Multiple sequence alignment - TraesCS6A01G337000

Loading Multiple Alignment...

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 TraesCS6A01G337000 chr6A 100.000 6142 0 0 1 6142 571018999 571025140 0.000000e+00 11343.0
1 TraesCS6A01G337000 chr6A 80.737 353 40 15 462 787 602458745 602458394 3.680000e-62 250.0
2 TraesCS6A01G337000 chr6A 80.745 161 24 4 227 383 74389309 74389152 1.080000e-22 119.0
3 TraesCS6A01G337000 chr6B 96.115 4427 114 21 788 5200 641394624 641399006 0.000000e+00 7169.0
4 TraesCS6A01G337000 chr6B 90.853 1126 91 7 2855 3974 82743855 82742736 0.000000e+00 1498.0
5 TraesCS6A01G337000 chr6B 88.819 635 66 4 1912 2544 82744482 82743851 0.000000e+00 774.0
6 TraesCS6A01G337000 chr6B 94.530 457 20 3 5420 5873 641400606 641401060 0.000000e+00 701.0
7 TraesCS6A01G337000 chr6B 82.857 630 92 10 870 1496 82746425 82745809 9.000000e-153 551.0
8 TraesCS6A01G337000 chr6B 92.683 287 12 1 5156 5433 641399017 641399303 7.410000e-109 405.0
9 TraesCS6A01G337000 chr6B 100.000 90 0 0 6053 6142 641401132 641401221 3.810000e-37 167.0
10 TraesCS6A01G337000 chr6B 96.296 54 0 2 5786 5838 641401074 641401126 3.050000e-13 87.9
11 TraesCS6A01G337000 chr6D 96.479 4033 108 9 1853 5873 426100673 426104683 0.000000e+00 6630.0
12 TraesCS6A01G337000 chr6D 88.776 1871 116 49 1 1850 426098418 426100215 0.000000e+00 2206.0
13 TraesCS6A01G337000 chr6D 98.889 90 1 0 6053 6142 426104755 426104844 1.770000e-35 161.0
14 TraesCS6A01G337000 chr6D 88.372 43 5 0 178 220 10715283 10715325 1.100000e-02 52.8
15 TraesCS6A01G337000 chr7D 89.247 2855 257 26 2360 5209 39710662 39713471 0.000000e+00 3526.0
16 TraesCS6A01G337000 chr7D 86.117 886 110 6 4262 5146 40001876 40002749 0.000000e+00 942.0
17 TraesCS6A01G337000 chr7D 86.935 819 98 7 3563 4381 39633800 39634609 0.000000e+00 911.0
18 TraesCS6A01G337000 chr7D 91.797 512 41 1 4768 5279 39635337 39635847 0.000000e+00 712.0
19 TraesCS6A01G337000 chr7D 93.069 303 20 1 2043 2345 39705320 39705621 5.650000e-120 442.0
20 TraesCS6A01G337000 chr7D 91.228 285 25 0 4428 4712 39635060 39635344 7.470000e-104 388.0
21 TraesCS6A01G337000 chr7D 88.256 281 21 6 5250 5519 39729217 39729496 5.940000e-85 326.0
22 TraesCS6A01G337000 chr7D 89.035 228 14 6 2012 2231 39723810 39724034 7.840000e-69 272.0
23 TraesCS6A01G337000 chr7D 81.928 166 24 5 235 395 531824971 531824807 1.070000e-27 135.0
24 TraesCS6A01G337000 chr7D 79.882 169 28 6 3760 3924 15933738 15933904 1.080000e-22 119.0
25 TraesCS6A01G337000 chr7D 80.272 147 17 7 4068 4205 15934324 15934467 3.920000e-17 100.0
26 TraesCS6A01G337000 chr7A 91.151 1955 159 8 2092 4037 39587583 39589532 0.000000e+00 2639.0
27 TraesCS6A01G337000 chr7A 88.330 1491 132 20 4050 5508 39592150 39593630 0.000000e+00 1751.0
28 TraesCS6A01G337000 chr7A 80.059 341 48 12 466 787 72817484 72817145 1.030000e-57 235.0
29 TraesCS6A01G337000 chr7A 80.059 341 48 12 466 787 72855073 72854734 1.030000e-57 235.0
30 TraesCS6A01G337000 chr7A 79.290 169 29 6 3760 3924 14846517 14846683 5.030000e-21 113.0
31 TraesCS6A01G337000 chr4A 87.609 1727 167 21 3980 5691 645860409 645862103 0.000000e+00 1960.0
32 TraesCS6A01G337000 chr4A 82.927 164 23 5 224 383 121481498 121481660 6.420000e-30 143.0
33 TraesCS6A01G337000 chr4A 100.000 29 0 0 193 221 710777437 710777465 3.000000e-03 54.7
34 TraesCS6A01G337000 chr1B 84.320 338 35 9 466 787 582937562 582937897 1.290000e-81 315.0
35 TraesCS6A01G337000 chr1D 82.891 339 36 13 466 788 431805288 431805620 1.010000e-72 285.0
36 TraesCS6A01G337000 chr1D 83.750 160 21 4 227 383 62568503 62568346 4.960000e-31 147.0
37 TraesCS6A01G337000 chr2B 82.164 342 39 14 466 787 741204608 741204947 2.180000e-69 274.0
38 TraesCS6A01G337000 chr2B 82.164 342 39 14 466 787 741234341 741234680 2.180000e-69 274.0
39 TraesCS6A01G337000 chr2B 80.745 161 24 7 235 394 7447365 7447211 1.080000e-22 119.0
40 TraesCS6A01G337000 chr5D 83.959 293 31 10 510 787 476032924 476032633 3.650000e-67 267.0
41 TraesCS6A01G337000 chr5D 80.000 335 51 10 465 787 532659400 532659730 3.700000e-57 233.0
42 TraesCS6A01G337000 chr5D 100.000 28 0 0 193 220 84345688 84345661 1.100000e-02 52.8
43 TraesCS6A01G337000 chr5A 87.778 180 14 5 1653 1831 566219274 566219446 2.900000e-48 204.0
44 TraesCS6A01G337000 chr5A 82.870 216 29 4 6 221 138427175 138426968 2.920000e-43 187.0
45 TraesCS6A01G337000 chr4B 87.349 166 15 5 223 383 645312130 645311966 1.050000e-42 185.0
46 TraesCS6A01G337000 chr2D 84.000 200 22 7 227 417 174574563 174574761 3.780000e-42 183.0
47 TraesCS6A01G337000 chr2D 76.301 173 28 12 1669 1831 11172488 11172657 5.100000e-11 80.5
48 TraesCS6A01G337000 chr3B 83.221 149 21 3 249 394 622284501 622284648 3.860000e-27 134.0
49 TraesCS6A01G337000 chr3D 91.398 93 6 2 6 98 515236236 515236146 6.460000e-25 126.0
50 TraesCS6A01G337000 chr3D 80.473 169 26 7 3760 3924 584861759 584861594 8.360000e-24 122.0
51 TraesCS6A01G337000 chr3D 81.690 142 16 6 4071 4205 584861171 584861033 6.510000e-20 110.0
52 TraesCS6A01G337000 chrUn 83.594 128 19 2 267 394 387724268 387724143 1.080000e-22 119.0
53 TraesCS6A01G337000 chr7B 100.000 28 0 0 193 220 118638677 118638704 1.100000e-02 52.8


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 TraesCS6A01G337000 chr6A 571018999 571025140 6141 False 11343.000000 11343 100.000000 1 6142 1 chr6A.!!$F1 6141
1 TraesCS6A01G337000 chr6B 641394624 641401221 6597 False 1705.980000 7169 95.924800 788 6142 5 chr6B.!!$F1 5354
