037 0.00 0.00 0.00 2.73
1578 1828 9.070179 TGTATTACCTCGCACTAAATCATAGTA 57.930 33.333 0.00 0.00 0.00 1.82
1579 1829 7.866393 GTGTATTACCTCGCACTAAATCATAGT 59.134 37.037 0.00 0.00 0.00 2.12
1580 1830 7.328737 GGTGTATTACCTCGCACTAAATCATAG 59.671 40.741 0.00 0.00 46.51 2.23
1609 1859 4.810345 TCCATTTTAATCCCCGCCTAAAT 58.190 39.130 0.00 0.00 0.00 1.40
1613 1863 3.117131 AGAATCCATTTTAATCCCCGCCT 60.117 43.478 0.00 0.00 0.00 5.52
1617 1867 4.281941 GGAGCAGAATCCATTTTAATCCCC 59.718 45.833 0.00 0.00 39.34 4.81
1624 1874 2.094675 CACCGGAGCAGAATCCATTTT 58.905 47.619 9.46 0.00 39.53 1.82
1625 1875 1.683011 CCACCGGAGCAGAATCCATTT 60.683 52.381 9.46 0.00 39.53 2.32
1663 1913 2.299867 TCCTTGGTTTCACGGTAGTACC 59.700 50.000 9.50 9.50 34.30 3.34
1711 1962 0.684479 TCACACCATCCTCCTCCTCG 60.684 60.000 0.00 0.00 0.00 4.63
1715 1966 1.153549 GCGTCACACCATCCTCCTC 60.154 63.158 0.00 0.00 0.00 3.71
1716 1967 2.982130 GCGTCACACCATCCTCCT 59.018 61.111 0.00 0.00 0.00 3.69
1717 1968 2.509336 CGCGTCACACCATCCTCC 60.509 66.667 0.00 0.00 0.00 4.30
1781 2032 5.606749 AGGTTAGTACAATGCCTCATATGGA 59.393 40.000 2.13 0.00 0.00 3.41
1962 2226 4.025858 GGAGCCCTCACAGCAGCA 62.026 66.667 0.00 0.00 0.00 4.41
1973 2237 2.187946 CACGGTCTGATGGAGCCC 59.812 66.667 0.00 0.00 39.08 5.19
2082 2346 1.341209 TCACTACTGTCACCTGCACAG 59.659 52.381 0.02 0.02 45.86 3.66
2138 2407 6.943981 TGTCTTCTGTTACAAGAAAATGTCG 58.056 36.000 0.00 0.00 35.79 4.35
2237 2528 4.037803 CCAGTTTCACATGTTGATCCACAA 59.962 41.667 3.42 0.00 32.84 3.33
2328 2619 4.228824 TCCATAGTTCTTTACGGCCCTAT 58.771 43.478 0.00 0.00 0.00 2.57
2431 2723 3.589495 ACGAGTCCTAAACAGTTAGCC 57.411 47.619 0.00 0.00 36.19 3.93
2462 2754 6.855836 TGAGTGCACAAAATAATCCAGAATC 58.144 36.000 21.04 2.05 0.00 2.52
2533 2828 2.623416 GTCCAGGGTTTTCCAGAACAAG 59.377 50.000 0.00 0.00 42.91 3.16
2549 2844 5.836821 TCAGCAAGTACTATACAGTCCAG 57.163 43.478 0.00 0.00 36.14 3.86
2606 2903 4.210331 ACAAAATCAGAAGGCTTCACAGT 58.790 39.130 27.70 10.90 0.00 3.55
2632 2929 2.896685 CTCCAAACAGCCCAAACCATAA 59.103 45.455 0.00 0.00 0.00 1.90
3044 3341 1.453155 CAAGGTCATTTCCTGTCCCG 58.547 55.000 0.00 0.00 37.93 5.14
3056 3353 4.842531 TCCAAATGATCTAGCAAGGTCA 57.157 40.909 0.00 0.00 46.79 4.02
3129 3426 9.357652 GCTTGAGTTGATTAGCATTTTCAATTA 57.642 29.630 0.00 0.00 32.48 1.40
3258 3555 7.271511 AGAGAAATAACTCTCGAGCAATGATT 58.728 34.615 7.81 0.79 45.53 2.57
3307 3604 7.373493 CAAAATGTGTTCCTCAAATAGAGCTT 58.627 34.615 0.00 0.00 43.31 3.74
3403 3724 6.162079 GCAGATAGATGCTGAGCTTATGTAA 58.838 40.000 5.83 0.00 43.07 2.41
3459 3784 1.543802 AGAGTTGAGCCTCTTCACGAG 59.456 52.381 0.00 0.00 38.69 4.18
3501 3826 7.661437 AGCAAAAACAGATGAAGAGTGTATGTA 59.339 33.333 0.00 0.00 0.00 2.29
