Multiple sequence alignment - TraesCS6D01G030900

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 TraesCS6D01G030900 chr6D 100.000 5131 0 0 3284 8414 12360409 12365539 0.000000e+00 9476.0
1 TraesCS6D01G030900 chr6D 100.000 2882 0 0 1 2882 12357126 12360007 0.000000e+00 5323.0
2 TraesCS6D01G030900 chr6D 93.784 547 7 2 1 521 1943567 1944112 0.000000e+00 797.0
3 TraesCS6D01G030900 chr6D 93.297 552 11 1 1 526 20745503 20744952 0.000000e+00 791.0
4 TraesCS6D01G030900 chr6D 91.579 570 19 3 1 543 472035380 472034813 0.000000e+00 760.0
5 TraesCS6D01G030900 chr6D 76.783 659 111 26 1015 1658 11258138 11258769 1.750000e-86 331.0
6 TraesCS6D01G030900 chr6D 77.093 454 69 17 4436 4862 11259596 11260041 6.570000e-56 230.0
7 TraesCS6D01G030900 chr6D 79.781 183 25 7 1514 1687 11238398 11238577 1.150000e-23 122.0
8 TraesCS6D01G030900 chr6D 100.000 30 0 0 6816 6845 291239525 291239554 1.000000e-03 56.5
9 TraesCS6D01G030900 chr6A 93.709 2273 101 15 5970 8209 13739351 13741614 0.000000e+00 3367.0
10 TraesCS6D01G030900 chr6A 94.732 1974 71 15 853 2817 13733882 13735831 0.000000e+00 3038.0
11 TraesCS6D01G030900 chr6A 96.746 1721 46 7 3843 5560 13737195 13738908 0.000000e+00 2859.0
12 TraesCS6D01G030900 chr6A 77.479 1785 301 51 1018 2775 13672454 13674164 0.000000e+00 976.0
13 TraesCS6D01G030900 chr6A 92.796 583 22 6 3284 3847 13736561 13737142 0.000000e+00 826.0
14 TraesCS6D01G030900 chr6A 96.212 396 11 2 5573 5967 13738986 13739378 0.000000e+00 645.0
15 TraesCS6D01G030900 chr6A 76.024 659 116 26 1015 1658 12472929 12473560 3.820000e-78 303.0
16 TraesCS6D01G030900 chr6A 76.442 607 109 20 997 1597 12926018 12925440 1.780000e-76 298.0
17 TraesCS6D01G030900 chr6A 89.238 223 20 3 8195 8414 13741654 13741875 8.320000e-70 276.0
18 TraesCS6D01G030900 chr6A 85.806 155 19 2 8207 8358 479887550 479887396 2.430000e-35 161.0
19 TraesCS6D01G030900 chr6A 95.946 74 3 0 2809 2882 13736066 13736139 4.130000e-23 121.0
20 TraesCS6D01G030900 chr6A 81.757 148 17 8 1514 1653 12460343 12460488 1.920000e-21 115.0
21 TraesCS6D01G030900 chr6A 87.324 71 3 3 6773 6843 118355841 118355777 9.060000e-10 76.8
22 TraesCS6D01G030900 chr6B 93.472 2160 94 33 688 2825 22715253 22717387 0.000000e+00 3164.0
23 TraesCS6D01G030900 chr6B 95.989 1820 53 8 6334 8152 22720839 22722639 0.000000e+00 2939.0
24 TraesCS6D01G030900 chr6B 96.519 1063 35 2 4499 5560 22718747 22719808 0.000000e+00 1757.0
25 TraesCS6D01G030900 chr6B 94.961 774 29 4 5573 6342 22719886 22720653 0.000000e+00 1205.0
26 TraesCS6D01G030900 chr6B 90.909 583 31 3 3284 3847 22717875 22718454 0.000000e+00 763.0
27 TraesCS6D01G030900 chr6B 75.134 1122 184 48 1008 2090 22584462 22585527 1.000000e-118 438.0
28 TraesCS6D01G030900 chr6B 97.510 241 6 0 3845 4085 22718509 22718749 6.080000e-111 412.0
29 TraesCS6D01G030900 chr6B 95.671 231 8 2 8182 8411 22722628 22722857 3.710000e-98 370.0
30 TraesCS6D01G030900 chr6B 80.126 317 50 9 4436 4743 21133789 21134101 3.060000e-54 224.0