2 TraesCS6A01G337000 chr6B 82742736 82746425 3689 True 941.000000 1498 87.509667 870 3974 3 chr6B.!!$R1 3104
3 TraesCS6A01G337000 chr6D 426098418 426104844 6426 False 2999.000000 6630 94.714667 1 6142 3 chr6D.!!$F2 6141
4 TraesCS6A01G337000 chr7D 39710662 39713471 2809 False 3526.000000 3526 89.247000 2360 5209 1 chr7D.!!$F2 2849
5 TraesCS6A01G337000 chr7D 40001876 40002749 873 False 942.000000 942 86.117000 4262 5146 1 chr7D.!!$F5 884
6 TraesCS6A01G337000 chr7D 39633800 39635847 2047 False 670.333333 911 89.986667 3563 5279 3 chr7D.!!$F7 1716
7 TraesCS6A01G337000 chr7A 39587583 39593630 6047 False 2195.000000 2639 89.740500 2092 5508 2 chr7A.!!$F2 3416
8 TraesCS6A01G337000 chr4A 645860409 645862103 1694 False 1960.000000 1960 87.609000 3980 5691 1 chr4A.!!$F2 1711

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
476 485 0.036388 ACATCATGGAGAACGGCGTT 60.036 50.000 27.15 27.15 0.00 4.84 F
611 628 0.597568 TTTCATGGGAAACAGCAGCG 59.402 50.000 0.00 0.00 38.07 5.18 F
1556 2705 0.464373 AATCGCAGCATCCGAACCAT 60.464 50.000 0.00 0.00 38.31 3.55 F
1904 3513 0.475044 AAAACCTTGGTCCGCACCTA 59.525 50.000 0.00 0.00 44.17 3.08 F
1905 3514 0.696501 AAACCTTGGTCCGCACCTAT 59.303 50.000 0.00 0.00 44.17 2.57 F
2210 3841 1.303236 CCACGGCAAGGTGATCCAA 60.303 57.895 3.65 0.00 40.38 3.53 F
4272 8529 1.085091 CTGCACAAGAGCTAGGCTTG 58.915 55.000 11.11 11.11 46.20 4.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1531 2680 1.430632 GGATGCTGCGATTGTGTGG 59.569 57.895 0.00 0.0 0.00 4.17 R
1841 3000 1.538075 ACACGCCCCTTAACGAAATTG 59.462 47.619 0.00 0.0 0.00 2.32 R
3548 5187 0.659427 CATGGCATTGTAGACAGGCG 59.341 55.000 0.00 0.0 0.00 5.52 R
3778 5419 4.702131 CCTGAAACTTTCCTGGGAGTAATG 59.298 45.833 4.46 0.0 0.00 1.90 R
4272 8529 5.083389 GTGTATATCTTCTCGTCGATCAGC 58.917 45.833 0.00 0.0 0.00 4.26 R
4540 9201 6.596309 TCAGTCACAGTAGTCAATCTCAAT 57.404 37.500 0.00 0.0 0.00 2.57 R
6012 12077 0.250124 CCTGGCACGTTGACTGGTAA 60.250 55.000 8.09 0.0 39.41 2.85 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
59 60 6.617782 TTCTTTCTCTCTGTTCATCTCCAT 57.382 37.500 0.00 0.00 0.00 3.41
60 61 6.617782 TCTTTCTCTCTGTTCATCTCCATT 57.382 37.500 0.00 0.00 0.00 3.16
66 67 8.260099 TCTCTCTGTTCATCTCCATTAATCAT 57.740 34.615 0.00 0.00 0.00 2.45
78 79 6.261603 TCTCCATTAATCATGTGCAAGTGATC 59.738 38.462 13.62 0.00 34.14 2.92
87 88 4.664150 TGTGCAAGTGATCGGACATATA 57.336 40.909 0.00 0.00 0.00 0.86
90 91 5.163457 TGTGCAAGTGATCGGACATATAAGA 60.163 40.000 0.00 0.00 0.00 2.10
93 94 6.479990 TGCAAGTGATCGGACATATAAGAAAG 59.520 38.462 0.00 0.00 0.00 2.62
140 141 6.041069 TGAACGGACAAATAAGGGTTCAAAAT 59.959 34.615 2.27 0.00 40.29 1.82
141 142 5.778862 ACGGACAAATAAGGGTTCAAAATG 58.221 37.500 0.00 0.00 0.00 2.32
172 173 1.069765 CACTGACCCTGCGTGTCTT 59.930 57.895 2.40 0.00 33.83 3.01
176 177 2.915659 ACCCTGCGTGTCTTCGGA 60.916 61.111 0.00 0.00 0.00 4.55
189 190 1.205417 TCTTCGGACGTTTATGGGGTC 59.795 52.381 0.00 0.00 0.00 4.46
199 200 4.338118 ACGTTTATGGGGTCATATTTGCTG 59.662 41.667 0.00 0.00 35.94 4.41
206 207 2.158957 GGGTCATATTTGCTGAGTCCGA 60.159 50.000 0.00 0.00 0.00 4.55
213 214 1.905637 TTGCTGAGTCCGACTGTAGA 58.094 50.000 5.57 0.00 0.00 2.59
214 215 2.130272 TGCTGAGTCCGACTGTAGAT 57.870 50.000 5.57 0.00 0.00 1.98
215 216 1.745653 TGCTGAGTCCGACTGTAGATG 59.254 52.381 5.57 0.00 0.00 2.90
216 217 1.535015 GCTGAGTCCGACTGTAGATGC 60.535 57.143 5.57 0.00 0.00 3.91
217 218 2.020720 CTGAGTCCGACTGTAGATGCT 58.979 52.381 5.57 0.00 0.00 3.79
218 219 2.017782 TGAGTCCGACTGTAGATGCTC 58.982 52.381 5.57 0.00 0.00 4.26
219 220 2.294074 GAGTCCGACTGTAGATGCTCT 58.706 52.381 5.57 0.00 0.00 4.09
220 221 2.685897 GAGTCCGACTGTAGATGCTCTT 59.314 50.000 5.57 0.00 0.00 2.85
221 222 3.093057 AGTCCGACTGTAGATGCTCTTT 58.907 45.455 0.00 0.00 0.00 2.52
222 223 3.129638 AGTCCGACTGTAGATGCTCTTTC 59.870 47.826 0.00 0.00 0.00 2.62
223 224 2.097629 TCCGACTGTAGATGCTCTTTCG 59.902 50.000 0.00 0.00 0.00 3.46
224 225 2.455032 CGACTGTAGATGCTCTTTCGG 58.545 52.381 0.00 0.00 0.00 4.30
225 226 2.097629 CGACTGTAGATGCTCTTTCGGA 59.902 50.000 0.00 0.00 0.00 4.55
245 246 5.765677 TCGGAGAAGAGTTGTATAGGATCTG 59.234 44.000 0.00 0.00 0.00 2.90
252 253 8.484214 AAGAGTTGTATAGGATCTGCATTAGA 57.516 34.615 0.00 0.00 40.37 2.10
266 267 9.872721 GATCTGCATTAGATGAGATCAATAAGA 57.127 33.333 16.59 0.00 46.12 2.10
334 337 6.564709 TTGAAGACACTCATCCAATCTTTG 57.435 37.500 0.00 0.00 29.85 2.77
343 346 7.448161 ACACTCATCCAATCTTTGATGTACAAA 59.552 33.333 0.00 0.00 44.79 2.83
346 349 8.408043 TCATCCAATCTTTGATGTACAAACTT 57.592 30.769 0.00 0.00 42.57 2.66
375 378 7.674471 AGTTTCAGCTCCTAATTCAAACTAC 57.326 36.000 0.00 0.00 32.25 2.73
383 386 8.035984 AGCTCCTAATTCAAACTACACTTAGAC 58.964 37.037 0.00 0.00 0.00 2.59
429 438 4.922206 ACTATCAAAATCAGTGGAAGGCA 58.078 39.130 0.00 0.00 0.00 4.75
439 448 4.821589 GGAAGGCAGGCGTCCTCG 62.822 72.222 20.06 0.00 40.37 4.63
461 470 1.298157 TGCTGCGCCACTTACACATC 61.298 55.000 4.18 0.00 0.00 3.06
470 479 3.375299 GCCACTTACACATCATGGAGAAC 59.625 47.826 0.00 0.00 31.69 3.01
476 485 0.036388 ACATCATGGAGAACGGCGTT 60.036 50.000 27.15 27.15 0.00 4.84
486 495 2.494504 GAACGGCGTTTTGGCTCTCG 62.495 60.000 27.48 0.00 42.02 4.04
487 496 3.788766 CGGCGTTTTGGCTCTCGG 61.789 66.667 0.00 0.00 42.02 4.63
488 497 2.358247 GGCGTTTTGGCTCTCGGA 60.358 61.111 0.00 0.00 40.72 4.55
491 500 1.497722 CGTTTTGGCTCTCGGAAGC 59.502 57.895 1.80 1.80 41.73 3.86
573 590 2.831685 AGATGTTCGTGTTAGTGCCA 57.168 45.000 0.00 0.00 0.00 4.92
