Multiple sequence alignment - TraesCS3D01G495400

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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 TraesCS3D01G495400 chr3D 100.000 2236 0 0 2431 4666 587595087 587592852 0.000000e+00 4130.0
1 TraesCS3D01G495400 chr3D 100.000 2045 0 0 1 2045 587597517 587595473 0.000000e+00 3777.0
2 TraesCS3D01G495400 chr3D 83.213 828 88 30 932 1735 587586650 587585850 0.000000e+00 712.0
3 TraesCS3D01G495400 chr3D 81.720 837 105 29 998 1789 587648503 587647670 0.000000e+00 654.0
4 TraesCS3D01G495400 chr3D 80.952 777 89 31 998 1737 587745681 587746435 1.130000e-155 560.0
5 TraesCS3D01G495400 chr3D 91.111 45 3 1 1748 1792 587585786 587585743 5.040000e-05 60.2
6 TraesCS3D01G495400 chr3B 91.659 2086 113 20 2440 4504 784899582 784897537 0.000000e+00 2832.0
7 TraesCS3D01G495400 chr3B 94.286 1365 57 10 681 2045 784901199 784899856 0.000000e+00 2069.0
8 TraesCS3D01G495400 chr3B 81.840 826 91 28 1011 1792 784870599 784869789 1.420000e-179 640.0
9 TraesCS3D01G495400 chr3B 80.207 773 105 28 998 1737 785280735 785281492 1.910000e-148 536.0
10 TraesCS3D01G495400 chr3B 80.899 267 32 10 441 689 252947253 252947518 4.760000e-45 193.0
11 TraesCS3D01G495400 chr3B 100.000 57 0 0 386 442 784901253 784901197 6.390000e-19 106.0
12 TraesCS3D01G495400 chr3A 90.220 1953 133 25 2558 4488 716965203 716963287 0.000000e+00 2495.0
13 TraesCS3D01G495400 chr3A 95.525 1229 47 4 813 2037 716967139 716965915 0.000000e+00 1958.0
14 TraesCS3D01G495400 chr3A 81.818 880 106 32 942 1792 716948314 716947460 0.000000e+00 689.0
15 TraesCS3D01G495400 chr3A 93.694 444 25 3 1 442 716967896 716967454 0.000000e+00 662.0
16 TraesCS3D01G495400 chr3A 80.415 771 103 29 998 1737 717297220 717297973 1.140000e-150 544.0
17 TraesCS3D01G495400 chr3A 97.794 136 3 0 681 816 716967456 716967321 7.810000e-58 235.0
18 TraesCS3D01G495400 chr4A 92.268 194 14 1 441 633 674617054 674616861 1.650000e-69 274.0
19 TraesCS3D01G495400 chr1A 92.670 191 13 1 441 630 435053995 435054185 1.650000e-69 274.0
20 TraesCS3D01G495400 chr1A 89.091 220 22 2 440 658 498177808 498177590 5.950000e-69 272.0
21 TraesCS3D01G495400 chr1A 84.167 240 34 3 51 288 9205614 9205377 3.630000e-56 230.0
22 TraesCS3D01G495400 chr2D 86.235 247 31 3 439 683 121353342 121353587 9.960000e-67 265.0
23 TraesCS3D01G495400 chr2D 84.825 257 30 4 441 688 30440800 30440544 2.790000e-62 250.0
24 TraesCS3D01G495400 chr5D 90.863 197 17 1 438 633 279292868 279293064 3.580000e-66 263.0
25 TraesCS3D01G495400 chr7D 86.066 244 32 2 438 679 439997145 439997388 1.290000e-65 261.0
26 TraesCS3D01G495400 chr5B 86.307 241 30 3 51 290 366053610 366053372 4.630000e-65 259.0
27 TraesCS3D01G495400 chr5B 85.586 222 30 2 51 272 276957697 276957478 1.010000e-56 231.0
28 TraesCS3D01G495400 chrUn 85.366 246 33 3 440 683 105423940 105424184 7.750000e-63 252.0
29 TraesCS3D01G495400 chrUn 78.909 275 38 10 440 695 230312263 230312536 8.030000e-38 169.0
30 TraesCS3D01G495400 chrUn 89.231 65 5 2 633 695 452039146 452039082 3.870000e-11 80.5
31 TraesCS3D01G495400 chr4D 85.714 238 33 1 52 288 15552490 15552727 2.790000e-62 250.0
32 TraesCS3D01G495400 chr5A 85.020 247 28 5 441 683 180339369 180339610 4.660000e-60 243.0
33 TraesCS3D01G495400 chr1D 84.167 240 36 2 51 288 7770790 7770551 1.010000e-56 231.0
34 TraesCS3D01G495400 chr1D 84.255 235 35 2 54 288 347198689 347198457 1.310000e-55 228.0
35 TraesCS3D01G495400 chr1B 83.750 240 37 2 51 288 611522969 611523208 4.700000e-55 226.0
36 TraesCS3D01G495400 chr1B 78.909 275 38 10 440 695 59988859 59988586 8.030000e-38 169.0
37 TraesCS3D01G495400 chr4B 83.682 239 37 2 51 288 57270354 57270591 1.690000e-54 224.0


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 TraesCS3D01G495400 chr3D 587592852 587597517 4665 True 3953.5 4130 100.00000 1 4666 2 chr3D.!!$R3 4665
1 TraesCS3D01G495400 chr3D 587647670 587648503 833 True 654.0 654 81.72000 998 1789 1 chr3D.!!$R1 791
2 TraesCS3D01G495400 chr3D 587745681 587746435 754 False 560.0 560 80.95200 998 1737 1 chr3D.!!$F1 739
3 TraesCS3D01G495400 chr3D 587585743 587586650 907 True 386.1 712 87.16200 932 1792 2 chr3D.!!$R2 860
4 TraesCS3D01G495400 chr3B 784897537 784901253 3716 True 1669.0 2832 95.31500 386 4504 3 chr3B.!!$R2 4118
5 TraesCS3D01G495400 chr3B 784869789 784870599 810 True 640.0 640 81.84000 1011 1792 1 chr3B.!!$R1 781
6 TraesCS3D01G495400 chr3B 785280735 785281492 757 False 536.0 536 80.20700 998 1737 1 chr3B.!!$F2 739
7 TraesCS3D01G495400 chr3A 716963287 716967896 4609 True 1337.5 2495 94.30825 1 4488 4 chr3A.!!$R2 4487
8 TraesCS3D01G495400 chr3A 716947460 716948314 854 True 689.0 689 81.81800 942 1792 1 chr3A.!!$R1 850
9 TraesCS3D01G495400 chr3A 717297220 717297973 753 False 544.0 544 80.41500 998 1737 1 chr3A.!!$F1 739

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
