Multiple sequence alignment - TraesCS3D01G443000

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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 TraesCS3D01G443000 chr3D 100.000 2594 0 0 1 2594 552726803 552729396 0.000000e+00 4791.0
1 TraesCS3D01G443000 chr3D 87.685 609 68 6 999 1602 552733538 552734144 0.000000e+00 702.0
2 TraesCS3D01G443000 chr3D 80.964 851 105 32 764 1594 552417123 552416310 2.840000e-174 621.0
3 TraesCS3D01G443000 chr3D 88.418 354 29 8 1 349 552579309 552579655 1.440000e-112 416.0
4 TraesCS3D01G443000 chr3D 91.003 289 26 0 1992 2280 590365511 590365223 8.700000e-105 390.0
5 TraesCS3D01G443000 chr3D 83.747 363 42 11 1 355 552614112 552614465 6.920000e-86 327.0
6 TraesCS3D01G443000 chr3D 97.059 34 0 1 572 604 552289819 552289786 3.610000e-04 56.5
7 TraesCS3D01G443000 chr3A 89.116 1029 86 10 580 1600 688992635 688993645 0.000000e+00 1256.0
8 TraesCS3D01G443000 chr3A 87.145 669 68 13 940 1603 688965146 688964491 0.000000e+00 743.0
9 TraesCS3D01G443000 chr3A 89.018 601 61 4 1001 1600 688978026 688977430 0.000000e+00 739.0
10 TraesCS3D01G443000 chr3A 88.226 603 68 1 1001 1600 689002845 689003447 0.000000e+00 717.0
11 TraesCS3D01G443000 chr3A 90.141 355 27 5 1622 1974 688993634 688993982 3.040000e-124 455.0
12 TraesCS3D01G443000 chr3A 86.389 360 31 10 1 355 688990336 688990682 6.780000e-101 377.0
13 TraesCS3D01G443000 chr3A 90.506 158 13 2 418 573 688992310 688992467 9.410000e-50 207.0
14 TraesCS3D01G443000 chr3A 83.133 83 12 1 803 885 688987242 688987162 9.960000e-10 75.0
15 TraesCS3D01G443000 chr3A 83.117 77 11 1 809 885 688978237 688978163 4.630000e-08 69.4
16 TraesCS3D01G443000 chr3B 87.247 988 83 8 647 1600 733349483 733350461 0.000000e+00 1086.0
17 TraesCS3D01G443000 chr3B 92.808 723 39 5 880 1600 733270782 733271493 0.000000e+00 1035.0
18 TraesCS3D01G443000 chr3B 92.669 723 44 2 880 1600 733080122 733080837 0.000000e+00 1033.0
19 TraesCS3D01G443000 chr3B 89.862 651 51 9 962 1598 732841675 732841026 0.000000e+00 822.0
20 TraesCS3D01G443000 chr3B 93.789 322 19 1 2274 2594 733350804 733351125 1.400000e-132 483.0
21 TraesCS3D01G443000 chr3B 92.398 342 19 4 1655 1995 733271506 733271841 5.020000e-132 481.0
22 TraesCS3D01G443000 chr3B 90.801 337 25 3 1659 1994 733350480 733350811 1.830000e-121 446.0
23 TraesCS3D01G443000 chr3B 86.704 361 34 8 1 354 733001203 733001556 3.130000e-104 388.0
24 TraesCS3D01G443000 chr3B 85.596 361 38 8 1 354 733247440 733247793 1.470000e-97 366.0
25 TraesCS3D01G443000 chr3B 81.452 248 27 8 652 882 733079841 733080086 4.410000e-43 185.0
26 TraesCS3D01G443000 chr3B 88.387 155 11 4 427 576 733079452 733079604 2.050000e-41 180.0
27 TraesCS3D01G443000 chr3B 78.431 306 38 10 616 899 733270474 733270773 9.540000e-40 174.0
28 TraesCS3D01G443000 chr3B 89.167 120 13 0 2274 2393 733273077 733273196 1.610000e-32 150.0
29 TraesCS3D01G443000 chr3B 88.983 118 13 0 2476 2593 733273197 733273314 2.080000e-31 147.0
30 TraesCS3D01G443000 chr3B 75.540 139 20 7 572 696 732846228 732846090 3.610000e-04 56.5
31 TraesCS3D01G443000 chr7B 89.527 296 30 1 1985 2279 227590357 227590062 8.770000e-100 374.0
32 TraesCS3D01G443000 chr5B 89.527 296 30 1 1985 2279 564622001 564621706 8.770000e-100 374.0
33 TraesCS3D01G443000 chr5B 89.527 296 30 1 1985 2279 564723720 564723425 8.770000e-100 374.0
34 TraesCS3D01G443000 chr2D 89.273 289 31 0 1990 2278 351286895 351287183 1.900000e-96 363.0


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 TraesCS3D01G443000 chr3D 552726803 552729396 2593 False 4791.000000 4791 100.000000 1 2594 1 chr3D.!!$F3 2593
1 TraesCS3D01G443000 chr3D 552733538 552734144 606 False 702.000000 702 87.685000 999 1602 1 chr3D.!!$F4 603
2 TraesCS3D01G443000 chr3D 552416310 552417123 813 True 621.000000 621 80.964000 764 1594 1 chr3D.!!$R2 830
3 TraesCS3D01G443000 chr3A 688964491 688965146 655 True 743.000000 743 87.145000 940 1603 1 chr3A.!!$R1 663
4 TraesCS3D01G443000 chr3A 689002845 689003447 602 False 717.000000 717 88.226000 1001 1600 1 chr3A.!!$F1 599
5 TraesCS3D01G443000 chr3A 688990336 688993982 3646 False 573.750000 1256 89.038000 1 1974 4 chr3A.!!$F2 1973
6 TraesCS3D01G443000 chr3A 688977430 688978237 807 True 404.200000 739 86.067500 809 1600 2 chr3A.!!$R3 791
7 TraesCS3D01G443000 chr3B 732841026 732841675 649 True 822.000000 822 89.862000 962 1598 1 chr3B.!!$R1 636
8 TraesCS3D01G443000 chr3B 733349483 733351125 1642 False 671.666667 1086 90.612333 647 2594 3 chr3B.!!$F5 1947
9 TraesCS3D01G443000 chr3B 733079452 733080837 1385 False 466.000000 1033 87.502667 427 1600 3 chr3B.!!$F3 1173
10 TraesCS3D01G443000 chr3B 733270474 733273314 2840 False 397.400000 1035 88.357400 616 2593 5 chr3B.!!$F4 1977