577 594 1.937223 TGTTCGTGTTAGTGCCACAAG 59.063 47.619 0.00 0.00 33.00 3.16
599 616 7.820872 ACAAGCATCCTTAAAAAGATTTCATGG 59.179 33.333 0.00 0.00 0.00 3.66
604 621 9.154847 CATCCTTAAAAAGATTTCATGGGAAAC 57.845 33.333 0.00 0.00 45.22 2.78
605 622 8.256356 TCCTTAAAAAGATTTCATGGGAAACA 57.744 30.769 0.00 0.00 45.22 2.83
607 624 7.118245 CCTTAAAAAGATTTCATGGGAAACAGC 59.882 37.037 0.00 0.00 45.22 4.40
608 625 5.549742 AAAAGATTTCATGGGAAACAGCA 57.450 34.783 0.00 0.00 45.22 4.41
609 626 4.796038 AAGATTTCATGGGAAACAGCAG 57.204 40.909 0.00 0.00 45.22 4.24
610 627 2.494870 AGATTTCATGGGAAACAGCAGC 59.505 45.455 0.00 0.00 45.22 5.25
611 628 0.597568 TTTCATGGGAAACAGCAGCG 59.402 50.000 0.00 0.00 38.07 5.18
612 629 1.243342 TTCATGGGAAACAGCAGCGG 61.243 55.000 0.00 0.00 0.00 5.52
613 630 1.973281 CATGGGAAACAGCAGCGGT 60.973 57.895 0.00 0.00 0.00 5.68
614 631 1.973281 ATGGGAAACAGCAGCGGTG 60.973 57.895 10.98 10.98 37.06 4.94
615 632 2.594592 GGGAAACAGCAGCGGTGT 60.595 61.111 17.07 7.42 46.58 4.16
620 637 3.420943 ACAGCAGCGGTGTTTCAC 58.579 55.556 17.07 0.00 41.72 3.18
621 638 1.153168 ACAGCAGCGGTGTTTCACT 60.153 52.632 17.07 0.81 41.72 3.41
622 639 1.280746 CAGCAGCGGTGTTTCACTG 59.719 57.895 17.07 10.38 43.00 3.66
623 640 1.893808 AGCAGCGGTGTTTCACTGG 60.894 57.895 17.07 0.44 40.72 4.00
665 682 8.416329 AGGATGATATTTTGGAGTAACATTTGC 58.584 33.333 0.00 0.00 0.00 3.68
666 683 8.416329 GGATGATATTTTGGAGTAACATTTGCT 58.584 33.333 0.00 0.00 0.00 3.91
673 690 8.810652 TTTTGGAGTAACATTTGCTGTTTATC 57.189 30.769 0.00 0.00 45.98 1.75
674 691 7.759489 TTGGAGTAACATTTGCTGTTTATCT 57.241 32.000 0.00 0.00 45.98 1.98
675 692 7.759489 TGGAGTAACATTTGCTGTTTATCTT 57.241 32.000 0.00 0.00 45.98 2.40
676 693 8.177119 TGGAGTAACATTTGCTGTTTATCTTT 57.823 30.769 0.00 0.00 45.98 2.52
677 694 8.637986 TGGAGTAACATTTGCTGTTTATCTTTT 58.362 29.630 0.00 0.00 45.98 2.27
678 695 9.476202 GGAGTAACATTTGCTGTTTATCTTTTT 57.524 29.630 0.00 0.00 45.98 1.94
682 699 8.715191 AACATTTGCTGTTTATCTTTTTCACA 57.285 26.923 0.00 0.00 45.98 3.58
683 700 8.356533 ACATTTGCTGTTTATCTTTTTCACAG 57.643 30.769 0.00 0.00 38.32 3.66
684 701 7.439056 ACATTTGCTGTTTATCTTTTTCACAGG 59.561 33.333 0.00 0.00 36.22 4.00
685 702 4.870363 TGCTGTTTATCTTTTTCACAGGC 58.130 39.130 0.00 0.00 36.22 4.85
686 703 4.584325 TGCTGTTTATCTTTTTCACAGGCT 59.416 37.500 0.00 0.00 36.22 4.58
687 704 5.068987 TGCTGTTTATCTTTTTCACAGGCTT 59.931 36.000 0.00 0.00 36.22 4.35
688 705 6.264292 TGCTGTTTATCTTTTTCACAGGCTTA 59.736 34.615 0.00 0.00 36.22 3.09
689 706 7.145323 GCTGTTTATCTTTTTCACAGGCTTAA 58.855 34.615 0.00 0.00 36.22 1.85
690 707 7.651704 GCTGTTTATCTTTTTCACAGGCTTAAA 59.348 33.333 0.00 0.00 36.22 1.52
739 756 3.562973 GGATGTAGCATTGGATGTGACAG 59.437 47.826 0.00 0.00 32.95 3.51
740 757 3.701205 TGTAGCATTGGATGTGACAGT 57.299 42.857 0.00 0.00 0.00 3.55
741 758 4.817318 TGTAGCATTGGATGTGACAGTA 57.183 40.909 0.00 0.00 0.00 2.74
742 759 4.503910 TGTAGCATTGGATGTGACAGTAC 58.496 43.478 0.00 0.00 0.00 2.73
885 903 4.610333 TCTTTGAGCTGACCCAGATAGTA 58.390 43.478 0.00 0.00 32.44 1.82
1025 1045 1.457455 CTGCTCCTCCTCCTCCTCC 60.457 68.421 0.00 0.00 0.00 4.30
1026 1046 1.938596 TGCTCCTCCTCCTCCTCCT 60.939 63.158 0.00 0.00 0.00 3.69
1027 1047 1.152546 GCTCCTCCTCCTCCTCCTC 60.153 68.421 0.00 0.00 0.00 3.71
1531 2680 3.610911 CAGGTACAGAACAAGATTCCCC 58.389 50.000 0.00 0.00 0.00 4.81
1549 2698 1.430632 CCACACAATCGCAGCATCC 59.569 57.895 0.00 0.00 0.00 3.51
1556 2705 0.464373 AATCGCAGCATCCGAACCAT 60.464 50.000 0.00 0.00 38.31 3.55
1680 2829 6.471519 GCTAGTTGAACAATTCTGATTCATGC 59.528 38.462 0.00 0.00 32.61 4.06
1707 2864 7.596248 GTGTATAATCAACCAATGGATCATTGC 59.404 37.037 6.16 0.00 46.73 3.56
1781 2940 6.500041 TCTCGGTCATTTTTCGTTCAAAATT 58.500 32.000 0.00 0.00 34.70 1.82
1782 2941 6.635239 TCTCGGTCATTTTTCGTTCAAAATTC 59.365 34.615 0.00 0.00 34.70 2.17
1783 2942 6.266323 TCGGTCATTTTTCGTTCAAAATTCA 58.734 32.000 0.00 0.00 34.70 2.57
1823 2982 7.966246 TCAAGAATTCAAATTTTGGATGGTG 57.034 32.000 8.44 5.81 0.00 4.17
1851 3010 4.694177 CGAAAAGCTCGTCAATTTCGTTA 58.306 39.130 16.71 0.00 45.32 3.18
1859 3018 1.808343 GTCAATTTCGTTAAGGGGCGT 59.192 47.619 0.00 0.00 0.00 5.68
1860 3019 1.807742 TCAATTTCGTTAAGGGGCGTG 59.192 47.619 0.00 0.00 0.00 5.34
1861 3020 1.538075 CAATTTCGTTAAGGGGCGTGT 59.462 47.619 0.00 0.00 0.00 4.49
1862 3021 2.743126 CAATTTCGTTAAGGGGCGTGTA 59.257 45.455 0.00 0.00 0.00 2.90
1871 3480 5.927689 CGTTAAGGGGCGTGTATATATTTCA 59.072 40.000 0.00 0.00 0.00 2.69
1904 3513 0.475044 AAAACCTTGGTCCGCACCTA 59.525 50.000 0.00 0.00 44.17 3.08
1905 3514 0.696501 AAACCTTGGTCCGCACCTAT 59.303 50.000 0.00 0.00 44.17 2.57
2210 3841 1.303236 CCACGGCAAGGTGATCCAA 60.303 57.895 3.65 0.00 40.38 3.53
2657 4288 2.863704 GCAGCGCACTTTTGAGGAAATT 60.864 45.455 11.47 0.00 0.00 1.82
2753 4391 4.454728 TGATAAGGCATTGCAGGTTTTC 57.545 40.909 11.39 6.15 0.00 2.29
2765 4403 2.552315 GCAGGTTTTCGGTTTGATGAGA 59.448 45.455 0.00 0.00 0.00 3.27
2879 4517 3.054875 TCAGAGCTCTGTGCAAATATGGT 60.055 43.478 36.32 0.00 45.94 3.55
3219 4857 4.072088 GTTCGGCACTGAACGCGG 62.072 66.667 12.47 0.00 38.91 6.46
3450 5088 2.026822 GGGAGTCAAGCCTGAAGATTCA 60.027 50.000 0.00 0.00 31.88 2.57
3459 5097 2.915738 CTGAAGATTCAGCAACAGCC 57.084 50.000 9.50 0.00 46.97 4.85
3524 5163 4.327982 CAGAGGAACTGTTTGAGTCAGA 57.672 45.455 0.00 0.00 41.55 3.27
3548 5187 2.540101 CGACATCGTTTCCAATAGGAGC 59.460 50.000 0.00 0.00 38.84 4.70
3611 5250 2.786854 CAATATCGAGGAGGCGTATCG 58.213 52.381 7.07 7.07 37.79 2.92