490 493 0.663153 AGCTTTGGTCAACGTCAAGC 59.337 50.000 0.00 0.0 0.00 4.01 F
491 494 0.663153 GCTTTGGTCAACGTCAAGCT 59.337 50.000 0.00 0.0 0.00 3.74 F
1597 1885 0.915872 ATCATGGTCCAGGTCAGCCA 60.916 55.000 2.95 0.0 37.19 4.75 F
3004 3736 1.818674 GACCCGCATTGACCTCAATTT 59.181 47.619 0.00 0.0 43.48 1.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1834 2178 1.156736 CATCGCGGAAAAGGAAGTGT 58.843 50.000 6.13 0.0 0.0 3.55 R
1849 2193 1.739466 CCCACACCTCAATCAACATCG 59.261 52.381 0.00 0.0 0.0 3.84 R
3578 4316 0.449388 CCTCCTTGCTCATTGTTCGC 59.551 55.000 0.00 0.0 0.0 4.70 R
4640 5395 0.390472 GCCAGCCCATATAGTCGCTC 60.390 60.000 0.00 0.0 0.0 5.03 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 4.099419 AGTTGGGAGTTTTTAGGTTTGCTG 59.901 41.667 0.00 0.00 0.00 4.41
40 41 2.540101 GGTTTGCTGATTATCTCGGTCG 59.460 50.000 0.00 0.00 32.34 4.79
57 58 4.885907 TCGGTCGAATGAGAATTACTACCT 59.114 41.667 0.00 0.00 0.00 3.08
62 63 7.210873 GTCGAATGAGAATTACTACCTCCATT 58.789 38.462 0.00 0.00 0.00 3.16
66 67 7.921041 ATGAGAATTACTACCTCCATTCTGA 57.079 36.000 0.00 0.00 36.35 3.27
76 77 5.134725 ACCTCCATTCTGATTTATTGGCT 57.865 39.130 0.00 0.00 0.00 4.75
79 80 4.136796 TCCATTCTGATTTATTGGCTCCG 58.863 43.478 0.00 0.00 0.00 4.63
92 93 2.070783 TGGCTCCGTTCGTATTTTGTC 58.929 47.619 0.00 0.00 0.00 3.18
302 303 8.867097 ACAAAGGTAGTAGTTAAATCTCAGTCA 58.133 33.333 0.00 0.00 0.00 3.41
375 378 4.497006 CCTGACTCTGAAAACAAGCAACAG 60.497 45.833 0.00 0.00 0.00 3.16
376 379 4.260985 TGACTCTGAAAACAAGCAACAGA 58.739 39.130 0.00 0.00 36.42 3.41
442 445 5.871531 CAAGTGAACTTGTTTGCATGTAC 57.128 39.130 13.87 0.00 46.11 2.90
443 446 5.581605 CAAGTGAACTTGTTTGCATGTACT 58.418 37.500 13.87 0.00 46.11 2.73
444 447 5.424121 AGTGAACTTGTTTGCATGTACTC 57.576 39.130 0.00 0.00 33.39 2.59
445 448 4.275936 AGTGAACTTGTTTGCATGTACTCC 59.724 41.667 0.00 0.00 33.39 3.85
446 449 3.568007 TGAACTTGTTTGCATGTACTCCC 59.432 43.478 0.00 0.00 33.39 4.30
447 450 3.508845 ACTTGTTTGCATGTACTCCCT 57.491 42.857 0.00 0.00 32.19 4.20
448 451 3.832527 ACTTGTTTGCATGTACTCCCTT 58.167 40.909 0.00 0.00 32.19 3.95
449 452 3.821033 ACTTGTTTGCATGTACTCCCTTC 59.179 43.478 0.00 0.00 32.19 3.46
450 453 2.422597 TGTTTGCATGTACTCCCTTCG 58.577 47.619 0.00 0.00 0.00 3.79
451 454 2.224426 TGTTTGCATGTACTCCCTTCGT 60.224 45.455 0.00 0.00 0.00 3.85
452 455 2.812011 GTTTGCATGTACTCCCTTCGTT 59.188 45.455 0.00 0.00 0.00 3.85
453 456 2.851263 TGCATGTACTCCCTTCGTTT 57.149 45.000 0.00 0.00 0.00 3.60
454 457 3.134574 TGCATGTACTCCCTTCGTTTT 57.865 42.857 0.00 0.00 0.00 2.43
455 458 3.482436 TGCATGTACTCCCTTCGTTTTT 58.518 40.909 0.00 0.00 0.00 1.94
456 459 4.643463 TGCATGTACTCCCTTCGTTTTTA 58.357 39.130 0.00 0.00 0.00 1.52
457 460 5.250200 TGCATGTACTCCCTTCGTTTTTAT 58.750 37.500 0.00 0.00 0.00 1.40
458 461 5.708230 TGCATGTACTCCCTTCGTTTTTATT 59.292 36.000 0.00 0.00 0.00 1.40
459 462 6.207810 TGCATGTACTCCCTTCGTTTTTATTT 59.792 34.615 0.00 0.00 0.00 1.40
460 463 7.390996 TGCATGTACTCCCTTCGTTTTTATTTA 59.609 33.333 0.00 0.00 0.00 1.40
461 464 7.695201 GCATGTACTCCCTTCGTTTTTATTTAC 59.305 37.037 0.00 0.00 0.00 2.01
462 465 8.943002 CATGTACTCCCTTCGTTTTTATTTACT 58.057 33.333 0.00 0.00 0.00 2.24
463 466 8.538409 TGTACTCCCTTCGTTTTTATTTACTC 57.462 34.615 0.00 0.00 0.00 2.59
464 467 8.149647 TGTACTCCCTTCGTTTTTATTTACTCA 58.850 33.333 0.00 0.00 0.00 3.41
465 468 9.159364 GTACTCCCTTCGTTTTTATTTACTCAT 57.841 33.333 0.00 0.00 0.00 2.90
466 469 8.040716 ACTCCCTTCGTTTTTATTTACTCATG 57.959 34.615 0.00 0.00 0.00 3.07
467 470 7.664318 ACTCCCTTCGTTTTTATTTACTCATGT 59.336 33.333 0.00 0.00 0.00 3.21
468 471 9.158233 CTCCCTTCGTTTTTATTTACTCATGTA 57.842 33.333 0.00 0.00 0.00 2.29
469 472 9.675464 TCCCTTCGTTTTTATTTACTCATGTAT 57.325 29.630 0.00 0.00 0.00 2.29
482 485 8.856153 TTTACTCATGTATTAGCTTTGGTCAA 57.144 30.769 0.00 0.00 0.00 3.18
483 486 6.743575 ACTCATGTATTAGCTTTGGTCAAC 57.256 37.500 0.00 0.00 0.00 3.18
484 487 5.351465 ACTCATGTATTAGCTTTGGTCAACG 59.649 40.000 0.00 0.00 0.00 4.10
485 488 5.242434 TCATGTATTAGCTTTGGTCAACGT 58.758 37.500 0.00 0.00 0.00 3.99
486 489 5.350365 TCATGTATTAGCTTTGGTCAACGTC 59.650 40.000 0.00 0.00 0.00 4.34
487 490 4.633175 TGTATTAGCTTTGGTCAACGTCA 58.367 39.130 0.00 0.00 0.00 4.35
488 491 5.057819 TGTATTAGCTTTGGTCAACGTCAA 58.942 37.500 0.00 0.00 0.00 3.18
489 492 4.749245 ATTAGCTTTGGTCAACGTCAAG 57.251 40.909 0.00 0.00 0.00 3.02
490 493 0.663153 AGCTTTGGTCAACGTCAAGC 59.337 50.000 0.00 0.00 0.00 4.01
491 494 0.663153 GCTTTGGTCAACGTCAAGCT 59.337 50.000 0.00 0.00 0.00 3.74
492 495 1.065551 GCTTTGGTCAACGTCAAGCTT 59.934 47.619 0.00 0.00 0.00 3.74
493 496 2.479560 GCTTTGGTCAACGTCAAGCTTT 60.480 45.455 0.00 0.00 0.00 3.51
494 497 2.842208 TTGGTCAACGTCAAGCTTTG 57.158 45.000 0.00 0.00 0.00 2.77
495 498 1.745232 TGGTCAACGTCAAGCTTTGT 58.255 45.000 0.00 0.00 0.00 2.83
496 499 2.907634 TGGTCAACGTCAAGCTTTGTA 58.092 42.857 0.00 0.00 0.00 2.41