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
394 400 0.325671 TAGGAAGAGGTGGAGCAGGG 60.326 60.0 0.0 0.0 0.0 4.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2164 4058 0.030369 GCACTAATGCCAGCTGATGC 59.97 55.0 17.39 11.96 46.97 3.91 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
70 71 2.051334 TAATGCGCTTGCCTATGGTT 57.949 45.000 9.73 0.00 38.03 3.67
81 82 3.674997 TGCCTATGGTTCACTTGAGAAC 58.325 45.455 0.00 0.00 45.50 3.01
86 87 4.696479 ATGGTTCACTTGAGAACTGAGT 57.304 40.909 9.91 0.00 45.52 3.41
140 141 6.651225 ACTTAATTTTAGATAGCCGGCTGATC 59.349 38.462 38.98 30.91 0.00 2.92
145 146 2.255406 AGATAGCCGGCTGATCAAGAT 58.745 47.619 38.98 22.30 0.00 2.40
177 183 2.489938 TGCAAGTACCAAGATGTCCC 57.510 50.000 0.00 0.00 0.00 4.46
202 208 3.065786 TCGAATCGTTATTAGTGGCGACT 59.934 43.478 6.61 6.61 36.16 4.18
208 214 3.241552 CGTTATTAGTGGCGACTTCAACG 60.242 47.826 19.60 19.60 35.23 4.10
214 220 2.159282 AGTGGCGACTTCAACGGTATAG 60.159 50.000 0.00 0.00 0.00 1.31
335 341 4.364415 TGTTACACAAAAAGTCCAGTGC 57.636 40.909 0.00 0.00 35.47 4.40
338 344 5.648526 TGTTACACAAAAAGTCCAGTGCTTA 59.351 36.000 0.00 0.00 35.47 3.09
355 361 6.792250 CAGTGCTTAACAATCTTTACGTTGAG 59.208 38.462 0.00 0.00 31.45 3.02
356 362 6.704493 AGTGCTTAACAATCTTTACGTTGAGA 59.296 34.615 0.00 0.00 30.18 3.27
357 363 7.225931 AGTGCTTAACAATCTTTACGTTGAGAA 59.774 33.333 0.00 0.00 30.18 2.87
358 364 7.530861 GTGCTTAACAATCTTTACGTTGAGAAG 59.469 37.037 0.00 0.00 30.18 2.85
359 365 7.439955 TGCTTAACAATCTTTACGTTGAGAAGA 59.560 33.333 0.00 0.00 34.27 2.87
360 366 8.280497 GCTTAACAATCTTTACGTTGAGAAGAA 58.720 33.333 0.00 0.00 33.56 2.52
372 378 7.466193 ACGTTGAGAAGAAAGTAAAGAAGTC 57.534 36.000 0.00 0.00 0.00 3.01
375 381 7.224949 CGTTGAGAAGAAAGTAAAGAAGTCCTT 59.775 37.037 0.00 0.00 36.47 3.36
376 382 9.543783 GTTGAGAAGAAAGTAAAGAAGTCCTTA 57.456 33.333 0.00 0.00 34.00 2.69
377 383 9.765795 TTGAGAAGAAAGTAAAGAAGTCCTTAG 57.234 33.333 0.00 0.00 34.00 2.18
378 384 8.368668 TGAGAAGAAAGTAAAGAAGTCCTTAGG 58.631 37.037 0.00 0.00 34.00 2.69
379 385 8.493787 AGAAGAAAGTAAAGAAGTCCTTAGGA 57.506 34.615 0.00 0.00 34.00 2.94
380 386 8.935741 AGAAGAAAGTAAAGAAGTCCTTAGGAA 58.064 33.333 0.98 0.00 34.00 3.36
381 387 9.210329 GAAGAAAGTAAAGAAGTCCTTAGGAAG 57.790 37.037 0.98 0.00 34.00 3.46
382 388 8.493787 AGAAAGTAAAGAAGTCCTTAGGAAGA 57.506 34.615 0.98 0.00 34.00 2.87
383 389 8.590204 AGAAAGTAAAGAAGTCCTTAGGAAGAG 58.410 37.037 0.98 0.00 34.00 2.85
384 390 6.860790 AGTAAAGAAGTCCTTAGGAAGAGG 57.139 41.667 0.98 0.00 34.00 3.69
386 392 5.491323 AAAGAAGTCCTTAGGAAGAGGTG 57.509 43.478 0.98 0.00 35.71 4.00
387 393 3.445987 AGAAGTCCTTAGGAAGAGGTGG 58.554 50.000 0.98 0.00 35.71 4.61
388 394 3.077695 AGAAGTCCTTAGGAAGAGGTGGA 59.922 47.826 0.98 0.00 35.71 4.02
389 395 3.108847 AGTCCTTAGGAAGAGGTGGAG 57.891 52.381 0.98 0.00 35.71 3.86
390 396 1.483004 GTCCTTAGGAAGAGGTGGAGC 59.517 57.143 0.98 0.00 35.71 4.70
391 397 1.078823 TCCTTAGGAAGAGGTGGAGCA 59.921 52.381 0.00 0.00 35.71 4.26
392 398 1.484240 CCTTAGGAAGAGGTGGAGCAG 59.516 57.143 0.00 0.00 0.00 4.24
393 399 1.484240 CTTAGGAAGAGGTGGAGCAGG 59.516 57.143 0.00 0.00 0.00 4.85
394 400 0.325671 TAGGAAGAGGTGGAGCAGGG 60.326 60.000 0.00 0.00 0.00 4.45
395 401 1.613630 GGAAGAGGTGGAGCAGGGA 60.614 63.158 0.00 0.00 0.00 4.20
412 1964 7.380423 AGCAGGGAGAAGCTAAAGAATTATA 57.620 36.000 0.00 0.00 39.78 0.98
415 1967 7.717436 GCAGGGAGAAGCTAAAGAATTATACTT 59.283 37.037 0.00 0.00 0.00 2.24
416 1968 9.620259 CAGGGAGAAGCTAAAGAATTATACTTT 57.380 33.333 0.00 0.00 40.13 2.66
486 2060 5.440610 GACCTGATTACACAAATCCAGGAT 58.559 41.667 12.54 0.00 42.97 3.24
558 2134 9.546428 TCATGTGTGGATAAGTGATGTTATAAG 57.454 33.333 0.00 0.00 0.00 1.73
610 2373 7.678947 ATCTATTTTCTGACAAGTGTTCCAG 57.321 36.000 0.00 0.00 0.00 3.86
627 2390 3.487372 TCCAGATAGAACGATCATCGGT 58.513 45.455 12.67 3.99 45.79 4.69
628 2391 3.889538 TCCAGATAGAACGATCATCGGTT 59.110 43.478 12.67 3.28 41.51 4.44
629 2392 4.341235 TCCAGATAGAACGATCATCGGTTT 59.659 41.667 12.67 1.96 41.51 3.27
630 2393 4.681942 CCAGATAGAACGATCATCGGTTTC 59.318 45.833 12.67 7.14 41.51 2.78
634 2397 6.697892 AGATAGAACGATCATCGGTTTCTTTC 59.302 38.462 15.76 16.17 41.51 2.62
642 2405 5.216566 TCATCGGTTTCTTTCTAAATGCG 57.783 39.130 0.00 0.00 0.00 4.73
644 2407 5.584649 TCATCGGTTTCTTTCTAAATGCGAT 59.415 36.000 0.00 0.00 0.00 4.58
666 2434 3.686502 GCACACATGTTTTGTATTGCG 57.313 42.857 0.00 0.00 37.01 4.85
697 2465 8.866970 TTACGGTTTAATAAGATCCAGGTTTT 57.133 30.769 0.00 0.00 0.00 2.43
715 2489 4.324176 GGTTTTAACCCCATGCATTGGATT 60.324 41.667 18.24 10.10 46.06 3.01
727 2501 3.119280 TGCATTGGATTGATGTTCTGCAG 60.119 43.478 7.63 7.63 33.80 4.41
730 2504 5.681437 GCATTGGATTGATGTTCTGCAGAAT 60.681 40.000 30.65 17.09 36.33 2.40