4121 8374 1.895131 CACAGGAAAATGGGAGTTGGG 59.105 52.381 0.00 0.00 0.00 4.12
4272 8529 1.085091 CTGCACAAGAGCTAGGCTTG 58.915 55.000 11.11 11.11 46.20 4.01
4296 8553 5.106869 GCTGATCGACGAGAAGATATACACT 60.107 44.000 12.41 0.00 0.00 3.55
4526 9187 3.001330 CGTTGGTGTCTGACTTCTGAAAC 59.999 47.826 9.51 4.78 33.02 2.78
4540 9201 6.759272 ACTTCTGAAACTACAGTTATCTGCA 58.241 36.000 0.51 0.00 44.77 4.41
4815 9477 4.792068 CCCTCATTTTAGCCACCTCATTA 58.208 43.478 0.00 0.00 0.00 1.90
5288 10005 9.936759 TTGTTGTGTATGTTGTTCTAGATGATA 57.063 29.630 0.00 0.00 0.00 2.15
5451 11511 7.503521 TCAACTCACAGCATTTAACATGTTA 57.496 32.000 14.35 14.35 0.00 2.41
5490 11550 0.946221 AGTTCGCCGTCTGAAGCTTG 60.946 55.000 2.10 0.00 0.00 4.01
5540 11600 5.510861 GGTCTGTTACTCTGCTTCCACTTAA 60.511 44.000 0.00 0.00 0.00 1.85
5564 11626 4.934797 ATCCCATATACAGGGTGAATGG 57.065 45.455 10.98 0.00 46.82 3.16
5569 11631 5.073144 CCCATATACAGGGTGAATGGTTAGT 59.927 44.000 4.25 0.00 41.61 2.24
5618 11680 7.849322 AAAATAATAAACAGTTGACCAGGGT 57.151 32.000 0.00 0.00 0.00 4.34
5691 11753 5.662657 ACCCATTAAAGAATTGCCTGCTATT 59.337 36.000 0.00 0.00 0.00 1.73
5864 11929 5.874892 TTTGTGTTATAAGCACGCAAAAC 57.125 34.783 10.77 0.00 46.49 2.43
5873 11938 6.869421 ATAAGCACGCAAAACAATATGTTC 57.131 33.333 0.00 0.00 40.14 3.18
5874 11939 3.574614 AGCACGCAAAACAATATGTTCC 58.425 40.909 0.00 0.00 40.14 3.62
5875 11940 2.341168 GCACGCAAAACAATATGTTCCG 59.659 45.455 0.00 3.46 40.14 4.30
5876 11941 3.560503 CACGCAAAACAATATGTTCCGT 58.439 40.909 9.28 9.28 40.14 4.69
5877 11942 3.360463 CACGCAAAACAATATGTTCCGTG 59.640 43.478 19.45 19.45 43.42 4.94
5878 11943 3.003897 ACGCAAAACAATATGTTCCGTGT 59.996 39.130 12.44 9.17 40.14 4.49
5879 11944 3.360463 CGCAAAACAATATGTTCCGTGTG 59.640 43.478 0.00 0.00 40.14 3.82
5880 11945 4.541779 GCAAAACAATATGTTCCGTGTGA 58.458 39.130 0.00 0.00 40.14 3.58
5882 11947 5.633182 GCAAAACAATATGTTCCGTGTGATT 59.367 36.000 0.00 0.00 40.14 2.57
5883 11948 6.804295 GCAAAACAATATGTTCCGTGTGATTA 59.196 34.615 0.00 0.00 40.14 1.75
5884 11949 7.487829 GCAAAACAATATGTTCCGTGTGATTAT 59.512 33.333 0.00 0.00 40.14 1.28
5885 11950 9.352784 CAAAACAATATGTTCCGTGTGATTATT 57.647 29.630 0.00 0.00 40.14 1.40
5894 11959 8.780846 TGTTCCGTGTGATTATTAATGTTACT 57.219 30.769 0.00 0.00 0.00 2.24
5895 11960 8.875803 TGTTCCGTGTGATTATTAATGTTACTC 58.124 33.333 0.00 0.00 0.00 2.59
5896 11961 8.875803 GTTCCGTGTGATTATTAATGTTACTCA 58.124 33.333 0.00 0.00 0.00 3.41
5897 11962 8.642908 TCCGTGTGATTATTAATGTTACTCAG 57.357 34.615 0.00 0.00 0.00 3.35
5898 11963 8.471609 TCCGTGTGATTATTAATGTTACTCAGA 58.528 33.333 0.00 0.00 0.00 3.27
5899 11964 8.755941 CCGTGTGATTATTAATGTTACTCAGAG 58.244 37.037 0.00 0.00 0.00 3.35
5907 11972 4.392921 AATGTTACTCAGAGATGGGACG 57.607 45.455 3.79 0.00 0.00 4.79
5908 11973 3.081710 TGTTACTCAGAGATGGGACGA 57.918 47.619 3.79 0.00 0.00 4.20
5909 11974 3.427573 TGTTACTCAGAGATGGGACGAA 58.572 45.455 3.79 0.00 0.00 3.85
5910 11975 3.830178 TGTTACTCAGAGATGGGACGAAA 59.170 43.478 3.79 0.00 0.00 3.46
5911 11976 4.282449 TGTTACTCAGAGATGGGACGAAAA 59.718 41.667 3.79 0.00 0.00 2.29
5912 11977 5.046591 TGTTACTCAGAGATGGGACGAAAAT 60.047 40.000 3.79 0.00 0.00 1.82
5914 11979 5.878406 ACTCAGAGATGGGACGAAAATAT 57.122 39.130 3.79 0.00 0.00 1.28
5916 11981 6.987386 ACTCAGAGATGGGACGAAAATATAG 58.013 40.000 3.79 0.00 0.00 1.31
5917 11982 5.784177 TCAGAGATGGGACGAAAATATAGC 58.216 41.667 0.00 0.00 0.00 2.97
5918 11983 5.540337 TCAGAGATGGGACGAAAATATAGCT 59.460 40.000 0.00 0.00 0.00 3.32
5919 11984 5.636965 CAGAGATGGGACGAAAATATAGCTG 59.363 44.000 0.00 0.00 0.00 4.24
5920 11985 5.305644 AGAGATGGGACGAAAATATAGCTGT 59.694 40.000 0.00 0.00 0.00 4.40
5925 11990 7.004555 TGGGACGAAAATATAGCTGTCATAT 57.995 36.000 0.00 0.00 0.00 1.78
5926 11991 7.450074 TGGGACGAAAATATAGCTGTCATATT 58.550 34.615 0.00 0.00 31.40 1.28
5929 11994 8.988934 GGACGAAAATATAGCTGTCATATTTCA 58.011 33.333 11.57 0.00 37.51 2.69
5936 12001 6.889301 ATAGCTGTCATATTTCAATGTGGG 57.111 37.500 0.00 0.00 0.00 4.61
5937 12002 3.956199 AGCTGTCATATTTCAATGTGGGG 59.044 43.478 0.00 0.00 0.00 4.96
5938 12003 3.491447 GCTGTCATATTTCAATGTGGGGC 60.491 47.826 0.00 0.00 0.00 5.80
5939 12004 3.956199 CTGTCATATTTCAATGTGGGGCT 59.044 43.478 0.00 0.00 0.00 5.19
5940 12005 4.352009 TGTCATATTTCAATGTGGGGCTT 58.648 39.130 0.00 0.00 0.00 4.35
5941 12006 5.514169 TGTCATATTTCAATGTGGGGCTTA 58.486 37.500 0.00 0.00 0.00 3.09
5943 12008 6.438741 TGTCATATTTCAATGTGGGGCTTAAA 59.561 34.615 0.00 0.00 0.00 1.52
5944 12009 7.038729 TGTCATATTTCAATGTGGGGCTTAAAA 60.039 33.333 0.00 0.00 0.00 1.52
5945 12010 7.492344 GTCATATTTCAATGTGGGGCTTAAAAG 59.508 37.037 0.00 0.00 0.00 2.27
5946 12011 7.398618 TCATATTTCAATGTGGGGCTTAAAAGA 59.601 33.333 0.00 0.00 0.00 2.52
5947 12012 6.625532 ATTTCAATGTGGGGCTTAAAAGAT 57.374 33.333 0.00 0.00 0.00 2.40
5948 12013 5.404466 TTCAATGTGGGGCTTAAAAGATG 57.596 39.130 0.00 0.00 0.00 2.90
5949 12014 4.415596 TCAATGTGGGGCTTAAAAGATGT 58.584 39.130 0.00 0.00 0.00 3.06
5950 12015 5.575157 TCAATGTGGGGCTTAAAAGATGTA 58.425 37.500 0.00 0.00 0.00 2.29
5951 12016 5.417580 TCAATGTGGGGCTTAAAAGATGTAC 59.582 40.000 0.00 0.00 0.00 2.90
5952 12017 4.650972 TGTGGGGCTTAAAAGATGTACT 57.349 40.909 0.00 0.00 0.00 2.73
5953 12018 4.993028 TGTGGGGCTTAAAAGATGTACTT 58.007 39.130 0.00 0.00 40.98 2.24
5954 12019 6.129414 TGTGGGGCTTAAAAGATGTACTTA 57.871 37.500 0.00 0.00 37.93 2.24
5955 12020 6.727394 TGTGGGGCTTAAAAGATGTACTTAT 58.273 36.000 0.00 0.00 37.93 1.73