31 TraesCS6D01G030900 chr6B 84.574 188 28 1 6327 6513 22589419 22589606 1.440000e-42 185.0
32 TraesCS6D01G030900 chr6B 87.671 73 4 4 6773 6842 570062917 570062987 7.000000e-11 80.5
33 TraesCS6D01G030900 chr6B 84.211 76 11 1 6773 6847 541936654 541936729 1.170000e-08 73.1
34 TraesCS6D01G030900 chr6B 100.000 30 0 0 5938 5967 22720282 22720311 1.000000e-03 56.5
35 TraesCS6D01G030900 chr3D 94.150 547 6 1 1 521 614113526 614114072 0.000000e+00 809.0
36 TraesCS6D01G030900 chr3D 91.281 562 17 5 1 531 578645030 578644470 0.000000e+00 737.0
37 TraesCS6D01G030900 chr3D 78.857 175 32 5 8207 8376 377197948 377198122 6.900000e-21 113.0
38 TraesCS6D01G030900 chr3D 80.690 145 24 2 8207 8347 509168825 509168681 8.930000e-20 110.0
39 TraesCS6D01G030900 chr3D 89.041 73 5 1 6773 6842 515014773 515014845 4.180000e-13 87.9
40 TraesCS6D01G030900 chr3D 97.500 40 1 0 6775 6814 48041347 48041308 1.520000e-07 69.4
41 TraesCS6D01G030900 chr3D 91.892 37 3 0 6807 6843 263478502 263478538 1.500000e-02 52.8
42 TraesCS6D01G030900 chr2D 94.150 547 6 1 1 521 313229516 313228970 0.000000e+00 809.0
43 TraesCS6D01G030900 chr2D 94.000 550 5 2 1 522 28935420 28935969 0.000000e+00 808.0
44 TraesCS6D01G030900 chr2D 87.179 156 15 3 8206 8358 218019072 218019225 1.120000e-38 172.0
45 TraesCS6D01G030900 chr2D 88.462 52 2 3 6813 6863 74156936 74156984 9.120000e-05 60.2
46 TraesCS6D01G030900 chr2D 81.690 71 11 1 6773 6843 15196282 15196350 3.280000e-04 58.4
47 TraesCS6D01G030900 chr7D 94.818 521 21 5 1 520 578747556 578747041 0.000000e+00 808.0
48 TraesCS6D01G030900 chr7D 93.796 548 7 2 1 522 584230753 584231299 0.000000e+00 798.0
49 TraesCS6D01G030900 chr7D 92.540 563 13 3 1 534 61772348 61772910 0.000000e+00 780.0
50 TraesCS6D01G030900 chr7D 93.371 528 9 1 22 523 600582978 600582451 0.000000e+00 758.0
51 TraesCS6D01G030900 chr7D 87.342 158 16 3 8206 8360 625135334 625135490 2.410000e-40 178.0
52 TraesCS6D01G030900 chr7D 83.871 155 21 3 8202 8352 783275 783429 2.450000e-30 145.0
53 TraesCS6D01G030900 chr7D 94.595 37 2 0 6807 6843 291183029 291183065 3.280000e-04 58.4
54 TraesCS6D01G030900 chr7D 90.698 43 2 2 6813 6855 219092674 219092634 1.000000e-03 56.5
55 TraesCS6D01G030900 chr5D 93.967 547 7 1 1 521 563457213 563456667 0.000000e+00 804.0
56 TraesCS6D01G030900 chr5D 82.716 81 7 6 6788 6865 411841416 411841340 1.960000e-06 65.8
57 TraesCS6D01G030900 chr5D 100.000 31 0 0 6812 6842 370831376 370831346 3.280000e-04 58.4
58 TraesCS6D01G030900 chr5D 100.000 30 0 0 6813 6842 41316278 41316307 1.000000e-03 56.5
59 TraesCS6D01G030900 chr1D 93.514 555 8 3 1 527 30415156 30414602 0.000000e+00 800.0
60 TraesCS6D01G030900 chr1D 91.413 559 18 3 1 530 453359705 453360262 0.000000e+00 739.0
61 TraesCS6D01G030900 chr1D 84.277 159 21 3 8207 8361 149057863 149058021 1.460000e-32 152.0
62 TraesCS6D01G030900 chr1D 97.059 34 1 0 6816 6849 421923261 421923228 3.280000e-04 58.4
63 TraesCS6D01G030900 chr1D 91.892 37 3 0 6807 6843 243732143 243732179 1.500000e-02 52.8