731 2505 5.988310 TTGGATTGATGTTCTGCAGAATT 57.012 34.783 30.65 21.19 36.33 2.17
732 2506 5.988310 TGGATTGATGTTCTGCAGAATTT 57.012 34.783 30.65 20.84 36.33 1.82
733 2507 6.349243 TGGATTGATGTTCTGCAGAATTTT 57.651 33.333 30.65 18.44 36.33 1.82
781 2566 2.791158 GCAAAACGTGATGCTAATCGGG 60.791 50.000 16.20 0.00 39.46 5.14
796 2581 2.496817 GGGTGCTGACTAGGAGCG 59.503 66.667 10.47 0.00 42.83 5.03
803 2588 0.382515 CTGACTAGGAGCGGTACAGC 59.617 60.000 10.25 10.25 37.41 4.40
851 2641 2.093181 TGGTGTGCGGCACTATTCTATT 60.093 45.455 30.81 0.00 46.86 1.73
936 2783 2.435663 CACTGCACCCACCATCCA 59.564 61.111 0.00 0.00 0.00 3.41
989 2848 4.440758 GCAATCTTCTTCTTCGATCTCTCG 59.559 45.833 0.00 0.00 46.41 4.04
992 2851 4.254492 TCTTCTTCTTCGATCTCTCGTCA 58.746 43.478 0.00 0.00 45.25 4.35
993 2852 4.878971 TCTTCTTCTTCGATCTCTCGTCAT 59.121 41.667 0.00 0.00 45.25 3.06
996 2862 4.636206 TCTTCTTCGATCTCTCGTCATTCA 59.364 41.667 0.00 0.00 45.25 2.57
1323 3207 2.970324 GCAACGCCGTGGTTCAGA 60.970 61.111 0.00 0.00 0.00 3.27
1688 3581 4.557301 GGCGAAAATCTCCAATTTTGTACG 59.443 41.667 0.78 0.00 32.03 3.67
1689 3582 5.151389 GCGAAAATCTCCAATTTTGTACGT 58.849 37.500 0.00 0.00 32.03 3.57
1693 3586 7.799447 CGAAAATCTCCAATTTTGTACGTACAA 59.201 33.333 31.86 31.86 43.80 2.41
1715 3608 3.878699 ACTAGTTTAGAGTAGCCGAGAGC 59.121 47.826 0.00 0.00 44.25 4.09
1739 3632 6.140737 GCTTGTTTCACACGAACATTTAGAAG 59.859 38.462 0.00 0.00 36.92 2.85
1797 3690 5.930837 TGAAAACTCTTTTTGGTGGATGT 57.069 34.783 0.00 0.00 34.94 3.06
1900 3793 1.614996 TGGATGGAACGCAACAACAT 58.385 45.000 0.00 0.00 0.00 2.71
1903 3796 2.730928 GGATGGAACGCAACAACATTTG 59.269 45.455 0.00 0.00 0.00 2.32
1905 3798 2.803451 TGGAACGCAACAACATTTGAC 58.197 42.857 0.00 0.00 0.00 3.18
1906 3799 2.164422 TGGAACGCAACAACATTTGACA 59.836 40.909 0.00 0.00 0.00 3.58
1907 3800 3.182967 GGAACGCAACAACATTTGACAA 58.817 40.909 0.00 0.00 0.00 3.18
2005 3899 2.283145 CCCTAAGGGCATCTCCAATG 57.717 55.000 0.00 0.00 35.35 2.82
2009 3903 2.449137 AAGGGCATCTCCAATGGAAG 57.551 50.000 2.61 0.00 36.21 3.46
2010 3904 0.554792 AGGGCATCTCCAATGGAAGG 59.445 55.000 2.61 0.00 36.21 3.46
2012 3906 1.450531 GGCATCTCCAATGGAAGGCG 61.451 60.000 2.61 0.00 34.01 5.52
2013 3907 2.028130 CATCTCCAATGGAAGGCGC 58.972 57.895 2.61 0.00 0.00 6.53
2014 3908 0.465097 CATCTCCAATGGAAGGCGCT 60.465 55.000 7.64 0.00 0.00 5.92
2015 3909 0.257039 ATCTCCAATGGAAGGCGCTT 59.743 50.000 7.64 0.00 0.00 4.68
2016 3910 0.677731 TCTCCAATGGAAGGCGCTTG 60.678 55.000 7.64 2.09 0.00 4.01
2017 3911 2.182537 CCAATGGAAGGCGCTTGC 59.817 61.111 7.64 0.00 38.11 4.01
2018 3912 2.345760 CCAATGGAAGGCGCTTGCT 61.346 57.895 7.64 0.00 39.13 3.91
2020 3914 0.810648 CAATGGAAGGCGCTTGCTTA 59.189 50.000 7.64 0.00 39.13 3.09
2022 3916 0.749454 ATGGAAGGCGCTTGCTTAGG 60.749 55.000 7.64 0.00 39.13 2.69
2023 3917 2.115291 GGAAGGCGCTTGCTTAGGG 61.115 63.158 7.64 0.00 39.13 3.53
2029 3923 1.029947 GCGCTTGCTTAGGGGCTTAA 61.030 55.000 0.00 0.00 38.18 1.85
2030 3924 0.733150 CGCTTGCTTAGGGGCTTAAC 59.267 55.000 0.00 0.00 33.37 2.01
2031 3925 1.679032 CGCTTGCTTAGGGGCTTAACT 60.679 52.381 0.00 0.00 33.37 2.24
2032 3926 2.419574 CGCTTGCTTAGGGGCTTAACTA 60.420 50.000 0.00 0.00 33.37 2.24
2033 3927 3.206964 GCTTGCTTAGGGGCTTAACTAG 58.793 50.000 0.00 0.00 0.00 2.57
2064 3958 9.614792 AGTAAATGATTTAAATTCCTAGCGTCT 57.385 29.630 1.43 0.00 0.00 4.18
2066 3960 7.865706 AATGATTTAAATTCCTAGCGTCTGT 57.134 32.000 1.43 0.00 0.00 3.41
2067 3961 6.662414 TGATTTAAATTCCTAGCGTCTGTG 57.338 37.500 1.43 0.00 0.00 3.66
2068 3962 4.939509 TTTAAATTCCTAGCGTCTGTGC 57.060 40.909 0.00 0.00 0.00 4.57
2069 3963 2.472695 AAATTCCTAGCGTCTGTGCA 57.527 45.000 0.00 0.00 37.31 4.57
2070 3964 2.472695 AATTCCTAGCGTCTGTGCAA 57.527 45.000 0.00 0.00 37.31 4.08
2071 3965 2.015736 ATTCCTAGCGTCTGTGCAAG 57.984 50.000 0.00 0.00 37.31 4.01
2072 3966 0.966179 TTCCTAGCGTCTGTGCAAGA 59.034 50.000 0.00 0.00 37.31 3.02
2073 3967 0.528017 TCCTAGCGTCTGTGCAAGAG 59.472 55.000 0.00 0.00 34.84 2.85
2074 3968 0.244994 CCTAGCGTCTGTGCAAGAGT 59.755 55.000 0.00 0.00 34.84 3.24
2075 3969 1.623359 CTAGCGTCTGTGCAAGAGTC 58.377 55.000 0.00 0.00 34.84 3.36
2076 3970 0.243907 TAGCGTCTGTGCAAGAGTCC 59.756 55.000 0.00 0.00 34.84 3.85
2077 3971 2.375766 GCGTCTGTGCAAGAGTCCG 61.376 63.158 0.00 0.00 34.84 4.79
2079 3973 1.278172 CGTCTGTGCAAGAGTCCGTG 61.278 60.000 0.00 0.00 34.84 4.94
2080 3974 0.249489 GTCTGTGCAAGAGTCCGTGT 60.249 55.000 0.00 0.00 34.84 4.49
2081 3975 0.032130 TCTGTGCAAGAGTCCGTGTC 59.968 55.000 0.00 0.00 0.00 3.67
2082 3976 0.032678 CTGTGCAAGAGTCCGTGTCT 59.967 55.000 0.00 0.00 0.00 3.41
2083 3977 0.032130 TGTGCAAGAGTCCGTGTCTC 59.968 55.000 0.00 0.00 0.00 3.36