497 500 3.271729 TGGTCAACGTCAAGCTTTGTAA 58.728 40.909 0.00 0.00 0.00 2.41
498 501 3.690139 TGGTCAACGTCAAGCTTTGTAAA 59.310 39.130 0.00 0.00 0.00 2.01
499 502 4.033019 GGTCAACGTCAAGCTTTGTAAAC 58.967 43.478 0.00 0.00 0.00 2.01
500 503 4.201881 GGTCAACGTCAAGCTTTGTAAACT 60.202 41.667 0.00 0.00 0.00 2.66
501 504 5.329493 GTCAACGTCAAGCTTTGTAAACTT 58.671 37.500 0.00 0.00 0.00 2.66
502 505 5.798434 GTCAACGTCAAGCTTTGTAAACTTT 59.202 36.000 0.00 0.00 0.00 2.66
503 506 5.797934 TCAACGTCAAGCTTTGTAAACTTTG 59.202 36.000 0.00 1.50 0.00 2.77
504 507 5.554822 ACGTCAAGCTTTGTAAACTTTGA 57.445 34.783 0.00 0.00 0.00 2.69
505 508 5.329493 ACGTCAAGCTTTGTAAACTTTGAC 58.671 37.500 0.00 13.70 0.00 3.18
506 509 5.106475 ACGTCAAGCTTTGTAAACTTTGACA 60.106 36.000 18.87 0.00 0.00 3.58
507 510 5.797934 CGTCAAGCTTTGTAAACTTTGACAA 59.202 36.000 18.87 0.13 33.81 3.18
508 511 6.306837 CGTCAAGCTTTGTAAACTTTGACAAA 59.693 34.615 18.87 0.00 41.90 2.83
660 663 7.834068 GACTTCAGTCAACTCTAATATGCAA 57.166 36.000 1.86 0.00 44.18 4.08
661 664 8.256611 GACTTCAGTCAACTCTAATATGCAAA 57.743 34.615 1.86 0.00 44.18 3.68
662 665 8.621532 ACTTCAGTCAACTCTAATATGCAAAA 57.378 30.769 0.00 0.00 0.00 2.44
663 666 9.236006 ACTTCAGTCAACTCTAATATGCAAAAT 57.764 29.630 0.00 0.00 0.00 1.82
678 681 9.541143 AATATGCAAAATAATTAAAACCGAGGG 57.459 29.630 0.00 0.00 0.00 4.30
679 682 6.591750 TGCAAAATAATTAAAACCGAGGGA 57.408 33.333 0.00 0.00 0.00 4.20
680 683 6.626302 TGCAAAATAATTAAAACCGAGGGAG 58.374 36.000 0.00 0.00 0.00 4.30
681 684 6.209788 TGCAAAATAATTAAAACCGAGGGAGT 59.790 34.615 0.00 0.00 0.00 3.85
682 685 7.393796 TGCAAAATAATTAAAACCGAGGGAGTA 59.606 33.333 0.00 0.00 0.00 2.59
695 698 5.189145 ACCGAGGGAGTATATGAACAACTTT 59.811 40.000 0.00 0.00 0.00 2.66
825 1013 3.767673 ACGTCCAGGCTAAATCAGTTCTA 59.232 43.478 0.00 0.00 0.00 2.10
881 1069 4.383118 CGCCCTATATAAATGGGAGGTCAG 60.383 50.000 9.28 0.00 43.47 3.51
929 1117 1.409427 CTGGCTACTACCACACTAGGC 59.591 57.143 0.00 0.00 35.33 3.93
1104 1304 2.203728 TACCACCACCTCACGCCT 60.204 61.111 0.00 0.00 0.00 5.52
1143 1352 3.735820 GCTTGGATAACGACATACCGTCA 60.736 47.826 0.00 0.00 45.70 4.35
1284 1520 2.491022 CCTCCTCCCCGATGACGAC 61.491 68.421 0.00 0.00 42.66 4.34
1300 1539 6.681178 CGATGACGACCACAATGTAATTAAAC 59.319 38.462 0.00 0.00 42.66 2.01
1597 1885 0.915872 ATCATGGTCCAGGTCAGCCA 60.916 55.000 2.95 0.00 37.19 4.75
1849 2193 9.797556 ATTAATATAAAACACTTCCTTTTCCGC 57.202 29.630 0.00 0.00 0.00 5.54
1884 2228 4.406003 AGGTGTGGGTCTAGATAACATGAC 59.594 45.833 0.00 0.00 0.00 3.06
1886 2230 5.163301 GGTGTGGGTCTAGATAACATGACAT 60.163 44.000 0.00 0.00 0.00 3.06
1946 2290 2.103373 TCTGGCTAATCTTGTCGAGCT 58.897 47.619 0.00 0.00 35.23 4.09
1956 2300 2.826128 TCTTGTCGAGCTCTGTTATGGT 59.174 45.455 12.85 0.00 0.00 3.55
2461 2805 7.466804 TCAGTGGTGGAATTTAAAATCTACCT 58.533 34.615 28.67 14.47 44.81 3.08
2497 2841 3.955551 TGGTAGCATAGTATGACGAACCA 59.044 43.478 14.52 17.53 31.77 3.67
2623 3346 6.785076 TCCTCCACTAAAATGGTTCACAATA 58.215 36.000 0.00 0.00 40.95 1.90
2721 3450 5.850557 TCGTTCGGGGTTACATCTTATAA 57.149 39.130 0.00 0.00 0.00 0.98
2814 3543 6.491062 AGGATGAGTTCATTGTGTTTTGATCA 59.509 34.615 0.00 0.00 36.57 2.92
2815 3544 7.014518 AGGATGAGTTCATTGTGTTTTGATCAA 59.985 33.333 3.38 3.38 36.57 2.57
2870 3601 3.091545 TCAGGTGGATGAGAATTTTGCC 58.908 45.455 0.00 0.00 0.00 4.52
2989 3721 2.803203 TCCTTCGTGGATAGACCCG 58.197 57.895 0.00 0.00 40.56 5.28
3004 3736 1.818674 GACCCGCATTGACCTCAATTT 59.181 47.619 0.00 0.00 43.48 1.82
3088 3821 5.413833 GCCAATACAACTGATGGGATAGATG 59.586 44.000 0.00 0.00 33.45 2.90
3108 3841 4.790810 TGTAGCTTGTCGTATCTAGACG 57.209 45.455 0.00 0.00 44.29 4.18
3238 3971 3.996150 ACAAGCAGACAAGGAACATTG 57.004 42.857 0.00 0.00 36.22 2.82
3257 3990 5.186992 ACATTGCCCTTAATTTGTTAGGACC 59.813 40.000 0.00 0.00 0.00 4.46
3301 4034 2.685106 TCTCCTACCCTCTAGGCATG 57.315 55.000 0.00 0.00 40.58 4.06
3397 4130 9.571816 TTCATGCATATTTCTACATGTTATCCA 57.428 29.630 2.30 0.00 40.57 3.41
3398 4131 9.002600 TCATGCATATTTCTACATGTTATCCAC 57.997 33.333 2.30 0.00 40.57 4.02
3531 4269 6.262273 GGTGACGGAATGGAAATTGTATACAT 59.738 38.462 6.36 0.00 0.00 2.29
3578 4316 6.633500 TTTGTATTGAAACAGAGAACCCAG 57.367 37.500 0.00 0.00 0.00 4.45
3628 4366 3.441496 TTGTAACGAACTGGAGAACGT 57.559 42.857 0.00 0.00 40.64 3.99
3672 4410 6.183360 ACAACATCTGCATCATTAGTGGATTG 60.183 38.462 0.00 0.00 0.00 2.67
3772 4513 9.703892 AATCTCAGATAAATAGTACTGATGCAC 57.296 33.333 5.39 0.00 38.43 4.57
3779 4520 2.609427 AGTACTGATGCACGCATGAT 57.391 45.000 9.70 0.00 36.70 2.45
3781 4522 3.646946 AGTACTGATGCACGCATGATAG 58.353 45.455 9.70 7.49 36.70 2.08
3934 4676 7.824779 GGAGAAAATAAATATAGAGATGGCCGT 59.175 37.037 0.00 0.00 0.00 5.68
3960 4702 2.988493 CAGTGGCATGCATAAAACACAC 59.012 45.455 21.36 14.95 0.00 3.82
3983 4725 5.758296 ACGCCATTGTCGATGTAATTCTTAT 59.242 36.000 0.00 0.00 33.71 1.73
4093 4843 0.736053 TGTTCGTGTTCAGGTTTGGC 59.264 50.000 0.00 0.00 0.00 4.52