64 TraesCS6D01G030900 chr1D 96.774 31 1 0 6813 6843 303428051 303428081 1.500000e-02 52.8
65 TraesCS6D01G030900 chrUn 93.715 541 8 1 1 515 221589729 221590269 0.000000e+00 787.0
66 TraesCS6D01G030900 chrUn 93.223 546 11 1 1 520 29126722 29127267 0.000000e+00 780.0
67 TraesCS6D01G030900 chrUn 92.308 546 16 1 1 520 28434823 28435368 0.000000e+00 752.0
68 TraesCS6D01G030900 chrUn 90.727 550 21 4 1 520 95588272 95588821 0.000000e+00 706.0
69 TraesCS6D01G030900 chrUn 92.132 394 5 1 1 368 21541140 21540747 4.470000e-147 532.0
70 TraesCS6D01G030900 chrUn 91.878 394 6 1 1 368 111265486 111265093 2.080000e-145 527.0
71 TraesCS6D01G030900 chrUn 91.624 394 7 1 1 368 9969496 9969889 9.680000e-144 521.0
72 TraesCS6D01G030900 chrUn 91.624 394 7 1 1 368 21245446 21245839 9.680000e-144 521.0
73 TraesCS6D01G030900 chrUn 82.581 155 24 2 8210 8361 102152054 102151900 5.300000e-27 134.0
74 TraesCS6D01G030900 chrUn 100.000 29 0 0 6817 6845 52972590 52972562 4.000000e-03 54.7
75 TraesCS6D01G030900 chrUn 96.774 31 1 0 6813 6843 22763171 22763201 1.500000e-02 52.8
76 TraesCS6D01G030900 chr4D 91.773 547 19 1 1 521 497077909 497078455 0.000000e+00 737.0
77 TraesCS6D01G030900 chr4D 84.153 183 23 5 8208 8387 424471809 424471630 1.120000e-38 172.0
78 TraesCS6D01G030900 chr4D 85.714 77 5 2 6773 6843 416070633 416070709 9.060000e-10 76.8
79 TraesCS6D01G030900 chr4D 100.000 31 0 0 6813 6843 213708383 213708413 3.280000e-04 58.4
80 TraesCS6D01G030900 chr4D 97.059 34 1 0 6813 6846 236617120 236617087 3.280000e-04 58.4
81 TraesCS6D01G030900 chr4D 100.000 28 0 0 6814 6841 30006489 30006516 1.500000e-02 52.8
82 TraesCS6D01G030900 chr2A 95.380 303 13 1 983 1285 348246432 348246131 1.640000e-131 481.0
83 TraesCS6D01G030900 chr2A 93.980 299 18 0 983 1281 345169659 345169361 3.580000e-123 453.0
84 TraesCS6D01G030900 chr2A 93.993 283 16 1 999 1281 344899640 344899359 2.170000e-115 427.0
85 TraesCS6D01G030900 chr4B 86.228 167 19 3 6603 6767 99064861 99065025 2.410000e-40 178.0
86 TraesCS6D01G030900 chr4B 87.919 149 15 2 8207 8352 654063485 654063633 1.120000e-38 172.0
87 TraesCS6D01G030900 chr4B 83.511 188 25 5 8203 8387 520402240 520402056 4.040000e-38 171.0
88 TraesCS6D01G030900 chr4B 100.000 31 0 0 6813 6843 545874440 545874470 3.280000e-04 58.4
89 TraesCS6D01G030900 chr2B 86.792 159 17 3 8207 8362 154933535 154933378 3.120000e-39 174.0
90 TraesCS6D01G030900 chr2B 81.643 207 35 2 8210 8413 355308331 355308125 1.450000e-37 169.0
91 TraesCS6D01G030900 chr4A 86.275 153 17 3 8203 8352 40247229 40247380 6.760000e-36 163.0
92 TraesCS6D01G030900 chr4A 84.024 169 24 2 8207 8372 737773874 737773706 8.740000e-35 159.0
93 TraesCS6D01G030900 chr4A 92.105 38 2 1 6768 6805 17481974 17481938 1.500000e-02 52.8
94 TraesCS6D01G030900 chr3A 80.488 205 35 3 8207 8406 314628381 314628177 1.460000e-32 152.0
95 TraesCS6D01G030900 chr5B 85.915 71 9 1 6773 6843 244412427 244412496 3.260000e-09 75.0
96 TraesCS6D01G030900 chr5B 85.915 71 8 1 6773 6843 571231547 571231615 3.260000e-09 75.0