2085 3979 1.112916 TGCAAGAGTCCGTGTCTCCA 61.113 55.000 0.00 0.00 32.93 3.86
2087 3981 1.784525 CAAGAGTCCGTGTCTCCAAC 58.215 55.000 0.00 0.00 32.93 3.77
2088 3982 0.314302 AAGAGTCCGTGTCTCCAACG 59.686 55.000 0.00 0.00 40.70 4.10
2093 3987 4.164252 CGTGTCTCCAACGGTAGC 57.836 61.111 0.00 0.00 37.39 3.58
2094 3988 1.287815 CGTGTCTCCAACGGTAGCA 59.712 57.895 0.00 0.00 37.39 3.49
2095 3989 0.732880 CGTGTCTCCAACGGTAGCAG 60.733 60.000 0.00 0.00 37.39 4.24
2096 3990 1.014564 GTGTCTCCAACGGTAGCAGC 61.015 60.000 0.00 0.00 0.00 5.25
2097 3991 1.185618 TGTCTCCAACGGTAGCAGCT 61.186 55.000 0.00 0.00 0.00 4.24
2098 3992 0.815734 GTCTCCAACGGTAGCAGCTA 59.184 55.000 0.00 0.00 0.00 3.32
2099 3993 1.409427 GTCTCCAACGGTAGCAGCTAT 59.591 52.381 5.14 0.00 0.00 2.97
2100 3994 1.681793 TCTCCAACGGTAGCAGCTATC 59.318 52.381 5.14 3.57 0.00 2.08
2101 3995 0.750850 TCCAACGGTAGCAGCTATCC 59.249 55.000 5.14 8.05 0.00 2.59
2103 3997 1.134521 CCAACGGTAGCAGCTATCCAA 60.135 52.381 5.14 0.00 0.00 3.53
2104 3998 2.485479 CCAACGGTAGCAGCTATCCAAT 60.485 50.000 5.14 0.00 0.00 3.16
2106 4000 3.944055 ACGGTAGCAGCTATCCAATAG 57.056 47.619 5.14 0.00 35.94 1.73
2107 4001 2.563179 ACGGTAGCAGCTATCCAATAGG 59.437 50.000 5.14 0.00 33.43 2.57
2108 4002 2.675317 CGGTAGCAGCTATCCAATAGGC 60.675 54.545 5.14 0.00 33.43 3.93
2111 4005 1.301677 GCAGCTATCCAATAGGCGCC 61.302 60.000 21.89 21.89 33.43 6.53
2112 4006 0.322975 CAGCTATCCAATAGGCGCCT 59.677 55.000 34.85 34.85 33.43 5.52
2114 4008 0.674895 GCTATCCAATAGGCGCCTGG 60.675 60.000 38.98 30.79 33.43 4.45
2116 4010 2.124507 TATCCAATAGGCGCCTGGGC 62.125 60.000 38.98 5.72 42.69 5.36
2126 4020 2.892640 GCCTGGGCCGATTTTTCC 59.107 61.111 0.00 0.00 34.56 3.13
2128 4022 1.667154 GCCTGGGCCGATTTTTCCTC 61.667 60.000 0.00 0.00 34.56 3.71
2130 4024 1.383523 CTGGGCCGATTTTTCCTCTC 58.616 55.000 0.00 0.00 0.00 3.20
2131 4025 0.034477 TGGGCCGATTTTTCCTCTCC 60.034 55.000 0.00 0.00 0.00 3.71
2133 4027 1.489230 GGGCCGATTTTTCCTCTCCTA 59.511 52.381 0.00 0.00 0.00 2.94
2135 4029 3.435169 GGGCCGATTTTTCCTCTCCTAAT 60.435 47.826 0.00 0.00 0.00 1.73
2136 4030 4.202430 GGGCCGATTTTTCCTCTCCTAATA 60.202 45.833 0.00 0.00 0.00 0.98
2137 4031 4.755629 GGCCGATTTTTCCTCTCCTAATAC 59.244 45.833 0.00 0.00 0.00 1.89
2138 4032 4.448060 GCCGATTTTTCCTCTCCTAATACG 59.552 45.833 0.00 0.00 0.00 3.06
2140 4034 5.462398 CCGATTTTTCCTCTCCTAATACGTG 59.538 44.000 0.00 0.00 0.00 4.49
2141 4035 6.270815 CGATTTTTCCTCTCCTAATACGTGA 58.729 40.000 0.00 0.00 0.00 4.35
2142 4036 6.755141 CGATTTTTCCTCTCCTAATACGTGAA 59.245 38.462 0.00 0.00 0.00 3.18
2144 4038 8.857694 ATTTTTCCTCTCCTAATACGTGAAAA 57.142 30.769 0.00 0.00 0.00 2.29
2147 4041 8.857694 TTTCCTCTCCTAATACGTGAAAAATT 57.142 30.769 0.00 0.00 0.00 1.82
2148 4042 8.488651 TTCCTCTCCTAATACGTGAAAAATTC 57.511 34.615 0.00 0.00 0.00 2.17
2149 4043 7.046033 TCCTCTCCTAATACGTGAAAAATTCC 58.954 38.462 0.00 0.00 0.00 3.01
2150 4044 7.048512 CCTCTCCTAATACGTGAAAAATTCCT 58.951 38.462 0.00 0.00 0.00 3.36
2151 4045 7.553044 CCTCTCCTAATACGTGAAAAATTCCTT 59.447 37.037 0.00 0.00 0.00 3.36
2153 4047 7.881232 TCTCCTAATACGTGAAAAATTCCTTGT 59.119 33.333 0.00 0.00 0.00 3.16
2154 4048 9.158233 CTCCTAATACGTGAAAAATTCCTTGTA 57.842 33.333 0.00 0.00 0.00 2.41
2155 4049 9.158233 TCCTAATACGTGAAAAATTCCTTGTAG 57.842 33.333 0.00 0.00 0.00 2.74
2156 4050 7.908601 CCTAATACGTGAAAAATTCCTTGTAGC 59.091 37.037 0.00 0.00 0.00 3.58
2157 4051 4.141855 ACGTGAAAAATTCCTTGTAGCG 57.858 40.909 0.00 0.00 0.00 4.26
2158 4052 2.908626 CGTGAAAAATTCCTTGTAGCGC 59.091 45.455 0.00 0.00 0.00 5.92
2159 4053 3.242518 GTGAAAAATTCCTTGTAGCGCC 58.757 45.455 2.29 0.00 0.00 6.53
2160 4054 2.230266 TGAAAAATTCCTTGTAGCGCCC 59.770 45.455 2.29 0.00 0.00 6.13
2161 4055 0.808755 AAAATTCCTTGTAGCGCCCG 59.191 50.000 2.29 0.00 0.00 6.13
2163 4057 4.770874 TTCCTTGTAGCGCCCGGC 62.771 66.667 2.29 0.00 44.05 6.13
2179 4073 2.188829 GGCGCATCAGCTGGCATTA 61.189 57.895 15.13 0.00 38.78 1.90
2180 4074 1.281960 GCGCATCAGCTGGCATTAG 59.718 57.895 15.13 2.29 39.10 1.73
2182 4076 0.306840 CGCATCAGCTGGCATTAGTG 59.693 55.000 15.13 3.31 39.10 2.74
2183 4077 0.030369 GCATCAGCTGGCATTAGTGC 59.970 55.000 15.13 0.74 43.62 4.40
2198 4092 6.211515 GCATTAGTGCCAAAGATAATCCTTG 58.788 40.000 0.00 0.00 45.76 3.61
2199 4093 6.736794 GCATTAGTGCCAAAGATAATCCTTGG 60.737 42.308 0.00 5.28 45.76 3.61
2204 4984 4.141505 TGCCAAAGATAATCCTTGGATCGA 60.142 41.667 12.56 0.00 0.00 3.59
2206 4986 4.757149 CCAAAGATAATCCTTGGATCGACC 59.243 45.833 2.27 0.00 39.54 4.79
2219 4999 2.678336 GGATCGACCAGGAATTGAACAC 59.322 50.000 0.00 0.00 38.79 3.32
2221 5001 3.201353 TCGACCAGGAATTGAACACAA 57.799 42.857 0.00 0.00 0.00 3.33
2229 5009 0.673437 AATTGAACACAACGGCCAGG 59.327 50.000 2.24 0.00 0.00 4.45