5956 12021 7.179269 TGTGGGGCTTAAAAGATGTACTTATT 58.821 34.615 0.00 0.00 37.93 1.40
5957 12022 7.672239 TGTGGGGCTTAAAAGATGTACTTATTT 59.328 33.333 0.00 0.00 37.93 1.40
5958 12023 8.188799 GTGGGGCTTAAAAGATGTACTTATTTC 58.811 37.037 2.28 0.00 37.93 2.17
5959 12024 7.891183 TGGGGCTTAAAAGATGTACTTATTTCA 59.109 33.333 2.28 0.00 37.93 2.69
5960 12025 8.914011 GGGGCTTAAAAGATGTACTTATTTCAT 58.086 33.333 2.28 0.00 37.93 2.57
5972 12037 8.835467 TGTACTTATTTCATAAAAATCGCAGC 57.165 30.769 0.00 0.00 0.00 5.25
5973 12038 8.454894 TGTACTTATTTCATAAAAATCGCAGCA 58.545 29.630 0.00 0.00 0.00 4.41
5974 12039 9.284594 GTACTTATTTCATAAAAATCGCAGCAA 57.715 29.630 0.00 0.00 0.00 3.91
5975 12040 8.931385 ACTTATTTCATAAAAATCGCAGCAAT 57.069 26.923 0.00 0.00 0.00 3.56
5976 12041 9.369904 ACTTATTTCATAAAAATCGCAGCAATT 57.630 25.926 0.00 0.00 0.00 2.32
5977 12042 9.627657 CTTATTTCATAAAAATCGCAGCAATTG 57.372 29.630 0.00 0.00 0.00 2.32
5990 12055 4.978083 CAGCAATTGCACCTTTCTATCT 57.022 40.909 30.89 3.86 45.16 1.98
5992 12057 6.630444 CAGCAATTGCACCTTTCTATCTAT 57.370 37.500 30.89 3.18 45.16 1.98
5993 12058 7.035840 CAGCAATTGCACCTTTCTATCTATT 57.964 36.000 30.89 2.50 45.16 1.73
5994 12059 7.486647 CAGCAATTGCACCTTTCTATCTATTT 58.513 34.615 30.89 2.10 45.16 1.40
5995 12060 7.434307 CAGCAATTGCACCTTTCTATCTATTTG 59.566 37.037 30.89 11.04 45.16 2.32
5996 12061 7.340232 AGCAATTGCACCTTTCTATCTATTTGA 59.660 33.333 30.89 0.00 45.16 2.69
5997 12062 7.975616 GCAATTGCACCTTTCTATCTATTTGAA 59.024 33.333 25.36 0.00 41.59 2.69
6001 12066 8.579850 TGCACCTTTCTATCTATTTGAATTGT 57.420 30.769 0.00 0.00 0.00 2.71
6002 12067 8.677300 TGCACCTTTCTATCTATTTGAATTGTC 58.323 33.333 0.00 0.00 0.00 3.18
6003 12068 8.897752 GCACCTTTCTATCTATTTGAATTGTCT 58.102 33.333 0.00 0.00 0.00 3.41
6017 12082 9.739276 ATTTGAATTGTCTGAGATAGTTTACCA 57.261 29.630 0.00 0.00 0.00 3.25
6018 12083 8.777865 TTGAATTGTCTGAGATAGTTTACCAG 57.222 34.615 0.00 0.00 0.00 4.00
6019 12084 7.907389 TGAATTGTCTGAGATAGTTTACCAGT 58.093 34.615 0.00 0.00 0.00 4.00
6020 12085 8.035394 TGAATTGTCTGAGATAGTTTACCAGTC 58.965 37.037 0.00 0.00 0.00 3.51
6021 12086 6.911250 TTGTCTGAGATAGTTTACCAGTCA 57.089 37.500 0.00 0.00 0.00 3.41
6022 12087 6.911250 TGTCTGAGATAGTTTACCAGTCAA 57.089 37.500 0.00 0.00 0.00 3.18
6023 12088 6.688578 TGTCTGAGATAGTTTACCAGTCAAC 58.311 40.000 0.00 0.00 0.00 3.18
6024 12089 5.800941 GTCTGAGATAGTTTACCAGTCAACG 59.199 44.000 0.00 0.00 0.00 4.10
6025 12090 5.475909 TCTGAGATAGTTTACCAGTCAACGT 59.524 40.000 0.00 0.00 0.00 3.99
6026 12091 5.466819 TGAGATAGTTTACCAGTCAACGTG 58.533 41.667 0.00 0.00 0.00 4.49
6027 12092 4.243270 AGATAGTTTACCAGTCAACGTGC 58.757 43.478 0.00 0.00 0.00 5.34
6028 12093 1.589803 AGTTTACCAGTCAACGTGCC 58.410 50.000 0.00 0.00 0.00 5.01
6029 12094 1.134340 AGTTTACCAGTCAACGTGCCA 60.134 47.619 0.00 0.00 0.00 4.92
6030 12095 1.263217 GTTTACCAGTCAACGTGCCAG 59.737 52.381 0.00 0.00 0.00 4.85
6031 12096 0.250124 TTACCAGTCAACGTGCCAGG 60.250 55.000 0.00 0.00 0.00 4.45
6032 12097 1.116536 TACCAGTCAACGTGCCAGGA 61.117 55.000 0.00 0.00 0.00 3.86
6033 12098 1.227823 CCAGTCAACGTGCCAGGAA 60.228 57.895 0.00 0.00 0.00 3.36
6034 12099 0.817634 CCAGTCAACGTGCCAGGAAA 60.818 55.000 0.00 0.00 0.00 3.13
6035 12100 1.238439 CAGTCAACGTGCCAGGAAAT 58.762 50.000 0.00 0.00 0.00 2.17
6036 12101 1.608590 CAGTCAACGTGCCAGGAAATT 59.391 47.619 0.00 0.00 0.00 1.82
6037 12102 2.811431 CAGTCAACGTGCCAGGAAATTA 59.189 45.455 0.00 0.00 0.00 1.40
6038 12103 3.252215 CAGTCAACGTGCCAGGAAATTAA 59.748 43.478 0.00 0.00 0.00 1.40
6039 12104 3.886505 AGTCAACGTGCCAGGAAATTAAA 59.113 39.130 0.00 0.00 0.00 1.52
6040 12105 4.023193 AGTCAACGTGCCAGGAAATTAAAG 60.023 41.667 0.00 0.00 0.00 1.85
6041 12106 3.886505 TCAACGTGCCAGGAAATTAAAGT 59.113 39.130 0.00 0.00 0.00 2.66
6042 12107 3.915437 ACGTGCCAGGAAATTAAAGTG 57.085 42.857 0.00 0.00 0.00 3.16
6043 12108 2.030274 ACGTGCCAGGAAATTAAAGTGC 60.030 45.455 0.00 0.00 0.00 4.40
6044 12109 2.228822 CGTGCCAGGAAATTAAAGTGCT 59.771 45.455 0.00 0.00 0.00 4.40
6045 12110 3.578688 GTGCCAGGAAATTAAAGTGCTG 58.421 45.455 0.00 3.99 33.35 4.41
6050 12115 5.051891 CAGGAAATTAAAGTGCTGGACTG 57.948 43.478 1.54 0.00 34.02 3.51
6051 12116 4.082125 AGGAAATTAAAGTGCTGGACTGG 58.918 43.478 1.54 0.00 34.02 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
48 49 6.381481 TGCACATGATTAATGGAGATGAAC 57.619 37.500 0.00 0.00 40.94 3.18
59 60 4.332543 GTCCGATCACTTGCACATGATTAA 59.667 41.667 12.09 1.03 35.67 1.40
60 61 3.871006 GTCCGATCACTTGCACATGATTA 59.129 43.478 12.09 1.29 35.67 1.75
66 67 3.541996 ATATGTCCGATCACTTGCACA 57.458 42.857 0.00 0.00 0.00 4.57
78 79 8.662781 TCCTCATTTTCTTTCTTATATGTCCG 57.337 34.615 0.00 0.00 0.00 4.79
87 88 5.694995 TCCACACTCCTCATTTTCTTTCTT 58.305 37.500 0.00 0.00 0.00 2.52
90 91 5.388654 ACATCCACACTCCTCATTTTCTTT 58.611 37.500 0.00 0.00 0.00 2.52
93 94 6.115446 TCATACATCCACACTCCTCATTTTC 58.885 40.000 0.00 0.00 0.00 2.29
108 109 5.238650 CCCTTATTTGTCCGTTCATACATCC 59.761 44.000 0.00 0.00 0.00 3.51
140 141 1.227527 CAGTGACCAGGCGTGTTCA 60.228 57.895 2.19 2.19 0.00 3.18
141 142 1.069090 TCAGTGACCAGGCGTGTTC 59.931 57.895 5.57 0.78 0.00 3.18
161 162 2.805353 CGTCCGAAGACACGCAGG 60.805 66.667 0.00 0.00 43.73 4.85
162 163 1.213094 AAACGTCCGAAGACACGCAG 61.213 55.000 0.00 0.00 43.73 5.18
163 164 0.030504 TAAACGTCCGAAGACACGCA 59.969 50.000 0.00 0.00 43.73 5.24
167 168 1.066716 CCCCATAAACGTCCGAAGACA 60.067 52.381 0.00 0.00 43.73 3.41
172 173 1.196911 ATGACCCCATAAACGTCCGA 58.803 50.000 0.00 0.00 0.00 4.55