97 TraesCS6D01G030900 chr1A 100.000 35 0 0 6813 6847 589607618 589607584 1.960000e-06 65.8
98 TraesCS6D01G030900 chr1A 100.000 31 0 0 6813 6843 500986354 500986324 3.280000e-04 58.4


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 TraesCS6D01G030900 chr6D 12357126 12365539 8413 False 7399.500000 9476 100.000000 1 8414 2 chr6D.!!$F5 8413
1 TraesCS6D01G030900 chr6D 1943567 1944112 545 False 797.000000 797 93.784000 1 521 1 chr6D.!!$F1 520
2 TraesCS6D01G030900 chr6D 20744952 20745503 551 True 791.000000 791 93.297000 1 526 1 chr6D.!!$R1 525
3 TraesCS6D01G030900 chr6D 472034813 472035380 567 True 760.000000 760 91.579000 1 543 1 chr6D.!!$R2 542
4 TraesCS6D01G030900 chr6D 11258138 11260041 1903 False 280.500000 331 76.938000 1015 4862 2 chr6D.!!$F4 3847
5 TraesCS6D01G030900 chr6A 13733882 13741875 7993 False 1590.285714 3367 94.197000 853 8414 7 chr6A.!!$F4 7561
6 TraesCS6D01G030900 chr6A 13672454 13674164 1710 False 976.000000 976 77.479000 1018 2775 1 chr6A.!!$F3 1757
7 TraesCS6D01G030900 chr6A 12472929 12473560 631 False 303.000000 303 76.024000 1015 1658 1 chr6A.!!$F2 643
8 TraesCS6D01G030900 chr6A 12925440 12926018 578 True 298.000000 298 76.442000 997 1597 1 chr6A.!!$R1 600
9 TraesCS6D01G030900 chr6B 22715253 22722857 7604 False 1333.312500 3164 95.628875 688 8411 8 chr6B.!!$F5 7723
10 TraesCS6D01G030900 chr6B 22584462 22589606 5144 False 311.500000 438 79.854000 1008 6513 2 chr6B.!!$F4 5505
11 TraesCS6D01G030900 chr3D 614113526 614114072 546 False 809.000000 809 94.150000 1 521 1 chr3D.!!$F4 520
12 TraesCS6D01G030900 chr3D 578644470 578645030 560 True 737.000000 737 91.281000 1 531 1 chr3D.!!$R3 530
13 TraesCS6D01G030900 chr2D 313228970 313229516 546 True 809.000000 809 94.150000 1 521 1 chr2D.!!$R1 520
14 TraesCS6D01G030900 chr2D 28935420 28935969 549 False 808.000000 808 94.000000 1 522 1 chr2D.!!$F2 521
15 TraesCS6D01G030900 chr7D 578747041 578747556 515 True 808.000000 808 94.818000 1 520 1 chr7D.!!$R2 519
16 TraesCS6D01G030900 chr7D 584230753 584231299 546 False 798.000000 798 93.796000 1 522 1 chr7D.!!$F4 521
17 TraesCS6D01G030900 chr7D 61772348 61772910 562 False 780.000000 780 92.540000 1 534 1 chr7D.!!$F2 533
18 TraesCS6D01G030900 chr7D 600582451 600582978 527 True 758.000000 758 93.371000 22 523 1 chr7D.!!$R3 501
19 TraesCS6D01G030900 chr5D 563456667 563457213 546 True 804.000000 804 93.967000 1 521 1 chr5D.!!$R3 520
20 TraesCS6D01G030900 chr1D 30414602 30415156 554 True 800.000000 800 93.514000 1 527 1 chr1D.!!$R1 526
21 TraesCS6D01G030900 chr1D 453359705 453360262 557 False 739.000000 739 91.413000 1 530 1 chr1D.!!$F4 529
22 TraesCS6D01G030900 chrUn 221589729 221590269 540 False 787.000000 787 93.715000 1 515 1 chrUn.!!$F7 514
23 TraesCS6D01G030900 chrUn 29126722 29127267 545 False 780.000000 780 93.223000 1 520 1 chrUn.!!$F5 519
24 TraesCS6D01G030900 chrUn 28434823 28435368 545 False 752.000000 752 92.308000 1 520 1 chrUn.!!$F4 519
25 TraesCS6D01G030900 chrUn 95588272 95588821 549 False 706.000000 706 90.727000 1 520 1 chrUn.!!$F6 519