2230 5010 1.178534 ATTGAACACAACGGCCAGGG 61.179 55.000 2.24 0.00 0.00 4.45
2232 5012 1.527380 GAACACAACGGCCAGGGAA 60.527 57.895 2.24 0.00 0.00 3.97
2233 5013 1.076632 AACACAACGGCCAGGGAAA 60.077 52.632 2.24 0.00 0.00 3.13
2234 5014 1.388837 AACACAACGGCCAGGGAAAC 61.389 55.000 2.24 0.00 0.00 2.78
2235 5015 1.826054 CACAACGGCCAGGGAAACA 60.826 57.895 2.24 0.00 0.00 2.83
2236 5016 1.076632 ACAACGGCCAGGGAAACAA 60.077 52.632 2.24 0.00 0.00 2.83
2238 5018 0.243636 CAACGGCCAGGGAAACAATC 59.756 55.000 2.24 0.00 0.00 2.67
2248 5028 1.287425 GGAAACAATCCTAGCGTCGG 58.713 55.000 0.00 0.00 45.56 4.79
2249 5029 1.287425 GAAACAATCCTAGCGTCGGG 58.713 55.000 0.00 0.00 0.00 5.14
2250 5030 0.743345 AAACAATCCTAGCGTCGGGC 60.743 55.000 0.00 0.00 44.05 6.13
2305 5156 0.329596 GGAGGACTTGGGCTGTTCAT 59.670 55.000 0.00 0.00 0.00 2.57
2361 5212 2.886523 TGGTGTTGGAAGCTTTCTCATG 59.113 45.455 6.25 0.00 0.00 3.07
2388 5239 0.251916 GGGGTTGTGGATGACGATCA 59.748 55.000 0.00 0.00 0.00 2.92
2567 5419 1.200020 CAACGCCCCTTCATGAGAAAC 59.800 52.381 0.00 0.00 32.35 2.78
2576 5428 3.496692 CCTTCATGAGAAACACCCTCACA 60.497 47.826 0.00 0.00 42.68 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 9.967451 TCCATGTGGAAATTTAGAATACACTAA 57.033 29.630 0.00 0.00 42.18 2.24
48 49 2.958355 ACCATAGGCAAGCGCATTAATT 59.042 40.909 11.47 0.00 41.24 1.40
49 50 2.586425 ACCATAGGCAAGCGCATTAAT 58.414 42.857 11.47 0.00 41.24 1.40
50 51 2.051334 ACCATAGGCAAGCGCATTAA 57.949 45.000 11.47 0.00 41.24 1.40
51 52 1.946768 GAACCATAGGCAAGCGCATTA 59.053 47.619 11.47 0.00 41.24 1.90
52 53 0.740737 GAACCATAGGCAAGCGCATT 59.259 50.000 11.47 0.00 41.24 3.56
70 71 4.402474 TCAAGTGACTCAGTTCTCAAGTGA 59.598 41.667 0.00 0.00 38.47 3.41
112 113 7.656137 TCAGCCGGCTATCTAAAATTAAGTAAG 59.344 37.037 32.30 10.20 0.00 2.34
113 114 7.502696 TCAGCCGGCTATCTAAAATTAAGTAA 58.497 34.615 32.30 0.00 0.00 2.24
114 115 7.058023 TCAGCCGGCTATCTAAAATTAAGTA 57.942 36.000 32.30 0.00 0.00 2.24
115 116 5.925509 TCAGCCGGCTATCTAAAATTAAGT 58.074 37.500 32.30 0.00 0.00 2.24
123 124 3.230976 TCTTGATCAGCCGGCTATCTAA 58.769 45.455 32.30 20.25 0.00 2.10
154 160 4.564821 GGGACATCTTGGTACTTGCAAGTA 60.565 45.833 30.81 30.81 40.37 2.24
164 170 2.061509 TCGATCGGGACATCTTGGTA 57.938 50.000 16.41 0.00 0.00 3.25
166 172 2.408050 GATTCGATCGGGACATCTTGG 58.592 52.381 16.41 0.00 0.00 3.61
187 193 3.061697 CCGTTGAAGTCGCCACTAATAAC 59.938 47.826 0.00 0.00 30.14 1.89
252 258 6.795399 CGAGGAGCACCAATAATACAAATTT 58.205 36.000 2.07 0.00 38.94 1.82
270 276 4.452455 ACACTTCTTTTAATGTGCGAGGAG 59.548 41.667 0.00 0.00 34.14 3.69
320 326 5.652994 TTGTTAAGCACTGGACTTTTTGT 57.347 34.783 0.00 0.00 0.00 2.83
322 328 6.715347 AGATTGTTAAGCACTGGACTTTTT 57.285 33.333 0.00 0.00 0.00 1.94
332 338 6.884187 TCTCAACGTAAAGATTGTTAAGCAC 58.116 36.000 0.00 0.00 0.00 4.40
338 344 8.209917 ACTTTCTTCTCAACGTAAAGATTGTT 57.790 30.769 10.77 0.00 32.72 2.83
355 361 9.210329 CTTCCTAAGGACTTCTTTACTTTCTTC 57.790 37.037 0.00 0.00 36.93 2.87
356 362 8.935741 TCTTCCTAAGGACTTCTTTACTTTCTT 58.064 33.333 0.00 0.00 36.93 2.52
357 363 8.493787 TCTTCCTAAGGACTTCTTTACTTTCT 57.506 34.615 0.00 0.00 36.93 2.52
358 364 7.820386 CCTCTTCCTAAGGACTTCTTTACTTTC 59.180 40.741 0.00 0.00 35.83 2.62
359 365 7.292827 ACCTCTTCCTAAGGACTTCTTTACTTT 59.707 37.037 0.00 0.00 37.35 2.66
360 366 6.788456 ACCTCTTCCTAAGGACTTCTTTACTT 59.212 38.462 0.00 0.00 37.35 2.24
361 367 6.211785 CACCTCTTCCTAAGGACTTCTTTACT 59.788 42.308 0.00 0.00 37.35 2.24
362 368 6.399743 CACCTCTTCCTAAGGACTTCTTTAC 58.600 44.000 0.00 0.00 37.35 2.01
367 373 3.442076 TCCACCTCTTCCTAAGGACTTC 58.558 50.000 0.00 0.00 37.35 3.01
369 375 2.890602 GCTCCACCTCTTCCTAAGGACT 60.891 54.545 0.00 0.00 37.35 3.85
370 376 1.483004 GCTCCACCTCTTCCTAAGGAC 59.517 57.143 0.00 0.00 37.35 3.85
372 378 1.484240 CTGCTCCACCTCTTCCTAAGG 59.516 57.143 0.00 0.00 39.96 2.69
375 381 0.325671 CCCTGCTCCACCTCTTCCTA 60.326 60.000 0.00 0.00 0.00 2.94
376 382 1.614824 CCCTGCTCCACCTCTTCCT 60.615 63.158 0.00 0.00 0.00 3.36
377 383 1.613630 TCCCTGCTCCACCTCTTCC 60.614 63.158 0.00 0.00 0.00 3.46
378 384 0.616111 TCTCCCTGCTCCACCTCTTC 60.616 60.000 0.00 0.00 0.00 2.87
379 385 0.178891 TTCTCCCTGCTCCACCTCTT 60.179 55.000 0.00 0.00 0.00 2.85
380 386 0.617249 CTTCTCCCTGCTCCACCTCT 60.617 60.000 0.00 0.00 0.00 3.69
381 387 1.904032 CTTCTCCCTGCTCCACCTC 59.096 63.158 0.00 0.00 0.00 3.85
382 388 2.297129 GCTTCTCCCTGCTCCACCT 61.297 63.158 0.00 0.00 0.00 4.00
383 389 0.978146 TAGCTTCTCCCTGCTCCACC 60.978 60.000 0.00 0.00 40.35 4.61
384 390 0.905357 TTAGCTTCTCCCTGCTCCAC 59.095 55.000 0.00 0.00 40.35 4.02
386 392 1.834263 TCTTTAGCTTCTCCCTGCTCC 59.166 52.381 0.00 0.00 40.35 4.70
387 393 3.618690 TTCTTTAGCTTCTCCCTGCTC 57.381 47.619 0.00 0.00 40.35 4.26