3536 3861 4.562394 CCAACTGCAAAAATATTGGTAGCG 59.438 41.667 0.00 0.00 35.98 4.26
3684 4009 8.246871 AGCTAAAATCTGTTTTCTATTTCAGGC 58.753 33.333 0.00 0.00 38.44 4.85
3703 4028 7.553334 ACCGAGTGTATAGATTTGAGCTAAAA 58.447 34.615 0.00 0.00 0.00 1.52
3861 4186 9.865321 GGATTTTCAGAATTGAATTCATCTCAA 57.135 29.630 19.02 0.00 42.60 3.02
3863 4188 9.865321 TTGGATTTTCAGAATTGAATTCATCTC 57.135 29.630 19.02 8.88 42.60 2.75
3871 4196 6.580788 TGCAACTTGGATTTTCAGAATTGAA 58.419 32.000 0.00 0.00 41.44 2.69
3968 4380 1.134128 TGCAGAGTCAAAGAGTGGCAA 60.134 47.619 0.00 0.00 32.63 4.52
4107 4525 9.077885 GACAAAATATAGGAGGGATTGCAATAA 57.922 33.333 12.97 0.00 0.00 1.40
4110 4528 6.672593 AGACAAAATATAGGAGGGATTGCAA 58.327 36.000 0.00 0.00 0.00 4.08
4112 4530 7.503902 AGAAAGACAAAATATAGGAGGGATTGC 59.496 37.037 0.00 0.00 0.00 3.56
4114 4532 8.781951 TGAGAAAGACAAAATATAGGAGGGATT 58.218 33.333 0.00 0.00 0.00 3.01
4197 4615 1.000506 TCGGTTAACTCACTGCCACTC 59.999 52.381 5.42 0.00 0.00 3.51
4280 4698 9.877178 TTAGCTTAAGGAAAGAAAGTAGATGAG 57.123 33.333 4.29 0.00 37.38 2.90
4301 4719 5.657474 TCACGAGAATTAACCGAATTAGCT 58.343 37.500 0.00 0.00 37.90 3.32
4310 4728 7.094933 ACCATGTAAAGTTCACGAGAATTAACC 60.095 37.037 0.00 0.00 35.92 2.85
4315 4733 5.547465 TCACCATGTAAAGTTCACGAGAAT 58.453 37.500 0.00 0.00 35.92 2.40
4564 4984 9.344772 ACAACTTTATATTATCATAAACCCGCA 57.655 29.630 0.00 0.00 0.00 5.69
4601 5021 5.895636 ACATTCATATCTTGCGGTTTCAA 57.104 34.783 0.00 0.00 0.00 2.69
4609 5029 7.734924 TTGATCTGGTACATTCATATCTTGC 57.265 36.000 0.00 0.00 38.20 4.01
4686 5106 5.375417 TGGCACACTTAACAATGAATCAG 57.625 39.130 0.00 0.00 0.00 2.90
4994 5419 8.144478 GTGATCTATCAGACTGCCATACTTAAA 58.856 37.037 0.00 0.00 37.51 1.52
4995 5420 7.522236 CGTGATCTATCAGACTGCCATACTTAA 60.522 40.741 0.00 0.00 37.51 1.85
5008 5433 4.142182 TGCAACATCACGTGATCTATCAGA 60.142 41.667 27.79 6.59 37.51 3.27
5049 5474 0.251341 ATGGGAGAACTTGGGTGCAC 60.251 55.000 8.80 8.80 0.00 4.57
5240 5863 5.537300 AAACAGTCACCTATAGATCGCAT 57.463 39.130 0.00 0.00 0.00 4.73
5312 5935 2.188817 GGAGTACAGAACCATCCCTGT 58.811 52.381 0.00 0.00 44.81 4.00
5389 6013 8.635765 ATTTGATACTTTAAAAGTCCAGCTCA 57.364 30.769 0.00 0.00 41.77 4.26
5420 6044 4.695455 TCTCGAGGATGGATCAAAACAAAC 59.305 41.667 13.56 0.00 0.00 2.93
5467 6093 2.932614 GTTCTGTGGGTCGAATCTCATG 59.067 50.000 0.00 0.00 0.00 3.07
5647 6379 7.659390 GAAGAATATCTTAGCACTATTGCAGGT 59.341 37.037 7.88 0.00 43.54 4.00
5648 6380 7.877097 AGAAGAATATCTTAGCACTATTGCAGG 59.123 37.037 7.88 0.00 43.54 4.85
5649 6381 8.830201 AGAAGAATATCTTAGCACTATTGCAG 57.170 34.615 7.88 0.00 43.54 4.41
5650 6382 9.265901 GAAGAAGAATATCTTAGCACTATTGCA 57.734 33.333 7.88 0.00 44.40 4.08