176 177 4.338118 CAGCAAATATGACCCCATAAACGT 59.662 41.667 0.00 0.00 38.62 3.99
184 185 2.576615 GGACTCAGCAAATATGACCCC 58.423 52.381 0.00 0.00 0.00 4.95
189 190 3.525537 ACAGTCGGACTCAGCAAATATG 58.474 45.455 7.89 0.00 0.00 1.78
199 200 2.766970 GAGCATCTACAGTCGGACTC 57.233 55.000 7.89 0.00 0.00 3.36
217 218 6.185511 TCCTATACAACTCTTCTCCGAAAGA 58.814 40.000 0.00 0.00 34.22 2.52
218 219 6.452494 TCCTATACAACTCTTCTCCGAAAG 57.548 41.667 0.00 0.00 0.00 2.62
219 220 6.834451 AGATCCTATACAACTCTTCTCCGAAA 59.166 38.462 0.00 0.00 0.00 3.46
220 221 6.263392 CAGATCCTATACAACTCTTCTCCGAA 59.737 42.308 0.00 0.00 0.00 4.30
221 222 5.765677 CAGATCCTATACAACTCTTCTCCGA 59.234 44.000 0.00 0.00 0.00 4.55
222 223 5.563867 GCAGATCCTATACAACTCTTCTCCG 60.564 48.000 0.00 0.00 0.00 4.63
223 224 5.303078 TGCAGATCCTATACAACTCTTCTCC 59.697 44.000 0.00 0.00 0.00 3.71
224 225 6.398234 TGCAGATCCTATACAACTCTTCTC 57.602 41.667 0.00 0.00 0.00 2.87
225 226 6.992664 ATGCAGATCCTATACAACTCTTCT 57.007 37.500 0.00 0.00 0.00 2.85
306 309 7.824672 AGATTGGATGAGTGTCTTCAATTTTC 58.175 34.615 0.00 0.00 0.00 2.29
307 310 7.771927 AGATTGGATGAGTGTCTTCAATTTT 57.228 32.000 0.00 0.00 0.00 1.82
320 323 8.048534 AGTTTGTACATCAAAGATTGGATGAG 57.951 34.615 15.34 0.00 45.15 2.90
343 346 9.131791 TGAATTAGGAGCTGAAACTTTTTAAGT 57.868 29.630 0.00 0.00 45.46 2.24
346 349 9.744468 GTTTGAATTAGGAGCTGAAACTTTTTA 57.256 29.630 0.00 0.00 0.00 1.52
355 358 6.360370 AGTGTAGTTTGAATTAGGAGCTGA 57.640 37.500 0.00 0.00 0.00 4.26
401 410 9.347240 CCTTCCACTGATTTTGATAGTATTCAT 57.653 33.333 0.00 0.00 0.00 2.57
410 419 3.094572 CCTGCCTTCCACTGATTTTGAT 58.905 45.455 0.00 0.00 0.00 2.57
448 457 3.266510 TCTCCATGATGTGTAAGTGGC 57.733 47.619 0.00 0.00 0.00 5.01
461 470 0.109781 CCAAAACGCCGTTCTCCATG 60.110 55.000 1.60 0.00 0.00 3.66
470 479 3.788766 CCGAGAGCCAAAACGCCG 61.789 66.667 0.00 0.00 0.00 6.46
476 485 2.742372 GCGCTTCCGAGAGCCAAA 60.742 61.111 0.00 0.00 42.14 3.28
494 503 2.526304 TACTATTCACATGGGAGCGC 57.474 50.000 0.00 0.00 0.00 5.92
495 504 4.188462 TGTTTACTATTCACATGGGAGCG 58.812 43.478 0.00 0.00 0.00 5.03
570 587 4.519540 TCTTTTTAAGGATGCTTGTGGC 57.480 40.909 10.10 0.00 42.22 5.01
571 588 7.153985 TGAAATCTTTTTAAGGATGCTTGTGG 58.846 34.615 10.10 0.00 0.00 4.17
573 590 7.820872 CCATGAAATCTTTTTAAGGATGCTTGT 59.179 33.333 10.10 0.00 0.00 3.16
577 594 6.877236 TCCCATGAAATCTTTTTAAGGATGC 58.123 36.000 0.00 0.00 0.00 3.91
582 599 7.656948 TGCTGTTTCCCATGAAATCTTTTTAAG 59.343 33.333 0.00 0.00 42.20 1.85
585 602 5.927819 TGCTGTTTCCCATGAAATCTTTTT 58.072 33.333 0.00 0.00 42.20 1.94
590 607 2.733227 CGCTGCTGTTTCCCATGAAATC 60.733 50.000 0.00 0.00 42.20 2.17
599 616 0.317854 GAAACACCGCTGCTGTTTCC 60.318 55.000 25.24 14.11 46.34 3.13
604 621 1.280746 CAGTGAAACACCGCTGCTG 59.719 57.895 0.00 0.00 41.43 4.41
605 622 1.893808 CCAGTGAAACACCGCTGCT 60.894 57.895 0.00 0.00 41.84 4.24
607 624 0.813610 TCACCAGTGAAACACCGCTG 60.814 55.000 0.00 0.00 41.43 5.18
608 625 0.107410 TTCACCAGTGAAACACCGCT 60.107 50.000 10.71 0.00 45.56 5.52
609 626 2.399856 TTCACCAGTGAAACACCGC 58.600 52.632 10.71 0.00 45.56 5.68
665 682 9.696917 ATTTAAGCCTGTGAAAAAGATAAACAG 57.303 29.630 0.00 0.00 38.36 3.16
666 683 9.474920 CATTTAAGCCTGTGAAAAAGATAAACA 57.525 29.630 0.00 0.00 0.00 2.83
680 697 8.773645 GCAAAAAGATTAAACATTTAAGCCTGT 58.226 29.630 8.38 0.00 39.22 4.00
681 698 8.229811 GGCAAAAAGATTAAACATTTAAGCCTG 58.770 33.333 15.94 3.95 39.22 4.85
682 699 8.156820 AGGCAAAAAGATTAAACATTTAAGCCT 58.843 29.630 18.25 18.25 39.22 4.58
683 700 8.322906 AGGCAAAAAGATTAAACATTTAAGCC 57.677 30.769 15.66 15.66 39.22 4.35
739 756 7.961325 ATTTCAACAAAAATCCCATGTGTAC 57.039 32.000 0.00 0.00 0.00 2.90
740 757 8.970859 AAATTTCAACAAAAATCCCATGTGTA 57.029 26.923 0.00 0.00 0.00 2.90
741 758 7.878547 AAATTTCAACAAAAATCCCATGTGT 57.121 28.000 0.00 0.00 0.00 3.72
805 823 8.149647 AGCAAGTTGGAAAAACAAATGATATCA 58.850 29.630 8.10 8.10 31.17 2.15
885 903 1.134098 CCACCTGTCAGTGTGAAGGTT 60.134 52.381 17.94 0.00 36.47 3.50
947 965 3.650139 CGATTACGAGATAAGGTTGGGG 58.350 50.000 0.00 0.00 42.66 4.96
948 966 3.057734 GCGATTACGAGATAAGGTTGGG 58.942 50.000 0.00 0.00 42.66 4.12
1025 1045 2.126307 CGGCGAGTGGAGTGTGAG 60.126 66.667 0.00 0.00 0.00 3.51
1026 1046 4.357947 GCGGCGAGTGGAGTGTGA 62.358 66.667 12.98 0.00 0.00 3.58
1131 1154 3.878519 GACGACGGCGAGGAGGAG 61.879 72.222 22.49 0.00 41.64 3.69
1531 2680 1.430632 GGATGCTGCGATTGTGTGG 59.569 57.895 0.00 0.00 0.00 4.17
1680 2829 6.859420 TGATCCATTGGTTGATTATACACG 57.141 37.500 1.86 0.00 0.00 4.49
1754 2913 5.682943 TGAACGAAAAATGACCGAGATTT 57.317 34.783 0.00 0.00 0.00 2.17
1781 2940 6.859420 TCTTGAATGAAAAACGAGTGATGA 57.141 33.333 0.00 0.00 0.00 2.92
1782 2941 8.511465 AATTCTTGAATGAAAAACGAGTGATG 57.489 30.769 0.00 0.00 0.00 3.07
1783 2942 8.352201 TGAATTCTTGAATGAAAAACGAGTGAT 58.648 29.630 7.05 0.00 0.00 3.06
1841 3000 1.538075 ACACGCCCCTTAACGAAATTG 59.462 47.619 0.00 0.00 0.00 2.32
1851 3010 5.298989 TGTGAAATATATACACGCCCCTT 57.701 39.130 14.15 0.00 37.35 3.95
1898 3507 3.248266 CAGCTGCAAGAAAAATAGGTGC 58.752 45.455 0.00 0.00 34.07 5.01
1904 3513 3.610114 CGTAGCACAGCTGCAAGAAAAAT 60.610 43.478 15.27 0.00 46.97 1.82
1905 3514 2.286950 CGTAGCACAGCTGCAAGAAAAA 60.287 45.455 15.27 0.00 46.97 1.94
2210 3841 4.371624 TTCCATCATGTGTTTCCAGAGT 57.628 40.909 0.00 0.00 0.00 3.24
2648 4279 1.522668 CCGCACTGTCAATTTCCTCA 58.477 50.000 0.00 0.00 0.00 3.86
2657 4288 1.112916 TCAGAAGACCCGCACTGTCA 61.113 55.000 0.00 0.00 35.15 3.58