388 394 4.582973 AATTCTTTAGCTTCTCCCTGCT 57.417 40.909 0.00 0.00 42.67 4.24
389 395 7.220740 AGTATAATTCTTTAGCTTCTCCCTGC 58.779 38.462 0.00 0.00 0.00 4.85
390 396 9.620259 AAAGTATAATTCTTTAGCTTCTCCCTG 57.380 33.333 0.00 0.00 34.02 4.45
391 397 9.839817 GAAAGTATAATTCTTTAGCTTCTCCCT 57.160 33.333 0.00 0.00 35.62 4.20
392 398 9.614792 TGAAAGTATAATTCTTTAGCTTCTCCC 57.385 33.333 0.00 0.00 35.62 4.30
412 1964 3.131396 AGCGACGACAGAAAATGAAAGT 58.869 40.909 0.00 0.00 0.00 2.66
415 1967 3.673338 CAGTAGCGACGACAGAAAATGAA 59.327 43.478 0.00 0.00 0.00 2.57
416 1968 3.057806 TCAGTAGCGACGACAGAAAATGA 60.058 43.478 0.00 0.00 0.00 2.57
428 1999 3.250040 ACAATTGGTTGTTCAGTAGCGAC 59.750 43.478 10.83 0.00 46.07 5.19
529 2104 5.748402 ACATCACTTATCCACACATGACAT 58.252 37.500 0.00 0.00 0.00 3.06
530 2105 5.164620 ACATCACTTATCCACACATGACA 57.835 39.130 0.00 0.00 0.00 3.58
531 2106 7.792374 ATAACATCACTTATCCACACATGAC 57.208 36.000 0.00 0.00 0.00 3.06
532 2107 9.546428 CTTATAACATCACTTATCCACACATGA 57.454 33.333 0.00 0.00 0.00 3.07
558 2134 1.452145 TTGGCGACCCTCAACTTTGC 61.452 55.000 0.00 0.00 0.00 3.68
610 2373 6.697892 AGAAAGAAACCGATGATCGTTCTATC 59.302 38.462 17.36 7.79 39.18 2.08
642 2405 4.030529 GCAATACAAAACATGTGTGCGATC 59.969 41.667 0.00 0.00 43.77 3.69
644 2407 3.304257 GCAATACAAAACATGTGTGCGA 58.696 40.909 0.00 0.00 43.77 5.10
666 2434 8.441312 TGGATCTTATTAAACCGTAATCCAAC 57.559 34.615 0.00 0.00 32.27 3.77
731 2505 6.491745 TGCTTGTATGGTAGATGTTCCAAAAA 59.508 34.615 0.00 0.00 37.27 1.94
732 2506 6.007076 TGCTTGTATGGTAGATGTTCCAAAA 58.993 36.000 0.00 0.00 37.27 2.44
733 2507 5.414454 GTGCTTGTATGGTAGATGTTCCAAA 59.586 40.000 0.00 0.00 37.27 3.28
742 2516 5.414789 TTTGCTAGTGCTTGTATGGTAGA 57.585 39.130 0.00 0.00 40.48 2.59
781 2566 0.100861 GTACCGCTCCTAGTCAGCAC 59.899 60.000 10.65 0.00 36.61 4.40
803 2588 7.268586 AGTTGTTTATGCTCCATCTAGTACTG 58.731 38.462 5.39 0.00 0.00 2.74
904 2747 3.058224 GTGCAGTGGTTGGTTTCATCTAC 60.058 47.826 0.00 0.00 0.00 2.59
936 2783 0.883153 TGCTGCTGTTGCGATGATTT 59.117 45.000 0.00 0.00 43.34 2.17
960 2816 2.351111 CGAAGAAGAAGATTGCTCTGCC 59.649 50.000 0.00 0.00 0.00 4.85
989 2848 4.261909 GGATCTTGGCCATTGATGAATGAC 60.262 45.833 21.75 9.53 41.49 3.06
992 2851 3.895656 CTGGATCTTGGCCATTGATGAAT 59.104 43.478 21.75 3.71 34.33 2.57
993 2852 3.293337 CTGGATCTTGGCCATTGATGAA 58.707 45.455 21.75 11.34 34.33 2.57
996 2862 1.700955 GCTGGATCTTGGCCATTGAT 58.299 50.000 18.19 18.19 34.33 2.57
1308 3192 1.594293 CACTCTGAACCACGGCGTT 60.594 57.895 11.19 0.00 0.00 4.84
1617 3510 5.349270 CGTTGCATTCATCCATCACATTTTT 59.651 36.000 0.00 0.00 0.00 1.94
1618 3511 4.865925 CGTTGCATTCATCCATCACATTTT 59.134 37.500 0.00 0.00 0.00 1.82
1619 3512 4.426416 CGTTGCATTCATCCATCACATTT 58.574 39.130 0.00 0.00 0.00 2.32
1620 3513 3.181484 CCGTTGCATTCATCCATCACATT 60.181 43.478 0.00 0.00 0.00 2.71
1621 3514 2.359848 CCGTTGCATTCATCCATCACAT 59.640 45.455 0.00 0.00 0.00 3.21
1622 3515 1.744522 CCGTTGCATTCATCCATCACA 59.255 47.619 0.00 0.00 0.00 3.58
1623 3516 1.066002 CCCGTTGCATTCATCCATCAC 59.934 52.381 0.00 0.00 0.00 3.06
1624 3517 1.340893 ACCCGTTGCATTCATCCATCA 60.341 47.619 0.00 0.00 0.00 3.07
1625 3518 1.066002 CACCCGTTGCATTCATCCATC 59.934 52.381 0.00 0.00 0.00 3.51
1626 3519 1.105457 CACCCGTTGCATTCATCCAT 58.895 50.000 0.00 0.00 0.00 3.41
1627 3520 2.565647 CACCCGTTGCATTCATCCA 58.434 52.632 0.00 0.00 0.00 3.41
1688 3581 6.314896 TCTCGGCTACTCTAAACTAGTTGTAC 59.685 42.308 9.34 2.81 0.00 2.90
1689 3582 6.409704 TCTCGGCTACTCTAAACTAGTTGTA 58.590 40.000 9.34 6.15 0.00 2.41
1693 3586 3.878699 GCTCTCGGCTACTCTAAACTAGT 59.121 47.826 0.00 0.00 38.06 2.57
1739 3632 4.155826 GGCTAAAAATGTTCCCAAAATGGC 59.844 41.667 0.00 0.00 35.79 4.40
1865 3758 3.803778 CCATCCAAACAGAAAACACTTGC 59.196 43.478 0.00 0.00 0.00 4.01
1869 3762 4.041723 CGTTCCATCCAAACAGAAAACAC 58.958 43.478 0.00 0.00 0.00 3.32
1905 3798 8.092521 TCAAAAGAATCTAGCTCTGACTTTTG 57.907 34.615 23.91 23.91 46.14 2.44
1906 3799 7.390162 CCTCAAAAGAATCTAGCTCTGACTTTT 59.610 37.037 0.00 1.17 36.82 2.27
1907 3800 6.878389 CCTCAAAAGAATCTAGCTCTGACTTT 59.122 38.462 0.00 0.00 0.00 2.66
1966 3860 2.158696 GGTGCAAAGCTCTATCCATCCT 60.159 50.000 0.00 0.00 0.00 3.24
1978 3872 0.972471 ATGCCCTTAGGGTGCAAAGC 60.972 55.000 19.76 2.70 46.51 3.51
1995 3889 0.465097 AGCGCCTTCCATTGGAGATG 60.465 55.000 2.29 0.04 31.21 2.90
1996 3890 0.257039 AAGCGCCTTCCATTGGAGAT 59.743 50.000 2.29 0.00 31.21 2.75
1998 3892 1.805254 CAAGCGCCTTCCATTGGAG 59.195 57.895 2.29 0.00 31.21 3.86
1999 3893 2.342650 GCAAGCGCCTTCCATTGGA 61.343 57.895 2.29 0.00 0.00 3.53
2000 3894 1.880819 AAGCAAGCGCCTTCCATTGG 61.881 55.000 2.29 0.00 39.83 3.16
2001 3895 0.810648 TAAGCAAGCGCCTTCCATTG 59.189 50.000 2.29 1.37 39.83 2.82