4095 4845 1.336755 GTTCGTGTTCAGGTTTGGCAT 59.663 47.619 0.00 0.00 0.00 4.40
4101 4851 3.245048 GTGTTCAGGTTTGGCATTTTTCG 59.755 43.478 0.00 0.00 0.00 3.46
4102 4852 2.799978 GTTCAGGTTTGGCATTTTTCGG 59.200 45.455 0.00 0.00 0.00 4.30
4103 4853 1.342819 TCAGGTTTGGCATTTTTCGGG 59.657 47.619 0.00 0.00 0.00 5.14
4104 4854 0.684535 AGGTTTGGCATTTTTCGGGG 59.315 50.000 0.00 0.00 0.00 5.73
4105 4855 0.321210 GGTTTGGCATTTTTCGGGGG 60.321 55.000 0.00 0.00 0.00 5.40
4301 5051 2.364632 CAATGTGTCCGGCCTATCAAA 58.635 47.619 0.00 0.00 0.00 2.69
4402 5154 5.811399 AAAAACATCAGTTCAGACGTTCA 57.189 34.783 0.00 0.00 36.84 3.18
4409 5161 6.929049 ACATCAGTTCAGACGTTCATTTTCTA 59.071 34.615 0.00 0.00 0.00 2.10
4488 5243 9.588096 ACACATCCTATAACTGTATCATACTCA 57.412 33.333 0.00 0.00 0.00 3.41
4504 5259 8.674263 ATCATACTCAGCATTCTTTTTCTAGG 57.326 34.615 0.00 0.00 0.00 3.02
4505 5260 6.540189 TCATACTCAGCATTCTTTTTCTAGGC 59.460 38.462 0.00 0.00 0.00 3.93
4506 5261 4.013050 ACTCAGCATTCTTTTTCTAGGCC 58.987 43.478 0.00 0.00 0.00 5.19
4507 5262 4.012374 CTCAGCATTCTTTTTCTAGGCCA 58.988 43.478 5.01 0.00 0.00 5.36
4508 5263 3.758554 TCAGCATTCTTTTTCTAGGCCAC 59.241 43.478 5.01 0.00 0.00 5.01
4509 5264 3.092301 AGCATTCTTTTTCTAGGCCACC 58.908 45.455 5.01 0.00 0.00 4.61
4510 5265 2.166459 GCATTCTTTTTCTAGGCCACCC 59.834 50.000 5.01 0.00 0.00 4.61
4511 5266 3.701664 CATTCTTTTTCTAGGCCACCCT 58.298 45.455 5.01 0.00 45.61 4.34
4512 5267 3.434940 TTCTTTTTCTAGGCCACCCTC 57.565 47.619 5.01 0.00 41.75 4.30
4513 5268 1.278127 TCTTTTTCTAGGCCACCCTCG 59.722 52.381 5.01 0.00 41.75 4.63
4514 5269 0.326927 TTTTTCTAGGCCACCCTCGG 59.673 55.000 5.01 0.00 41.75 4.63
4515 5270 1.559065 TTTTCTAGGCCACCCTCGGG 61.559 60.000 5.01 0.00 41.75 5.14
4525 5280 2.735237 CCCTCGGGGTAGCGAATC 59.265 66.667 0.00 0.00 38.25 2.52
4526 5281 1.833049 CCCTCGGGGTAGCGAATCT 60.833 63.158 0.00 0.00 38.25 2.40
4527 5282 0.538977 CCCTCGGGGTAGCGAATCTA 60.539 60.000 0.00 0.00 38.25 1.98
4528 5283 1.546961 CCTCGGGGTAGCGAATCTAT 58.453 55.000 0.00 0.00 0.00 1.98
4529 5284 1.202582 CCTCGGGGTAGCGAATCTATG 59.797 57.143 0.00 0.00 0.00 2.23
4530 5285 2.160205 CTCGGGGTAGCGAATCTATGA 58.840 52.381 0.00 0.00 0.00 2.15
4531 5286 2.160205 TCGGGGTAGCGAATCTATGAG 58.840 52.381 0.00 0.00 0.00 2.90
4532 5287 1.887198 CGGGGTAGCGAATCTATGAGT 59.113 52.381 0.00 0.00 0.00 3.41
4533 5288 2.296471 CGGGGTAGCGAATCTATGAGTT 59.704 50.000 0.00 0.00 0.00 3.01
4534 5289 3.243771 CGGGGTAGCGAATCTATGAGTTT 60.244 47.826 0.00 0.00 0.00 2.66
4535 5290 4.058817 GGGGTAGCGAATCTATGAGTTTG 58.941 47.826 0.00 0.00 0.00 2.93
4536 5291 4.443034 GGGGTAGCGAATCTATGAGTTTGT 60.443 45.833 0.00 0.00 0.00 2.83
4537 5292 5.116882 GGGTAGCGAATCTATGAGTTTGTT 58.883 41.667 0.00 0.00 0.00 2.83
4538 5293 5.585047 GGGTAGCGAATCTATGAGTTTGTTT 59.415 40.000 0.00 0.00 0.00 2.83
4539 5294 6.456988 GGGTAGCGAATCTATGAGTTTGTTTG 60.457 42.308 0.00 0.00 0.00 2.93
4540 5295 5.551760 AGCGAATCTATGAGTTTGTTTGG 57.448 39.130 0.00 0.00 0.00 3.28
4541 5296 5.245531 AGCGAATCTATGAGTTTGTTTGGA 58.754 37.500 0.00 0.00 0.00 3.53
4542 5297 5.122396 AGCGAATCTATGAGTTTGTTTGGAC 59.878 40.000 0.00 0.00 0.00 4.02
4543 5298 5.550981 CGAATCTATGAGTTTGTTTGGACG 58.449 41.667 0.00 0.00 0.00 4.79
4544 5299 5.445939 CGAATCTATGAGTTTGTTTGGACGG 60.446 44.000 0.00 0.00 0.00 4.79
4545 5300 3.670625 TCTATGAGTTTGTTTGGACGGG 58.329 45.455 0.00 0.00 0.00 5.28
4546 5301 2.649531 ATGAGTTTGTTTGGACGGGA 57.350 45.000 0.00 0.00 0.00 5.14
4547 5302 1.961793 TGAGTTTGTTTGGACGGGAG 58.038 50.000 0.00 0.00 0.00 4.30
4548 5303 0.591659 GAGTTTGTTTGGACGGGAGC 59.408 55.000 0.00 0.00 0.00 4.70
4549 5304 0.822121 AGTTTGTTTGGACGGGAGCC 60.822 55.000 0.00 0.00 0.00 4.70
4565 5320 1.803289 GCCGTGAGCTGGAATTTCC 59.197 57.895 8.59 8.59 38.99 3.13
4566 5321 0.678048 GCCGTGAGCTGGAATTTCCT 60.678 55.000 16.25 0.00 37.46 3.36
4567 5322 1.406887 GCCGTGAGCTGGAATTTCCTA 60.407 52.381 16.25 2.72 37.46 2.94
4568 5323 2.746472 GCCGTGAGCTGGAATTTCCTAT 60.746 50.000 16.25 2.53 37.46 2.57
4569 5324 3.494398 GCCGTGAGCTGGAATTTCCTATA 60.494 47.826 16.25 0.00 37.46 1.31
4570 5325 4.058817 CCGTGAGCTGGAATTTCCTATAC 58.941 47.826 16.25 7.61 37.46 1.47
4571 5326 3.736252 CGTGAGCTGGAATTTCCTATACG 59.264 47.826 16.25 14.19 37.46 3.06
4572 5327 4.499188 CGTGAGCTGGAATTTCCTATACGA 60.499 45.833 16.25 0.00 37.46 3.43
4573 5328 5.542779 GTGAGCTGGAATTTCCTATACGAT 58.457 41.667 16.25 0.00 37.46 3.73
4574 5329 5.406780 GTGAGCTGGAATTTCCTATACGATG 59.593 44.000 16.25 0.00 37.46 3.84
4575 5330 4.319177 AGCTGGAATTTCCTATACGATGC 58.681 43.478 16.25 7.69 37.46 3.91
4576 5331 4.040952 AGCTGGAATTTCCTATACGATGCT 59.959 41.667 16.25 9.44 37.46 3.79
4577 5332 4.757149 GCTGGAATTTCCTATACGATGCTT 59.243 41.667 16.25 0.00 37.46 3.91
4578 5333 5.932303 GCTGGAATTTCCTATACGATGCTTA 59.068 40.000 16.25 0.00 37.46 3.09
4579 5334 6.595716 GCTGGAATTTCCTATACGATGCTTAT 59.404 38.462 16.25 0.00 37.46 1.73