2753 4391 2.871182 TCCTCGATCTCATCAAACCG 57.129 50.000 0.00 0.00 0.00 4.44
2765 4403 2.237143 TGAAGGCTTCACATTCCTCGAT 59.763 45.455 25.38 0.00 34.08 3.59
2879 4517 1.277273 CAGCAGAACACATCAGGGAGA 59.723 52.381 0.00 0.00 0.00 3.71
3219 4857 2.032799 TGTCCAACAATGACTTCAACGC 59.967 45.455 0.00 0.00 33.83 4.84
3450 5088 1.202855 ACAATGAGAGTGGCTGTTGCT 60.203 47.619 0.00 0.00 39.59 3.91
3459 5097 4.825546 GCCATATTGGACAATGAGAGTG 57.174 45.455 7.76 0.30 40.96 3.51
3524 5163 5.018539 TCCTATTGGAAACGATGTCGATT 57.981 39.130 9.67 3.32 39.69 3.34
3548 5187 0.659427 CATGGCATTGTAGACAGGCG 59.341 55.000 0.00 0.00 0.00 5.52
3611 5250 7.325660 TGATCAGCCATTTTCATAAAGAGAC 57.674 36.000 0.00 0.00 0.00 3.36
3778 5419 4.702131 CCTGAAACTTTCCTGGGAGTAATG 59.298 45.833 4.46 0.00 0.00 1.90
4272 8529 5.083389 GTGTATATCTTCTCGTCGATCAGC 58.917 45.833 0.00 0.00 0.00 4.26
4296 8553 7.067008 GCCTTTCCATAGAAGTTAAGCATGTTA 59.933 37.037 0.00 0.00 32.35 2.41
4526 9187 7.710044 AGTCAATCTCAATGCAGATAACTGTAG 59.290 37.037 1.65 0.00 45.04 2.74
4540 9201 6.596309 TCAGTCACAGTAGTCAATCTCAAT 57.404 37.500 0.00 0.00 0.00 2.57
4863 9525 0.822532 CCAATCTCCTGCATCTGGCC 60.823 60.000 0.00 0.00 43.89 5.36
5109 9771 6.183360 GGTTCCAACTTTGATCCAACCTTTAA 60.183 38.462 0.00 0.00 30.99 1.52
5246 9963 2.621998 CAACAATGGGCTCATCTGGATC 59.378 50.000 0.00 0.00 32.24 3.36
5451 11511 7.630924 CGAACTGTTAAGTCTTCATTCTTTGT 58.369 34.615 0.00 0.00 34.77 2.83
5490 11550 5.691754 CCTTTGCTGTTGAAAATACACCTTC 59.308 40.000 0.00 0.00 0.00 3.46
5618 11680 4.889409 ACTTGCAGATTGAACTTGGAAGAA 59.111 37.500 15.37 0.00 33.27 2.52
5673 11735 4.142182 GGCACAATAGCAGGCAATTCTTTA 60.142 41.667 0.00 0.00 35.83 1.85
5851 11916 5.157781 GGAACATATTGTTTTGCGTGCTTA 58.842 37.500 0.00 0.00 41.28 3.09
5852 11917 3.987220 GGAACATATTGTTTTGCGTGCTT 59.013 39.130 0.00 0.00 41.28 3.91
5857 11922 3.360463 CACACGGAACATATTGTTTTGCG 59.640 43.478 0.00 0.00 41.28 4.85
5873 11938 8.642908 TCTGAGTAACATTAATAATCACACGG 57.357 34.615 0.00 0.00 0.00 4.94
5874 11939 9.516314 TCTCTGAGTAACATTAATAATCACACG 57.484 33.333 4.32 0.00 0.00 4.49
5882 11947 7.504574 TCGTCCCATCTCTGAGTAACATTAATA 59.495 37.037 4.32 0.00 0.00 0.98
5883 11948 6.323996 TCGTCCCATCTCTGAGTAACATTAAT 59.676 38.462 4.32 0.00 0.00 1.40
5884 11949 5.655090 TCGTCCCATCTCTGAGTAACATTAA 59.345 40.000 4.32 0.00 0.00 1.40
5885 11950 5.198207 TCGTCCCATCTCTGAGTAACATTA 58.802 41.667 4.32 0.00 0.00 1.90
5888 11953 3.081710 TCGTCCCATCTCTGAGTAACA 57.918 47.619 4.32 0.00 0.00 2.41
5889 11954 4.451629 TTTCGTCCCATCTCTGAGTAAC 57.548 45.455 4.32 0.00 0.00 2.50
5891 11956 6.978674 ATATTTTCGTCCCATCTCTGAGTA 57.021 37.500 4.32 0.00 0.00 2.59
5892 11957 5.878406 ATATTTTCGTCCCATCTCTGAGT 57.122 39.130 4.32 0.00 0.00 3.41
5893 11958 5.866633 GCTATATTTTCGTCCCATCTCTGAG 59.133 44.000 0.00 0.00 0.00 3.35
5894 11959 5.540337 AGCTATATTTTCGTCCCATCTCTGA 59.460 40.000 0.00 0.00 0.00 3.27
5895 11960 5.636965 CAGCTATATTTTCGTCCCATCTCTG 59.363 44.000 0.00 0.00 0.00 3.35
5896 11961 5.305644 ACAGCTATATTTTCGTCCCATCTCT 59.694 40.000 0.00 0.00 0.00 3.10
5897 11962 5.542779 ACAGCTATATTTTCGTCCCATCTC 58.457 41.667 0.00 0.00 0.00 2.75
5898 11963 5.070446 TGACAGCTATATTTTCGTCCCATCT 59.930 40.000 0.00 0.00 0.00 2.90
5899 11964 5.297547 TGACAGCTATATTTTCGTCCCATC 58.702 41.667 0.00 0.00 0.00 3.51
5901 11966 4.746535 TGACAGCTATATTTTCGTCCCA 57.253 40.909 0.00 0.00 0.00 4.37
5902 11967 7.907214 AATATGACAGCTATATTTTCGTCCC 57.093 36.000 0.00 0.00 28.87 4.46
5903 11968 8.988934 TGAAATATGACAGCTATATTTTCGTCC 58.011 33.333 12.19 3.30 39.52 4.79
5910 11975 9.017509 CCCACATTGAAATATGACAGCTATATT 57.982 33.333 0.00 0.00 33.37 1.28
5911 11976 7.613022 CCCCACATTGAAATATGACAGCTATAT 59.387 37.037 0.00 0.00 0.00 0.86
5912 11977 6.942005 CCCCACATTGAAATATGACAGCTATA 59.058 38.462 0.00 0.00 0.00 1.31
5914 11979 5.132502 CCCCACATTGAAATATGACAGCTA 58.867 41.667 0.00 0.00 0.00 3.32
5916 11981 3.491447 GCCCCACATTGAAATATGACAGC 60.491 47.826 0.00 0.00 0.00 4.40
5917 11982 3.956199 AGCCCCACATTGAAATATGACAG 59.044 43.478 0.00 0.00 0.00 3.51
5918 11983 3.979911 AGCCCCACATTGAAATATGACA 58.020 40.909 0.00 0.00 0.00 3.58
5919 11984 6.463995 TTAAGCCCCACATTGAAATATGAC 57.536 37.500 0.00 0.00 0.00 3.06
5920 11985 7.398618 TCTTTTAAGCCCCACATTGAAATATGA 59.601 33.333 0.00 0.00 0.00 2.15
5925 11990 5.306678 ACATCTTTTAAGCCCCACATTGAAA 59.693 36.000 0.00 0.00 0.00 2.69
5926 11991 4.837860 ACATCTTTTAAGCCCCACATTGAA 59.162 37.500 0.00 0.00 0.00 2.69
5929 11994 5.580022 AGTACATCTTTTAAGCCCCACATT 58.420 37.500 0.00 0.00 0.00 2.71
5932 11997 7.640597 AATAAGTACATCTTTTAAGCCCCAC 57.359 36.000 0.00 0.00 37.56 4.61
5933 11998 7.891183 TGAAATAAGTACATCTTTTAAGCCCCA 59.109 33.333 0.00 0.00 37.56 4.96
5934 11999 8.288689 TGAAATAAGTACATCTTTTAAGCCCC 57.711 34.615 0.00 0.00 37.56 5.80
5946 12011 9.450807 GCTGCGATTTTTATGAAATAAGTACAT 57.549 29.630 0.00 0.00 40.40 2.29
5947 12012 8.454894 TGCTGCGATTTTTATGAAATAAGTACA 58.545 29.630 0.00 0.00 40.40 2.90
5948 12013 8.835467 TGCTGCGATTTTTATGAAATAAGTAC 57.165 30.769 0.00 0.00 40.40 2.73
5950 12015 8.931385 ATTGCTGCGATTTTTATGAAATAAGT 57.069 26.923 0.00 0.00 40.40 2.24
5951 12016 9.627657 CAATTGCTGCGATTTTTATGAAATAAG 57.372 29.630 12.38 0.00 40.40 1.73
5952 12017 8.115520 GCAATTGCTGCGATTTTTATGAAATAA 58.884 29.630 23.21 0.00 42.37 1.40
5953 12018 7.620215 GCAATTGCTGCGATTTTTATGAAATA 58.380 30.769 23.21 0.00 42.37 1.40
5954 12019 6.480285 GCAATTGCTGCGATTTTTATGAAAT 58.520 32.000 23.21 0.00 42.37 2.17