2002 3896 1.098050 CTAAGCAAGCGCCTTCCATT 58.902 50.000 2.29 0.00 39.83 3.16
2003 3897 0.749454 CCTAAGCAAGCGCCTTCCAT 60.749 55.000 2.29 0.00 39.83 3.41
2004 3898 1.377202 CCTAAGCAAGCGCCTTCCA 60.377 57.895 2.29 0.00 39.83 3.53
2005 3899 2.115291 CCCTAAGCAAGCGCCTTCC 61.115 63.158 2.29 0.00 39.83 3.46
2009 3903 2.886730 TAAGCCCCTAAGCAAGCGCC 62.887 60.000 2.29 0.00 39.83 6.53
2010 3904 1.029947 TTAAGCCCCTAAGCAAGCGC 61.030 55.000 0.00 0.00 38.99 5.92
2012 3906 2.130272 AGTTAAGCCCCTAAGCAAGC 57.870 50.000 0.00 0.00 34.23 4.01
2013 3907 3.206964 GCTAGTTAAGCCCCTAAGCAAG 58.793 50.000 0.00 0.00 46.25 4.01
2014 3908 3.277142 GCTAGTTAAGCCCCTAAGCAA 57.723 47.619 0.00 0.00 46.25 3.91
2038 3932 9.614792 AGACGCTAGGAATTTAAATCATTTACT 57.385 29.630 0.10 0.00 0.00 2.24
2039 3933 9.651718 CAGACGCTAGGAATTTAAATCATTTAC 57.348 33.333 0.10 0.00 0.00 2.01
2040 3934 9.391006 ACAGACGCTAGGAATTTAAATCATTTA 57.609 29.630 0.10 0.00 0.00 1.40
2041 3935 8.184192 CACAGACGCTAGGAATTTAAATCATTT 58.816 33.333 0.10 0.00 0.00 2.32
2042 3936 7.679638 GCACAGACGCTAGGAATTTAAATCATT 60.680 37.037 0.10 0.00 0.00 2.57
2044 3938 5.064707 GCACAGACGCTAGGAATTTAAATCA 59.935 40.000 0.10 0.00 0.00 2.57
2045 3939 5.064707 TGCACAGACGCTAGGAATTTAAATC 59.935 40.000 0.10 0.00 0.00 2.17
2046 3940 4.941263 TGCACAGACGCTAGGAATTTAAAT 59.059 37.500 0.00 0.00 0.00 1.40
2049 3943 3.603158 TGCACAGACGCTAGGAATTTA 57.397 42.857 0.00 0.00 0.00 1.40
2050 3944 2.472695 TGCACAGACGCTAGGAATTT 57.527 45.000 0.00 0.00 0.00 1.82
2052 3946 1.550524 TCTTGCACAGACGCTAGGAAT 59.449 47.619 0.00 0.00 35.74 3.01
2053 3947 0.966179 TCTTGCACAGACGCTAGGAA 59.034 50.000 0.00 0.00 35.74 3.36
2054 3948 0.528017 CTCTTGCACAGACGCTAGGA 59.472 55.000 0.00 0.00 35.74 2.94
2055 3949 0.244994 ACTCTTGCACAGACGCTAGG 59.755 55.000 0.00 0.00 35.74 3.02
2056 3950 1.623359 GACTCTTGCACAGACGCTAG 58.377 55.000 0.00 0.00 36.28 3.42
2058 3952 1.005630 GGACTCTTGCACAGACGCT 60.006 57.895 0.00 0.00 0.00 5.07
2060 3954 1.007271 ACGGACTCTTGCACAGACG 60.007 57.895 0.00 5.74 0.00 4.18
2062 3956 0.032130 GACACGGACTCTTGCACAGA 59.968 55.000 0.00 0.00 0.00 3.41
2063 3957 0.032678 AGACACGGACTCTTGCACAG 59.967 55.000 0.00 0.00 0.00 3.66
2064 3958 0.032130 GAGACACGGACTCTTGCACA 59.968 55.000 0.00 0.00 0.00 4.57
2066 3960 1.112916 TGGAGACACGGACTCTTGCA 61.113 55.000 0.00 0.00 35.10 4.08
2067 3961 0.033504 TTGGAGACACGGACTCTTGC 59.966 55.000 0.00 0.00 42.67 4.01
2068 3962 1.784525 GTTGGAGACACGGACTCTTG 58.215 55.000 0.00 0.00 42.67 3.02
2069 3963 0.314302 CGTTGGAGACACGGACTCTT 59.686 55.000 0.00 0.00 42.67 2.85
2070 3964 1.957562 CGTTGGAGACACGGACTCT 59.042 57.895 0.00 0.00 42.67 3.24
2071 3965 4.554163 CGTTGGAGACACGGACTC 57.446 61.111 0.00 0.00 42.67 3.36
2076 3970 0.732880 CTGCTACCGTTGGAGACACG 60.733 60.000 0.00 0.00 42.67 4.49
2077 3971 1.014564 GCTGCTACCGTTGGAGACAC 61.015 60.000 5.71 0.00 42.67 3.67
2079 3973 0.815734 TAGCTGCTACCGTTGGAGAC 59.184 55.000 5.02 0.00 0.00 3.36
2080 3974 1.681793 GATAGCTGCTACCGTTGGAGA 59.318 52.381 12.26 0.00 0.00 3.71
2081 3975 1.269831 GGATAGCTGCTACCGTTGGAG 60.270 57.143 12.26 0.00 0.00 3.86
2082 3976 0.750850 GGATAGCTGCTACCGTTGGA 59.249 55.000 12.26 0.00 0.00 3.53
2083 3977 0.464036 TGGATAGCTGCTACCGTTGG 59.536 55.000 12.26 0.00 0.00 3.77
2085 3979 3.006967 CCTATTGGATAGCTGCTACCGTT 59.993 47.826 12.26 9.05 34.57 4.44
2087 3981 2.675317 GCCTATTGGATAGCTGCTACCG 60.675 54.545 12.26 4.20 34.57 4.02
2088 3982 2.675317 CGCCTATTGGATAGCTGCTACC 60.675 54.545 12.26 14.93 34.57 3.18
2089 3983 2.611518 CGCCTATTGGATAGCTGCTAC 58.388 52.381 12.26 6.15 34.57 3.58
2091 3985 0.321122 GCGCCTATTGGATAGCTGCT 60.321 55.000 7.57 7.57 34.57 4.24
2092 3986 1.301677 GGCGCCTATTGGATAGCTGC 61.302 60.000 22.15 0.00 34.57 5.25
2093 3987 0.322975 AGGCGCCTATTGGATAGCTG 59.677 55.000 31.86 0.00 34.57 4.24
2094 3988 0.322975 CAGGCGCCTATTGGATAGCT 59.677 55.000 32.30 0.00 34.57 3.32
2095 3989 0.674895 CCAGGCGCCTATTGGATAGC 60.675 60.000 32.30 0.00 33.76 2.97
2096 3990 0.036010 CCCAGGCGCCTATTGGATAG 60.036 60.000 32.30 14.35 33.76 2.08
2097 3991 2.066340 CCCAGGCGCCTATTGGATA 58.934 57.895 32.30 0.00 33.76 2.59
2098 3992 2.839098 CCCAGGCGCCTATTGGAT 59.161 61.111 32.30 1.18 33.76 3.41
2099 3993 4.189580 GCCCAGGCGCCTATTGGA 62.190 66.667 32.08 0.00 33.76 3.53
2111 4005 1.383523 GAGAGGAAAAATCGGCCCAG 58.616 55.000 0.00 0.00 0.00 4.45
2112 4006 0.034477 GGAGAGGAAAAATCGGCCCA 60.034 55.000 0.00 0.00 0.00 5.36
2114 4008 3.277142 TTAGGAGAGGAAAAATCGGCC 57.723 47.619 0.00 0.00 0.00 6.13
2116 4010 5.462398 CACGTATTAGGAGAGGAAAAATCGG 59.538 44.000 0.00 0.00 0.00 4.18
2118 4012 8.488651 TTTCACGTATTAGGAGAGGAAAAATC 57.511 34.615 0.00 0.00 0.00 2.17
2119 4013 8.857694 TTTTCACGTATTAGGAGAGGAAAAAT 57.142 30.769 0.00 0.00 32.12 1.82