4580 5335 7.119846 GCTGGAATTTCCTATACGATGCTTATT 59.880 37.037 16.25 0.00 37.46 1.40
4581 5336 9.653287 CTGGAATTTCCTATACGATGCTTATTA 57.347 33.333 16.25 0.00 37.46 0.98
4582 5337 9.653287 TGGAATTTCCTATACGATGCTTATTAG 57.347 33.333 16.25 0.00 37.46 1.73
4583 5338 8.604890 GGAATTTCCTATACGATGCTTATTAGC 58.395 37.037 8.25 0.00 39.69 3.09
4616 5371 8.500753 TTTTTGACATACGATGCTTATTACCT 57.499 30.769 0.00 0.00 0.00 3.08
4617 5372 7.477144 TTTGACATACGATGCTTATTACCTG 57.523 36.000 0.00 0.00 0.00 4.00
4618 5373 6.156748 TGACATACGATGCTTATTACCTGT 57.843 37.500 0.00 0.00 0.00 4.00
4619 5374 7.279750 TGACATACGATGCTTATTACCTGTA 57.720 36.000 0.00 0.00 0.00 2.74
4620 5375 7.718525 TGACATACGATGCTTATTACCTGTAA 58.281 34.615 0.00 0.00 0.00 2.41
4621 5376 7.650504 TGACATACGATGCTTATTACCTGTAAC 59.349 37.037 0.00 0.00 0.00 2.50
4622 5377 7.723324 ACATACGATGCTTATTACCTGTAACT 58.277 34.615 0.00 0.00 0.00 2.24
4623 5378 7.652105 ACATACGATGCTTATTACCTGTAACTG 59.348 37.037 0.00 0.00 0.00 3.16
4624 5379 5.974108 ACGATGCTTATTACCTGTAACTGT 58.026 37.500 0.00 0.00 0.00 3.55
4625 5380 6.403878 ACGATGCTTATTACCTGTAACTGTT 58.596 36.000 0.00 0.00 0.00 3.16
4626 5381 6.312918 ACGATGCTTATTACCTGTAACTGTTG 59.687 38.462 2.69 0.00 0.00 3.33
4627 5382 5.873179 TGCTTATTACCTGTAACTGTTGC 57.127 39.130 2.69 2.00 0.00 4.17
4628 5383 5.556915 TGCTTATTACCTGTAACTGTTGCT 58.443 37.500 9.94 0.00 0.00 3.91
4629 5384 5.411361 TGCTTATTACCTGTAACTGTTGCTG 59.589 40.000 9.94 9.02 0.00 4.41
4630 5385 5.163754 GCTTATTACCTGTAACTGTTGCTGG 60.164 44.000 25.19 25.19 39.61 4.85
4631 5386 4.634012 ATTACCTGTAACTGTTGCTGGA 57.366 40.909 30.65 16.29 37.69 3.86
4632 5387 4.634012 TTACCTGTAACTGTTGCTGGAT 57.366 40.909 30.65 20.35 37.69 3.41
4633 5388 3.059352 ACCTGTAACTGTTGCTGGATC 57.941 47.619 30.65 4.86 37.69 3.36
4634 5389 2.002586 CCTGTAACTGTTGCTGGATCG 58.997 52.381 23.50 2.85 36.68 3.69
4635 5390 1.394917 CTGTAACTGTTGCTGGATCGC 59.605 52.381 9.94 0.00 0.00 4.58
4636 5391 1.270571 TGTAACTGTTGCTGGATCGCA 60.271 47.619 9.94 0.00 38.31 5.10
4637 5392 1.128692 GTAACTGTTGCTGGATCGCAC 59.871 52.381 2.69 0.00 40.09 5.34
4638 5393 0.534877 AACTGTTGCTGGATCGCACA 60.535 50.000 0.00 0.00 40.09 4.57
4639 5394 0.321919 ACTGTTGCTGGATCGCACAT 60.322 50.000 0.00 0.00 40.09 3.21
4640 5395 0.098200 CTGTTGCTGGATCGCACATG 59.902 55.000 0.00 0.00 40.09 3.21
4641 5396 0.321475 TGTTGCTGGATCGCACATGA 60.321 50.000 0.00 0.00 40.09 3.07
4642 5397 0.376152 GTTGCTGGATCGCACATGAG 59.624 55.000 0.00 0.00 40.09 2.90
4643 5398 1.371337 TTGCTGGATCGCACATGAGC 61.371 55.000 4.89 4.89 40.09 4.26
4654 5409 2.341257 GCACATGAGCGACTATATGGG 58.659 52.381 0.00 0.00 0.00 4.00
4655 5410 2.341257 CACATGAGCGACTATATGGGC 58.659 52.381 0.00 0.00 0.00 5.36
4656 5411 2.028658 CACATGAGCGACTATATGGGCT 60.029 50.000 0.00 0.00 38.70 5.19
4657 5412 2.028658 ACATGAGCGACTATATGGGCTG 60.029 50.000 0.00 0.00 35.54 4.85
4658 5413 0.969149 TGAGCGACTATATGGGCTGG 59.031 55.000 0.00 0.00 35.54 4.85
4659 5414 0.390472 GAGCGACTATATGGGCTGGC 60.390 60.000 0.00 0.00 35.54 4.85
4660 5415 1.376037 GCGACTATATGGGCTGGCC 60.376 63.158 14.23 14.23 0.00 5.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 8.024285 AGTAATTCTCATTCGACCGAGATAATC 58.976 37.037 12.48 6.10 38.06 1.75
40 41 8.424918 TCAGAATGGAGGTAGTAATTCTCATTC 58.575 37.037 0.00 0.00 37.29 2.67
57 58 4.136796 CGGAGCCAATAAATCAGAATGGA 58.863 43.478 0.00 0.00 36.16 3.41
62 63 3.194861 CGAACGGAGCCAATAAATCAGA 58.805 45.455 0.00 0.00 0.00 3.27
66 67 6.127842 ACAAAATACGAACGGAGCCAATAAAT 60.128 34.615 0.00 0.00 0.00 1.40
70 71 3.078837 ACAAAATACGAACGGAGCCAAT 58.921 40.909 0.00 0.00 0.00 3.16
76 77 5.987777 TTTTGAGACAAAATACGAACGGA 57.012 34.783 5.70 0.00 0.00 4.69
272 273 9.537852 TGAGATTTAACTACTACCTTTGTCCTA 57.462 33.333 0.00 0.00 0.00 2.94
302 303 5.362717 TGACAGGTCAATGATACTCGGTATT 59.637 40.000 0.00 0.00 36.53 1.89
304 305 4.274978 TGACAGGTCAATGATACTCGGTA 58.725 43.478 0.00 0.00 36.53 4.02
353 356 4.333649 TCTGTTGCTTGTTTTCAGAGTCAG 59.666 41.667 0.00 0.00 32.49 3.51
442 445 8.040716 ACATGAGTAAATAAAAACGAAGGGAG 57.959 34.615 0.00 0.00 0.00 4.30
443 446 7.989416 ACATGAGTAAATAAAAACGAAGGGA 57.011 32.000 0.00 0.00 0.00 4.20
456 459 9.461312 TTGACCAAAGCTAATACATGAGTAAAT 57.539 29.630 0.00 0.00 33.13 1.40
457 460 8.726988 GTTGACCAAAGCTAATACATGAGTAAA 58.273 33.333 0.00 0.00 33.13 2.01
458 461 7.064134 CGTTGACCAAAGCTAATACATGAGTAA 59.936 37.037 0.00 0.00 33.13 2.24
459 462 6.533723 CGTTGACCAAAGCTAATACATGAGTA 59.466 38.462 0.00 0.00 34.10 2.59
460 463 5.351465 CGTTGACCAAAGCTAATACATGAGT 59.649 40.000 0.00 0.00 0.00 3.41
461 464 5.351465 ACGTTGACCAAAGCTAATACATGAG 59.649 40.000 0.00 0.00 0.00 2.90
462 465 5.242434 ACGTTGACCAAAGCTAATACATGA 58.758 37.500 0.00 0.00 0.00 3.07
463 466 5.121611 TGACGTTGACCAAAGCTAATACATG 59.878 40.000 0.00 0.00 0.00 3.21