5651 6383 8.716909 GGAAGAAGAATATCTTAGCACTATTGC 58.283 37.037 0.00 0.00 43.33 3.56
5652 6384 9.995003 AGGAAGAAGAATATCTTAGCACTATTG 57.005 33.333 0.00 0.00 39.70 1.90
5872 6614 5.590530 AGTCAGCTACTCGATTTTCTGAT 57.409 39.130 9.67 0.47 30.33 2.90
5970 6712 5.706916 CATTTCATGTTATCTGCATAGGCC 58.293 41.667 0.00 0.00 40.13 5.19
5973 6715 7.076362 GTCAGCATTTCATGTTATCTGCATAG 58.924 38.462 0.00 0.00 32.18 2.23
6093 6836 8.687292 TCCATTTCATCATTGAGAAAGATAGG 57.313 34.615 13.15 11.97 37.19 2.57
6203 6951 0.676782 CGGTTGAAGGTAAGGCCCAG 60.677 60.000 0.00 0.00 38.26 4.45
6585 7787 0.958091 TGTCCCATTTGGCAACTTCG 59.042 50.000 0.00 0.00 37.61 3.79
6603 7805 4.959596 ATGCTCACTTGCTGTCTATTTG 57.040 40.909 0.00 0.00 0.00 2.32
6635 7837 6.226052 TCTAAAAGCATATGTCAGCGATGAT 58.774 36.000 6.66 0.00 35.48 2.45
6647 7849 7.112779 AGCTACCACTTGTTCTAAAAGCATAT 58.887 34.615 0.00 0.00 0.00 1.78
6755 7965 4.566759 GCTTCAACAAAACCTTTCTGGAAC 59.433 41.667 0.00 0.00 39.71 3.62
6883 8093 0.531657 TCAATGCAAAATCAGGGCGG 59.468 50.000 0.00 0.00 0.00 6.13
6884 8094 2.589798 ATCAATGCAAAATCAGGGCG 57.410 45.000 0.00 0.00 0.00 6.13
6890 8100 7.887996 TTGACAGGTAAATCAATGCAAAATC 57.112 32.000 0.00 0.00 29.89 2.17
6906 8116 6.604795 CCAAATAGATCAATCCTTTGACAGGT 59.395 38.462 13.27 0.00 44.36 4.00
6955 8165 7.599621 TGCAATATTTTTGGACAGAAGTTCATG 59.400 33.333 5.50 3.46 31.99 3.07
6983 8193 3.033909 TGATAGCTGCAGCCTAAGAGAA 58.966 45.455 34.39 10.04 43.38 2.87
7054 8264 2.331893 TTGTTTCCATGGCTCGCCG 61.332 57.895 6.96 0.00 39.42 6.46
7120 8330 4.235360 CGTTTATCATCCGGGAGTGATAC 58.765 47.826 19.76 14.59 37.13 2.24
7156 8366 6.546484 CAATACCTGATTGACATAGGGGAAT 58.454 40.000 0.00 0.00 46.94 3.01
7230 8440 6.214819 GGTAATTGGATGGTTAGGGAGCTATA 59.785 42.308 0.00 0.00 0.00 1.31
7348 8558 5.818857 GGCCAATAAACATTGCATCATCTTT 59.181 36.000 0.00 0.00 0.00 2.52
7593 8804 2.156917 GGAACGTTTCGGAGGGAAAAT 58.843 47.619 0.46 0.00 45.74 1.82
7637 8848 6.583050 CACTAAGACAAGAACTTTAGGACGAG 59.417 42.308 0.00 0.00 0.00 4.18
7659 8870 8.522003 CAGATATATCTGCATCTAGACAACACT 58.478 37.037 25.81 0.00 46.63 3.55
7660 8871 8.686397 CAGATATATCTGCATCTAGACAACAC 57.314 38.462 25.81 0.00 46.63 3.32
7826 9044 7.650104 GGTTGTACACATAGCTAAAAGCAAAAA 59.350 33.333 0.00 0.00 45.56 1.94
8035 9256 1.004918 AAGGTCAAACGCCTCTCGG 60.005 57.895 0.00 0.00 43.86 4.63
8036 9257 1.901650 GCAAGGTCAAACGCCTCTCG 61.902 60.000 0.00 0.00 45.38 4.04
8044 9265 2.365293 AGTGGAAATGGCAAGGTCAAAC 59.635 45.455 0.00 0.00 0.00 2.93
8072 9293 0.835543 CAGAGGATAGAGGGGGCAGG 60.836 65.000 0.00 0.00 0.00 4.85


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

AutoCloner maintained by Alex Coulton.