2121 4015 8.857694 ATTTTTCACGTATTAGGAGAGGAAAA 57.142 30.769 0.00 0.00 32.91 2.29
2123 4017 7.551617 GGAATTTTTCACGTATTAGGAGAGGAA 59.448 37.037 0.00 0.00 0.00 3.36
2126 4020 8.391106 CAAGGAATTTTTCACGTATTAGGAGAG 58.609 37.037 0.00 0.00 0.00 3.20
2128 4022 8.040716 ACAAGGAATTTTTCACGTATTAGGAG 57.959 34.615 0.00 0.00 0.00 3.69
2130 4024 7.908601 GCTACAAGGAATTTTTCACGTATTAGG 59.091 37.037 0.00 0.00 0.00 2.69
2131 4025 7.634817 CGCTACAAGGAATTTTTCACGTATTAG 59.365 37.037 0.00 0.00 0.00 1.73
2133 4027 6.311723 CGCTACAAGGAATTTTTCACGTATT 58.688 36.000 0.00 0.00 0.00 1.89
2135 4029 4.377635 GCGCTACAAGGAATTTTTCACGTA 60.378 41.667 0.00 0.00 0.00 3.57
2136 4030 3.608474 GCGCTACAAGGAATTTTTCACGT 60.608 43.478 0.00 0.00 0.00 4.49
2137 4031 2.908626 GCGCTACAAGGAATTTTTCACG 59.091 45.455 0.00 0.00 0.00 4.35
2138 4032 3.242518 GGCGCTACAAGGAATTTTTCAC 58.757 45.455 7.64 0.00 0.00 3.18
2140 4034 2.731027 CGGGCGCTACAAGGAATTTTTC 60.731 50.000 7.64 0.00 0.00 2.29
2141 4035 1.201414 CGGGCGCTACAAGGAATTTTT 59.799 47.619 7.64 0.00 0.00 1.94
2142 4036 0.808755 CGGGCGCTACAAGGAATTTT 59.191 50.000 7.64 0.00 0.00 1.82
2144 4038 1.451387 CCGGGCGCTACAAGGAATT 60.451 57.895 7.64 0.00 0.00 2.17
2161 4055 2.126417 CTAATGCCAGCTGATGCGCC 62.126 60.000 17.39 0.00 45.42 6.53
2163 4057 0.306840 CACTAATGCCAGCTGATGCG 59.693 55.000 17.39 0.00 45.42 4.73
2164 4058 0.030369 GCACTAATGCCAGCTGATGC 59.970 55.000 17.39 11.96 46.97 3.91
2174 4068 6.736794 CCAAGGATTATCTTTGGCACTAATGC 60.737 42.308 20.43 0.00 44.78 3.56
2175 4069 6.742109 CCAAGGATTATCTTTGGCACTAATG 58.258 40.000 20.43 0.00 44.78 1.90
2184 4078 5.368145 TGGTCGATCCAAGGATTATCTTTG 58.632 41.667 9.69 9.69 44.12 2.77
2185 4079 5.455326 CCTGGTCGATCCAAGGATTATCTTT 60.455 44.000 2.62 0.00 46.59 2.52
2186 4080 4.040952 CCTGGTCGATCCAAGGATTATCTT 59.959 45.833 2.62 0.00 46.59 2.40
2187 4081 3.580458 CCTGGTCGATCCAAGGATTATCT 59.420 47.826 2.62 0.00 46.59 1.98
2189 4083 3.587498 TCCTGGTCGATCCAAGGATTAT 58.413 45.455 2.62 0.00 46.59 1.28
2190 4084 3.040655 TCCTGGTCGATCCAAGGATTA 57.959 47.619 2.62 0.00 46.59 1.75
2191 4085 1.879575 TCCTGGTCGATCCAAGGATT 58.120 50.000 2.62 0.00 46.59 3.01
2192 4086 1.879575 TTCCTGGTCGATCCAAGGAT 58.120 50.000 5.64 0.16 46.59 3.24
2195 4089 3.266510 TCAATTCCTGGTCGATCCAAG 57.733 47.619 7.90 3.06 46.59 3.61
2198 4092 2.678336 GTGTTCAATTCCTGGTCGATCC 59.322 50.000 0.00 0.00 0.00 3.36
2199 4093 3.334691 TGTGTTCAATTCCTGGTCGATC 58.665 45.455 0.00 0.00 0.00 3.69
2204 4984 1.953686 CCGTTGTGTTCAATTCCTGGT 59.046 47.619 0.00 0.00 35.92 4.00
2206 4986 1.335872 GGCCGTTGTGTTCAATTCCTG 60.336 52.381 0.00 0.00 35.92 3.86
2207 4987 0.958822 GGCCGTTGTGTTCAATTCCT 59.041 50.000 0.00 0.00 35.92 3.36
2208 4988 0.671251 TGGCCGTTGTGTTCAATTCC 59.329 50.000 0.00 0.00 35.92 3.01
2209 4989 1.335872 CCTGGCCGTTGTGTTCAATTC 60.336 52.381 0.00 0.00 35.92 2.17
2213 4993 2.203280 CCCTGGCCGTTGTGTTCA 60.203 61.111 0.00 0.00 0.00 3.18
2215 4995 1.076632 TTTCCCTGGCCGTTGTGTT 60.077 52.632 0.00 0.00 0.00 3.32
2216 4996 1.826487 GTTTCCCTGGCCGTTGTGT 60.826 57.895 0.00 0.00 0.00 3.72
2219 4999 0.243636 GATTGTTTCCCTGGCCGTTG 59.756 55.000 0.00 0.00 0.00 4.10
2221 5001 1.304134 GGATTGTTTCCCTGGCCGT 60.304 57.895 0.00 0.00 38.75 5.68
2229 5009 1.287425 CCGACGCTAGGATTGTTTCC 58.713 55.000 0.00 0.00 45.85 3.13
2230 5010 1.287425 CCCGACGCTAGGATTGTTTC 58.713 55.000 0.00 0.00 0.00 2.78
2232 5012 1.153429 GCCCGACGCTAGGATTGTT 60.153 57.895 0.00 0.00 0.00 2.83
2233 5013 2.355986 TGCCCGACGCTAGGATTGT 61.356 57.895 0.00 0.00 38.78 2.71
2234 5014 1.883084 GTGCCCGACGCTAGGATTG 60.883 63.158 0.00 0.00 38.78 2.67
2235 5015 0.754217 TAGTGCCCGACGCTAGGATT 60.754 55.000 0.00 0.00 40.44 3.01
2236 5016 1.152819 TAGTGCCCGACGCTAGGAT 60.153 57.895 0.00 0.00 40.44 3.24
2259 5039 2.587322 TTAGGGCATCTCCAACGCGG 62.587 60.000 12.47 0.00 36.21 6.46
2260 5040 1.153449 TTAGGGCATCTCCAACGCG 60.153 57.895 3.53 3.53 36.21 6.01
2261 5041 0.815615 CCTTAGGGCATCTCCAACGC 60.816 60.000 0.00 0.00 36.21 4.84
2262 5042 3.386543 CCTTAGGGCATCTCCAACG 57.613 57.895 0.00 0.00 36.21 4.10
2283 5134 1.360393 AACAGCCCAAGTCCTCCCAA 61.360 55.000 0.00 0.00 0.00 4.12
2321 5172 9.726232 CAACACCATTTCATGAGAAGTAATATG 57.274 33.333 0.00 0.00 34.71 1.78
2413 5264 7.791766 TGAGATCCTCTAGGTTATCCAAGAAAT 59.208 37.037 0.00 0.00 36.34 2.17
2439 5291 1.520666 CGGCTCCCGTTCCAAGTAT 59.479 57.895 0.00 0.00 42.73 2.12
2499 5351 4.402528 TGTCCCATCCGTTGCCCG 62.403 66.667 0.00 0.00 0.00 6.13
2525 5377 5.381757 TGTACTAAGCCATTTGGTGAACTT 58.618 37.500 0.00 0.00 37.57 2.66
2567 5419 2.867109 AGGACAAAGATGTGAGGGTG 57.133 50.000 0.00 0.00 40.74 4.61


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

AutoCloner maintained by Alex Coulton.