464 467 5.242434 TGACGTTGACCAAAGCTAATACAT 58.758 37.500 0.00 0.00 0.00 2.29
465 468 4.633175 TGACGTTGACCAAAGCTAATACA 58.367 39.130 0.00 0.00 0.00 2.29
466 469 5.600908 TTGACGTTGACCAAAGCTAATAC 57.399 39.130 0.00 0.00 0.00 1.89
467 470 4.153475 GCTTGACGTTGACCAAAGCTAATA 59.847 41.667 0.00 0.00 0.00 0.98
468 471 3.058224 GCTTGACGTTGACCAAAGCTAAT 60.058 43.478 0.00 0.00 0.00 1.73
469 472 2.289547 GCTTGACGTTGACCAAAGCTAA 59.710 45.455 0.00 0.00 0.00 3.09
470 473 1.871039 GCTTGACGTTGACCAAAGCTA 59.129 47.619 0.00 0.00 0.00 3.32
471 474 0.663153 GCTTGACGTTGACCAAAGCT 59.337 50.000 0.00 0.00 0.00 3.74
472 475 0.663153 AGCTTGACGTTGACCAAAGC 59.337 50.000 0.00 0.00 0.00 3.51
473 476 3.108144 CAAAGCTTGACGTTGACCAAAG 58.892 45.455 0.00 0.00 39.81 2.77
474 477 2.490115 ACAAAGCTTGACGTTGACCAAA 59.510 40.909 0.00 0.00 39.81 3.28
475 478 2.088423 ACAAAGCTTGACGTTGACCAA 58.912 42.857 0.00 0.00 39.81 3.67
476 479 1.745232 ACAAAGCTTGACGTTGACCA 58.255 45.000 0.00 0.00 39.81 4.02
477 480 3.955771 TTACAAAGCTTGACGTTGACC 57.044 42.857 0.00 0.00 39.81 4.02
478 481 4.905269 AGTTTACAAAGCTTGACGTTGAC 58.095 39.130 0.00 1.22 39.81 3.18
479 482 5.554822 AAGTTTACAAAGCTTGACGTTGA 57.445 34.783 0.00 0.00 39.81 3.18
480 483 5.797934 TCAAAGTTTACAAAGCTTGACGTTG 59.202 36.000 0.00 9.09 42.68 4.10
481 484 5.798434 GTCAAAGTTTACAAAGCTTGACGTT 59.202 36.000 0.00 0.00 34.11 3.99
482 485 5.106475 TGTCAAAGTTTACAAAGCTTGACGT 60.106 36.000 0.00 0.18 40.30 4.34
483 486 5.328691 TGTCAAAGTTTACAAAGCTTGACG 58.671 37.500 0.00 0.00 40.30 4.35
484 487 7.575332 TTTGTCAAAGTTTACAAAGCTTGAC 57.425 32.000 0.00 15.49 39.88 3.18
636 639 7.834068 TTGCATATTAGAGTTGACTGAAGTC 57.166 36.000 3.41 3.41 44.97 3.01
637 640 8.621532 TTTTGCATATTAGAGTTGACTGAAGT 57.378 30.769 0.00 0.00 0.00 3.01
652 655 9.541143 CCCTCGGTTTTAATTATTTTGCATATT 57.459 29.630 0.00 0.00 0.00 1.28
653 656 8.919145 TCCCTCGGTTTTAATTATTTTGCATAT 58.081 29.630 0.00 0.00 0.00 1.78
654 657 8.294954 TCCCTCGGTTTTAATTATTTTGCATA 57.705 30.769 0.00 0.00 0.00 3.14
655 658 7.093509 ACTCCCTCGGTTTTAATTATTTTGCAT 60.094 33.333 0.00 0.00 0.00 3.96
656 659 6.209788 ACTCCCTCGGTTTTAATTATTTTGCA 59.790 34.615 0.00 0.00 0.00 4.08
657 660 6.627243 ACTCCCTCGGTTTTAATTATTTTGC 58.373 36.000 0.00 0.00 0.00 3.68
663 666 9.768662 GTTCATATACTCCCTCGGTTTTAATTA 57.231 33.333 0.00 0.00 0.00 1.40
664 667 8.269317 TGTTCATATACTCCCTCGGTTTTAATT 58.731 33.333 0.00 0.00 0.00 1.40
665 668 7.798071 TGTTCATATACTCCCTCGGTTTTAAT 58.202 34.615 0.00 0.00 0.00 1.40
666 669 7.185318 TGTTCATATACTCCCTCGGTTTTAA 57.815 36.000 0.00 0.00 0.00 1.52
667 670 6.795144 TGTTCATATACTCCCTCGGTTTTA 57.205 37.500 0.00 0.00 0.00 1.52
668 671 5.687166 TGTTCATATACTCCCTCGGTTTT 57.313 39.130 0.00 0.00 0.00 2.43
669 672 5.189145 AGTTGTTCATATACTCCCTCGGTTT 59.811 40.000 0.00 0.00 0.00 3.27
670 673 4.715297 AGTTGTTCATATACTCCCTCGGTT 59.285 41.667 0.00 0.00 0.00 4.44
671 674 4.287552 AGTTGTTCATATACTCCCTCGGT 58.712 43.478 0.00 0.00 0.00 4.69
672 675 4.939052 AGTTGTTCATATACTCCCTCGG 57.061 45.455 0.00 0.00 0.00 4.63
673 676 6.338146 TCAAAGTTGTTCATATACTCCCTCG 58.662 40.000 0.00 0.00 0.00 4.63
674 677 8.561738 TTTCAAAGTTGTTCATATACTCCCTC 57.438 34.615 0.00 0.00 0.00 4.30
675 678 8.934023 TTTTCAAAGTTGTTCATATACTCCCT 57.066 30.769 0.00 0.00 0.00 4.20
825 1013 1.273606 CGACAGTGTCCAGAACTCCAT 59.726 52.381 17.57 0.00 0.00 3.41
881 1069 0.884704 TTGAGCAAGTTCCGGAGTGC 60.885 55.000 22.53 22.53 37.26 4.40
929 1117 0.401105 ATGGTGGAGATGAGAGGGGG 60.401 60.000 0.00 0.00 0.00 5.40
1284 1520 7.309920 AGTTAAGCGGTTTAATTACATTGTGG 58.690 34.615 4.64 0.00 33.99 4.17
1300 1539 2.915463 CGAGTTGTGTCTAGTTAAGCGG 59.085 50.000 0.00 0.00 0.00 5.52
1510 1792 4.393155 TCATGGCGCCTTGCTCGT 62.393 61.111 31.77 2.62 45.43 4.18
1834 2178 1.156736 CATCGCGGAAAAGGAAGTGT 58.843 50.000 6.13 0.00 0.00 3.55
1849 2193 1.739466 CCCACACCTCAATCAACATCG 59.261 52.381 0.00 0.00 0.00 3.84
1933 2277 4.081420 ACCATAACAGAGCTCGACAAGATT 60.081 41.667 8.37 0.00 0.00 2.40
2430 2774 9.573133 GATTTTAAATTCCACCACTGATAACTG 57.427 33.333 0.00 0.00 0.00 3.16
2431 2775 9.533831 AGATTTTAAATTCCACCACTGATAACT 57.466 29.630 6.50 0.00 0.00 2.24
2434 2778 9.403583 GGTAGATTTTAAATTCCACCACTGATA 57.596 33.333 17.47 0.00 0.00 2.15
2435 2779 8.116026 AGGTAGATTTTAAATTCCACCACTGAT 58.884 33.333 21.74 5.86 0.00 2.90
2436 2780 7.466804 AGGTAGATTTTAAATTCCACCACTGA 58.533 34.615 21.74 0.00 0.00 3.41
2437 2781 7.611855 AGAGGTAGATTTTAAATTCCACCACTG 59.388 37.037 21.74 0.00 0.00 3.66
2438 2782 7.699878 AGAGGTAGATTTTAAATTCCACCACT 58.300 34.615 21.74 18.90 0.00 4.00
2439 2783 7.939784 AGAGGTAGATTTTAAATTCCACCAC 57.060 36.000 21.74 17.53 0.00 4.16
2440 2784 8.167392 TCAAGAGGTAGATTTTAAATTCCACCA 58.833 33.333 21.74 5.86 0.00 4.17
2441 2785 8.575649 TCAAGAGGTAGATTTTAAATTCCACC 57.424 34.615 15.64 15.64 0.00 4.61
2442 2786 9.232473 ACTCAAGAGGTAGATTTTAAATTCCAC 57.768 33.333 6.50 3.92 0.00 4.02