5955 12020 5.856314 GCAATTGCTGCGATTTTTATGAAA 58.144 33.333 23.21 0.00 42.37 2.69
5956 12021 5.453281 GCAATTGCTGCGATTTTTATGAA 57.547 34.783 23.21 0.00 42.37 2.57
5969 12034 4.978083 AGATAGAAAGGTGCAATTGCTG 57.022 40.909 29.37 0.00 42.66 4.41
5970 12035 7.340232 TCAAATAGATAGAAAGGTGCAATTGCT 59.660 33.333 29.37 10.45 42.66 3.91
5971 12036 7.483307 TCAAATAGATAGAAAGGTGCAATTGC 58.517 34.615 23.69 23.69 42.50 3.56
5975 12040 9.023962 ACAATTCAAATAGATAGAAAGGTGCAA 57.976 29.630 0.00 0.00 0.00 4.08
5976 12041 8.579850 ACAATTCAAATAGATAGAAAGGTGCA 57.420 30.769 0.00 0.00 0.00 4.57
5977 12042 8.897752 AGACAATTCAAATAGATAGAAAGGTGC 58.102 33.333 0.00 0.00 0.00 5.01
5991 12056 9.739276 TGGTAAACTATCTCAGACAATTCAAAT 57.261 29.630 0.00 0.00 0.00 2.32
5992 12057 9.219603 CTGGTAAACTATCTCAGACAATTCAAA 57.780 33.333 0.00 0.00 0.00 2.69
5993 12058 8.375506 ACTGGTAAACTATCTCAGACAATTCAA 58.624 33.333 0.00 0.00 0.00 2.69
5994 12059 7.907389 ACTGGTAAACTATCTCAGACAATTCA 58.093 34.615 0.00 0.00 0.00 2.57
5995 12060 8.035394 TGACTGGTAAACTATCTCAGACAATTC 58.965 37.037 0.00 0.00 30.22 2.17
5996 12061 7.907389 TGACTGGTAAACTATCTCAGACAATT 58.093 34.615 0.00 0.00 30.22 2.32
5997 12062 7.482169 TGACTGGTAAACTATCTCAGACAAT 57.518 36.000 0.00 0.00 30.22 2.71
5998 12063 6.911250 TGACTGGTAAACTATCTCAGACAA 57.089 37.500 0.00 0.00 30.22 3.18
5999 12064 6.569801 CGTTGACTGGTAAACTATCTCAGACA 60.570 42.308 0.00 0.00 0.00 3.41
6000 12065 5.800941 CGTTGACTGGTAAACTATCTCAGAC 59.199 44.000 0.00 0.00 0.00 3.51
6001 12066 5.475909 ACGTTGACTGGTAAACTATCTCAGA 59.524 40.000 0.00 0.00 0.00 3.27
6002 12067 5.573282 CACGTTGACTGGTAAACTATCTCAG 59.427 44.000 0.00 0.00 0.00 3.35
6003 12068 5.466819 CACGTTGACTGGTAAACTATCTCA 58.533 41.667 0.00 0.00 0.00 3.27
6004 12069 4.326548 GCACGTTGACTGGTAAACTATCTC 59.673 45.833 0.00 0.00 0.00 2.75
6005 12070 4.243270 GCACGTTGACTGGTAAACTATCT 58.757 43.478 0.00 0.00 0.00 1.98
6006 12071 3.370061 GGCACGTTGACTGGTAAACTATC 59.630 47.826 0.00 0.00 0.00 2.08
6007 12072 3.244284 TGGCACGTTGACTGGTAAACTAT 60.244 43.478 0.00 0.00 0.00 2.12
6008 12073 2.102757 TGGCACGTTGACTGGTAAACTA 59.897 45.455 0.00 0.00 0.00 2.24
6009 12074 1.134340 TGGCACGTTGACTGGTAAACT 60.134 47.619 0.00 0.00 0.00 2.66
6010 12075 1.263217 CTGGCACGTTGACTGGTAAAC 59.737 52.381 0.00 0.00 0.00 2.01
6011 12076 1.588674 CTGGCACGTTGACTGGTAAA 58.411 50.000 0.00 0.00 0.00 2.01
6012 12077 0.250124 CCTGGCACGTTGACTGGTAA 60.250 55.000 8.09 0.00 39.41 2.85
6013 12078 1.116536 TCCTGGCACGTTGACTGGTA 61.117 55.000 13.61 2.58 44.08 3.25
6014 12079 1.978455 TTCCTGGCACGTTGACTGGT 61.978 55.000 13.61 0.00 44.08 4.00
6015 12080 0.817634 TTTCCTGGCACGTTGACTGG 60.818 55.000 9.49 9.49 44.96 4.00
6016 12081 1.238439 ATTTCCTGGCACGTTGACTG 58.762 50.000 0.00 0.00 0.00 3.51
6017 12082 1.981256 AATTTCCTGGCACGTTGACT 58.019 45.000 0.00 0.00 0.00 3.41
6018 12083 3.907894 TTAATTTCCTGGCACGTTGAC 57.092 42.857 0.00 0.00 0.00 3.18
6019 12084 3.886505 ACTTTAATTTCCTGGCACGTTGA 59.113 39.130 0.00 0.00 0.00 3.18
6020 12085 3.980775 CACTTTAATTTCCTGGCACGTTG 59.019 43.478 0.00 0.00 0.00 4.10
6021 12086 3.552068 GCACTTTAATTTCCTGGCACGTT 60.552 43.478 0.00 0.00 0.00 3.99
6022 12087 2.030274 GCACTTTAATTTCCTGGCACGT 60.030 45.455 0.00 0.00 0.00 4.49
6023 12088 2.228822 AGCACTTTAATTTCCTGGCACG 59.771 45.455 0.00 0.00 0.00 5.34
6024 12089 3.578688 CAGCACTTTAATTTCCTGGCAC 58.421 45.455 0.00 0.00 0.00 5.01
6025 12090 2.562298 CCAGCACTTTAATTTCCTGGCA 59.438 45.455 0.00 0.00 34.15 4.92
6026 12091 2.825532 TCCAGCACTTTAATTTCCTGGC 59.174 45.455 0.00 0.00 39.65 4.85
6027 12092 4.082125 AGTCCAGCACTTTAATTTCCTGG 58.918 43.478 0.00 0.00 40.84 4.45
6028 12093 4.082571 CCAGTCCAGCACTTTAATTTCCTG 60.083 45.833 0.00 0.00 30.26 3.86
6029 12094 4.082125 CCAGTCCAGCACTTTAATTTCCT 58.918 43.478 0.00 0.00 30.26 3.36
6030 12095 3.193479 CCCAGTCCAGCACTTTAATTTCC 59.807 47.826 0.00 0.00 30.26 3.13
6031 12096 3.826729 ACCCAGTCCAGCACTTTAATTTC 59.173 43.478 0.00 0.00 30.26 2.17
6032 12097 3.844640 ACCCAGTCCAGCACTTTAATTT 58.155 40.909 0.00 0.00 30.26 1.82
6033 12098 3.525800 ACCCAGTCCAGCACTTTAATT 57.474 42.857 0.00 0.00 30.26 1.40
6034 12099 3.157087 CAACCCAGTCCAGCACTTTAAT 58.843 45.455 0.00 0.00 30.26 1.40
6035 12100 2.582052 CAACCCAGTCCAGCACTTTAA 58.418 47.619 0.00 0.00 30.26 1.52
6036 12101 1.202879 CCAACCCAGTCCAGCACTTTA 60.203 52.381 0.00 0.00 30.26 1.85
6037 12102 0.468029 CCAACCCAGTCCAGCACTTT 60.468 55.000 0.00 0.00 30.26 2.66
6038 12103 1.151450 CCAACCCAGTCCAGCACTT 59.849 57.895 0.00 0.00 30.26 3.16
6039 12104 2.833913 CCCAACCCAGTCCAGCACT 61.834 63.158 0.00 0.00 34.67 4.40
6040 12105 2.282462 CCCAACCCAGTCCAGCAC 60.282 66.667 0.00 0.00 0.00 4.40
6041 12106 4.284550 GCCCAACCCAGTCCAGCA 62.285 66.667 0.00 0.00 0.00 4.41
6043 12108 4.722700 CGGCCCAACCCAGTCCAG 62.723 72.222 0.00 0.00 33.26 3.86
6045 12110 4.280019 AACGGCCCAACCCAGTCC 62.280 66.667 0.00 0.00 33.26 3.85
6046 12111 2.983592 CAACGGCCCAACCCAGTC 60.984 66.667 0.00 0.00 33.26 3.51
6047 12112 3.367907 AACAACGGCCCAACCCAGT 62.368 57.895 0.00 0.00 33.26 4.00
6048 12113 2.520741 AACAACGGCCCAACCCAG 60.521 61.111 0.00 0.00 33.26 4.45
6049 12114 2.835431 CAACAACGGCCCAACCCA 60.835 61.111 0.00 0.00 33.26 4.51
6050 12115 2.835895 ACAACAACGGCCCAACCC 60.836 61.111 0.00 0.00 33.26 4.11
6051 12116 1.668101 TTGACAACAACGGCCCAACC 61.668 55.000 0.00 0.00 0.00 3.77


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

AutoCloner maintained by Alex Coulton.