2443 2787 9.807921 AACTCAAGAGGTAGATTTTAAATTCCA 57.192 29.630 6.50 0.00 0.00 3.53
2461 2805 8.079211 ACTATGCTACCATCTTAAACTCAAGA 57.921 34.615 0.00 0.00 38.84 3.02
2581 3304 3.457749 GAGGAGAGACCCATTTTGATCCT 59.542 47.826 0.00 0.00 38.62 3.24
2623 3346 9.167311 CACTTAACTTCCAACTCATAAGCTATT 57.833 33.333 0.00 0.00 0.00 1.73
2721 3450 4.388378 GTAGTTCAAATCCTACGGAGCT 57.612 45.455 0.00 0.00 34.05 4.09
2742 3471 2.157668 CACCAAGGAACGTTCATCTTCG 59.842 50.000 28.24 17.62 0.00 3.79
2800 3529 9.603921 AGACAAAAGAATTGATCAAAACACAAT 57.396 25.926 13.09 0.00 36.07 2.71
2814 3543 4.516321 GCATGCCCAAAAGACAAAAGAATT 59.484 37.500 6.36 0.00 0.00 2.17
2815 3544 4.067192 GCATGCCCAAAAGACAAAAGAAT 58.933 39.130 6.36 0.00 0.00 2.40
2989 3721 7.656707 AAACAATACAAATTGAGGTCAATGC 57.343 32.000 5.98 0.00 45.06 3.56
3088 3821 4.792528 ACGTCTAGATACGACAAGCTAC 57.207 45.455 10.62 0.00 45.68 3.58
3238 3971 3.376234 GTCGGTCCTAACAAATTAAGGGC 59.624 47.826 0.00 0.00 0.00 5.19
3301 4034 2.284112 TCACGGGTGGTAGGGTCC 60.284 66.667 0.00 0.00 0.00 4.46
3421 4154 4.725556 TTTTTGACACATCTGTAGCGTC 57.274 40.909 0.00 0.00 0.00 5.19
3485 4222 9.302345 GTCACCGTAAGTTGGATCATATATATG 57.698 37.037 15.47 15.47 35.04 1.78
3486 4223 8.188799 CGTCACCGTAAGTTGGATCATATATAT 58.811 37.037 0.00 0.00 0.00 0.86
3552 4290 7.432869 TGGGTTCTCTGTTTCAATACAAAATG 58.567 34.615 0.00 0.00 0.00 2.32
3578 4316 0.449388 CCTCCTTGCTCATTGTTCGC 59.551 55.000 0.00 0.00 0.00 4.70
3628 4366 2.258013 CCCGCCTTTTGCTTCACGA 61.258 57.895 0.00 0.00 38.05 4.35
3672 4410 8.567104 TGATGACATGCACCATTATTATGTTAC 58.433 33.333 0.00 0.00 32.58 2.50
3751 4492 5.691754 TGCGTGCATCAGTACTATTTATCTG 59.308 40.000 0.00 0.00 0.00 2.90
3772 4513 8.520835 AACACACTGTATTATACTATCATGCG 57.479 34.615 3.92 0.00 0.00 4.73
3828 4569 9.512588 ACATGATGAAGATGAAAATATAGGACC 57.487 33.333 0.00 0.00 0.00 4.46
3842 4583 4.141321 ACATGCCTGGTACATGATGAAGAT 60.141 41.667 17.69 0.00 46.33 2.40
3858 4599 2.956987 GAAGTTGCGCACATGCCT 59.043 55.556 11.12 0.00 37.91 4.75
3884 4626 8.839343 TCCACTGTTTCATGCATACTAATTATG 58.161 33.333 0.00 0.00 40.74 1.90
3934 4676 1.836802 TTATGCATGCCACTGCTTCA 58.163 45.000 16.68 0.00 42.75 3.02
3960 4702 4.536364 AAGAATTACATCGACAATGGCG 57.464 40.909 0.05 0.05 39.90 5.69
4054 4796 3.239861 GCAAGAAGCACTACAGGCT 57.760 52.632 0.00 0.00 45.15 4.58
4108 4858 7.562088 TCCCTTGTACTCCTAAAACAAATTGTT 59.438 33.333 5.41 5.41 43.41 2.83
4109 4859 7.064229 TCCCTTGTACTCCTAAAACAAATTGT 58.936 34.615 0.00 0.00 33.05 2.71
4110 4860 7.519032 TCCCTTGTACTCCTAAAACAAATTG 57.481 36.000 0.00 0.00 33.05 2.32
4111 4861 8.418662 GTTTCCCTTGTACTCCTAAAACAAATT 58.581 33.333 0.00 0.00 33.05 1.82
4112 4862 7.562088 TGTTTCCCTTGTACTCCTAAAACAAAT 59.438 33.333 11.39 0.00 33.76 2.32
4113 4863 6.890814 TGTTTCCCTTGTACTCCTAAAACAAA 59.109 34.615 11.39 0.00 33.76 2.83
4116 4866 6.060136 ACTGTTTCCCTTGTACTCCTAAAAC 58.940 40.000 0.00 1.20 0.00 2.43
4128 4878 0.744281 AACGGCAACTGTTTCCCTTG 59.256 50.000 3.62 0.00 30.98 3.61
4129 4879 1.136110 CAAACGGCAACTGTTTCCCTT 59.864 47.619 3.62 0.00 39.88 3.95
4132 4882 2.570442 TTCAAACGGCAACTGTTTCC 57.430 45.000 1.60 0.00 39.88 3.13
4236 4986 2.681778 AGTCGCTCCTCCCCACTG 60.682 66.667 0.00 0.00 0.00 3.66
4301 5051 3.457610 TTACAAACTCGGTTCGGTTCT 57.542 42.857 0.00 0.00 0.00 3.01
4351 5101 7.147794 TGGGTACGTATGAACTTATGTGAATCT 60.148 37.037 0.00 0.00 0.00 2.40
4388 5140 8.835467 TTTTTAGAAAATGAACGTCTGAACTG 57.165 30.769 0.00 0.00 0.00 3.16
4417 5172 5.720202 TGAGTAGTCTGCAACGTATGATTT 58.280 37.500 0.00 0.00 0.00 2.17
4418 5173 5.324784 TGAGTAGTCTGCAACGTATGATT 57.675 39.130 0.00 0.00 0.00 2.57
4423 5178 4.983671 ATGATGAGTAGTCTGCAACGTA 57.016 40.909 0.00 0.00 0.00 3.57
4488 5243 3.092301 GGTGGCCTAGAAAAAGAATGCT 58.908 45.455 3.32 0.00 0.00 3.79
4509 5264 1.202582 CATAGATTCGCTACCCCGAGG 59.797 57.143 0.00 0.00 38.60 4.63
4510 5265 2.160205 TCATAGATTCGCTACCCCGAG 58.840 52.381 0.00 0.00 38.60 4.63
4511 5266 2.160205 CTCATAGATTCGCTACCCCGA 58.840 52.381 0.00 0.00 35.09 5.14
4512 5267 1.887198 ACTCATAGATTCGCTACCCCG 59.113 52.381 0.00 0.00 0.00 5.73
4513 5268 4.058817 CAAACTCATAGATTCGCTACCCC 58.941 47.826 0.00 0.00 0.00 4.95
4514 5269 4.694339 ACAAACTCATAGATTCGCTACCC 58.306 43.478 0.00 0.00 0.00 3.69
4515 5270 6.456988 CCAAACAAACTCATAGATTCGCTACC 60.457 42.308 0.00 0.00 0.00 3.18
4516 5271 6.312918 TCCAAACAAACTCATAGATTCGCTAC 59.687 38.462 0.00 0.00 0.00 3.58
4517 5272 6.312918 GTCCAAACAAACTCATAGATTCGCTA 59.687 38.462 0.00 0.00 0.00 4.26
4518 5273 5.122396 GTCCAAACAAACTCATAGATTCGCT 59.878 40.000 0.00 0.00 0.00 4.93
4519 5274 5.324697 GTCCAAACAAACTCATAGATTCGC 58.675 41.667 0.00 0.00 0.00 4.70
4520 5275 5.445939 CCGTCCAAACAAACTCATAGATTCG 60.446 44.000 0.00 0.00 0.00 3.34
4521 5276 5.163754 CCCGTCCAAACAAACTCATAGATTC 60.164 44.000 0.00 0.00 0.00 2.52
4522 5277 4.700213 CCCGTCCAAACAAACTCATAGATT 59.300 41.667 0.00 0.00 0.00 2.40
4523 5278 4.019681 TCCCGTCCAAACAAACTCATAGAT 60.020 41.667 0.00 0.00 0.00 1.98
4524 5279 3.325425 TCCCGTCCAAACAAACTCATAGA 59.675 43.478 0.00 0.00 0.00 1.98
4525 5280 3.670625 TCCCGTCCAAACAAACTCATAG 58.329 45.455 0.00 0.00 0.00 2.23
4526 5281 3.670625 CTCCCGTCCAAACAAACTCATA 58.329 45.455 0.00 0.00 0.00 2.15
4527 5282 2.504367 CTCCCGTCCAAACAAACTCAT 58.496 47.619 0.00 0.00 0.00 2.90
4528 5283 1.961793 CTCCCGTCCAAACAAACTCA 58.038 50.000 0.00 0.00 0.00 3.41
4529 5284 0.591659 GCTCCCGTCCAAACAAACTC 59.408 55.000 0.00 0.00 0.00 3.01
4530 5285 0.822121 GGCTCCCGTCCAAACAAACT 60.822 55.000 0.00 0.00 0.00 2.66
4531 5286 1.658114 GGCTCCCGTCCAAACAAAC 59.342 57.895 0.00 0.00 0.00 2.93
4532 5287 1.894756 CGGCTCCCGTCCAAACAAA 60.895 57.895 0.00 0.00 42.73 2.83
4533 5288 2.281208 CGGCTCCCGTCCAAACAA 60.281 61.111 0.00 0.00 42.73 2.83
4547 5302 0.678048 AGGAAATTCCAGCTCACGGC 60.678 55.000 15.21 0.00 39.61 5.68
4548 5303 2.691409 TAGGAAATTCCAGCTCACGG 57.309 50.000 15.21 0.00 39.61 4.94
4549 5304 3.736252 CGTATAGGAAATTCCAGCTCACG 59.264 47.826 15.21 11.53 39.61 4.35
4550 5305 4.945246 TCGTATAGGAAATTCCAGCTCAC 58.055 43.478 15.21 3.86 39.61 3.51
4551 5306 5.541845 CATCGTATAGGAAATTCCAGCTCA 58.458 41.667 15.21 0.00 39.61 4.26
4552 5307 4.390297 GCATCGTATAGGAAATTCCAGCTC 59.610 45.833 15.21 1.49 39.61 4.09
4553 5308 4.040952 AGCATCGTATAGGAAATTCCAGCT 59.959 41.667 15.21 7.03 39.61 4.24
4554 5309 4.319177 AGCATCGTATAGGAAATTCCAGC 58.681 43.478 15.21 4.99 39.61 4.85
4555 5310 8.553459 AATAAGCATCGTATAGGAAATTCCAG 57.447 34.615 15.21 0.43 39.61 3.86
4556 5311 9.653287 CTAATAAGCATCGTATAGGAAATTCCA 57.347 33.333 15.21 0.69 39.61 3.53
4591 5346 8.394877 CAGGTAATAAGCATCGTATGTCAAAAA 58.605 33.333 0.00 0.00 0.00 1.94
4592 5347 7.551262 ACAGGTAATAAGCATCGTATGTCAAAA 59.449 33.333 0.00 0.00 0.00 2.44
4593 5348 7.045416 ACAGGTAATAAGCATCGTATGTCAAA 58.955 34.615 0.00 0.00 0.00 2.69
4594 5349 6.578944 ACAGGTAATAAGCATCGTATGTCAA 58.421 36.000 0.00 0.00 0.00 3.18
4595 5350 6.156748 ACAGGTAATAAGCATCGTATGTCA 57.843 37.500 0.00 0.00 0.00 3.58
4596 5351 7.866393 AGTTACAGGTAATAAGCATCGTATGTC 59.134 37.037 0.00 0.00 0.00 3.06
4597 5352 7.652105 CAGTTACAGGTAATAAGCATCGTATGT 59.348 37.037 0.00 0.00 0.00 2.29
4598 5353 7.652105 ACAGTTACAGGTAATAAGCATCGTATG 59.348 37.037 0.00 0.00 0.00 2.39
4599 5354 7.723324 ACAGTTACAGGTAATAAGCATCGTAT 58.277 34.615 0.00 0.00 0.00 3.06
4600 5355 7.104043 ACAGTTACAGGTAATAAGCATCGTA 57.896 36.000 0.00 0.00 0.00 3.43
4601 5356 5.974108 ACAGTTACAGGTAATAAGCATCGT 58.026 37.500 0.00 0.00 0.00 3.73
4602 5357 6.705782 CAACAGTTACAGGTAATAAGCATCG 58.294 40.000 0.00 0.00 0.00 3.84
4603 5358 6.316390 AGCAACAGTTACAGGTAATAAGCATC 59.684 38.462 0.00 0.00 0.00 3.91
4604 5359 6.094048 CAGCAACAGTTACAGGTAATAAGCAT 59.906 38.462 0.00 0.00 0.00 3.79
4605 5360 5.411361 CAGCAACAGTTACAGGTAATAAGCA 59.589 40.000 0.00 0.00 0.00 3.91
4606 5361 5.163754 CCAGCAACAGTTACAGGTAATAAGC 60.164 44.000 0.00 0.00 0.00 3.09
4607 5362 6.170506 TCCAGCAACAGTTACAGGTAATAAG 58.829 40.000 0.00 0.00 0.00 1.73
4608 5363 6.116711 TCCAGCAACAGTTACAGGTAATAA 57.883 37.500 0.00 0.00 0.00 1.40
4609 5364 5.748670 TCCAGCAACAGTTACAGGTAATA 57.251 39.130 0.00 0.00 0.00 0.98
4610 5365 4.634012 TCCAGCAACAGTTACAGGTAAT 57.366 40.909 0.00 0.00 0.00 1.89
4611 5366 4.575885 GATCCAGCAACAGTTACAGGTAA 58.424 43.478 0.00 0.00 0.00 2.85
4612 5367 3.368013 CGATCCAGCAACAGTTACAGGTA 60.368 47.826 0.00 0.00 0.00 3.08
4613 5368 2.612972 CGATCCAGCAACAGTTACAGGT 60.613 50.000 0.00 0.00 0.00 4.00
4614 5369 2.002586 CGATCCAGCAACAGTTACAGG 58.997 52.381 0.00 0.00 0.00 4.00
4615 5370 1.394917 GCGATCCAGCAACAGTTACAG 59.605 52.381 0.00 0.00 37.05 2.74
4616 5371 1.270571 TGCGATCCAGCAACAGTTACA 60.271 47.619 0.00 0.00 45.06 2.41
4617 5372 1.438651 TGCGATCCAGCAACAGTTAC 58.561 50.000 0.00 0.00 45.06 2.50
4618 5373 3.925453 TGCGATCCAGCAACAGTTA 57.075 47.368 0.00 0.00 45.06 2.24
4619 5374 4.798433 TGCGATCCAGCAACAGTT 57.202 50.000 0.00 0.00 45.06 3.16
4625 5380 1.816679 GCTCATGTGCGATCCAGCA 60.817 57.895 3.67 0.00 45.96 4.41
4626 5381 3.020627 GCTCATGTGCGATCCAGC 58.979 61.111 3.67 0.00 37.71 4.85
4634 5389 2.341257 CCCATATAGTCGCTCATGTGC 58.659 52.381 9.72 9.72 0.00 4.57
4635 5390 2.028658 AGCCCATATAGTCGCTCATGTG 60.029 50.000 0.00 0.00 0.00 3.21
4636 5391 2.028658 CAGCCCATATAGTCGCTCATGT 60.029 50.000 0.00 0.00 0.00 3.21
4637 5392 2.614779 CAGCCCATATAGTCGCTCATG 58.385 52.381 0.00 0.00 0.00 3.07
4638 5393 1.552337 CCAGCCCATATAGTCGCTCAT 59.448 52.381 0.00 0.00 0.00 2.90
4639 5394 0.969149 CCAGCCCATATAGTCGCTCA 59.031 55.000 0.00 0.00 0.00 4.26
4640 5395 0.390472 GCCAGCCCATATAGTCGCTC 60.390 60.000 0.00 0.00 0.00 5.03
4641 5396 1.674057 GCCAGCCCATATAGTCGCT 59.326 57.895 0.00 0.00 0.00 4.93
4642 5397 1.376037 GGCCAGCCCATATAGTCGC 60.376 63.158 0.00 0.00 0.00 5.19


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

AutoCloner maintained by Alex Coulton.