26 TraesCS6D01G030900 chr4D 497077909 497078455 546 False 737.000000 737 91.773000 1 521 1 chr4D.!!$F4 520

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
945 1026 0.106619 CTCCCTGCGGTCTAGTAGGT 60.107 60.000 0.00 0.00 41.61 3.08 F
1770 1923 0.106268 ACTGGTTGTTGCATGGGTCA 60.106 50.000 0.00 0.00 0.00 4.02 F
1950 2112 2.150397 AACGCAAGGTCAGTAGTCAC 57.850 50.000 0.00 0.00 46.39 3.67 F
3698 4314 1.214305 TTGGGGAGCTATGCCAAGGT 61.214 55.000 0.00 0.00 39.08 3.50 F
3834 4450 1.135257 CCATCTCACTATCCGCGGATC 60.135 57.143 42.11 0.00 36.17 3.36 F
4897 6397 1.270550 GCCAACACAGCAGCAAAGTAT 59.729 47.619 0.00 0.00 0.00 2.12 F
6016 7735 0.031178 CTTTGCTTTTCCGCACAGCT 59.969 50.000 0.00 0.00 40.09 4.24 F
6017 7736 0.248990 TTTGCTTTTCCGCACAGCTG 60.249 50.000 13.48 13.48 40.09 4.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1812 1974 1.618343 GAAGGCCTCTCTATCAGAGCC 59.382 57.143 5.23 0.00 46.90 4.70 R
3306 3867 0.608130 TTGAGTATGAGCCGCACAGT 59.392 50.000 0.00 0.00 0.00 3.55 R
3834 4450 0.441533 GCAGCTTCAGTGATCACGTG 59.558 55.000 19.85 17.14 36.20 4.49 R
4897 6397 1.340889 GTGGCTCAATTGCTGGAACAA 59.659 47.619 0.00 0.00 38.70 2.83 R
5564 7072 2.158798 GGGTAGCTCTCCCACAATTACC 60.159 54.545 18.56 3.98 44.05 2.85 R
6253 7984 0.105964 CGCCGGATACCATGGAGAAA 59.894 55.000 21.47 0.56 0.00 2.52 R
6924 8857 0.527113 CGCAATCCTGATTTGTGCCA 59.473 50.000 0.00 0.00 0.00 4.92 R
7923 9887 4.036518 ACCAGAGCATAAGATCTCACCTT 58.963 43.478 0.00 0.00 38.74 3.50 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
561 599 2.622942 TCCAGTTCAGTGGAATGTTTGC 59.377 45.455 0.43 0.00 44.01 3.68
562 600 2.624838 CCAGTTCAGTGGAATGTTTGCT 59.375 45.455 0.00 0.00 40.44 3.91
563 601 3.068590 CCAGTTCAGTGGAATGTTTGCTT 59.931 43.478 0.00 0.00 40.44 3.91
564 602 4.293415 CAGTTCAGTGGAATGTTTGCTTC 58.707 43.478 0.00 0.00 35.05 3.86
565 603 3.003689 AGTTCAGTGGAATGTTTGCTTCG 59.996 43.478 0.00 0.00 35.05 3.79
566 604 2.844946 TCAGTGGAATGTTTGCTTCGA 58.155 42.857 0.00 0.00 0.00 3.71
567 605 3.210227 TCAGTGGAATGTTTGCTTCGAA 58.790 40.909 0.00 0.00 0.00 3.71
568 606 3.629855 TCAGTGGAATGTTTGCTTCGAAA 59.370 39.130 0.00 0.00 0.00 3.46
569 607 3.976942 CAGTGGAATGTTTGCTTCGAAAG 59.023 43.478 0.00 0.00 0.00 2.62
582 620 4.232641 CTTCGAAAGCTCGTCACATAAC 57.767 45.455 0.00 0.00 45.62 1.89
583 621 3.291809 TCGAAAGCTCGTCACATAACA 57.708 42.857 0.00 0.00 45.62 2.41
584 622 3.644823 TCGAAAGCTCGTCACATAACAA 58.355 40.909 0.00 0.00 45.62 2.83
585 623 4.052608 TCGAAAGCTCGTCACATAACAAA 58.947 39.130 0.00 0.00 45.62 2.83
586 624 4.084745 TCGAAAGCTCGTCACATAACAAAC 60.085 41.667 0.00 0.00 45.62 2.93
587 625 4.084537 CGAAAGCTCGTCACATAACAAACT 60.085 41.667 0.00 0.00 40.33 2.66
588 626 5.118050 CGAAAGCTCGTCACATAACAAACTA 59.882 40.000 0.00 0.00 40.33 2.24
589 627 6.346279 CGAAAGCTCGTCACATAACAAACTAA 60.346 38.462 0.00 0.00 40.33 2.24
590 628 6.467723 AAGCTCGTCACATAACAAACTAAG 57.532 37.500 0.00 0.00 0.00 2.18
591 629 5.539048 AGCTCGTCACATAACAAACTAAGT 58.461 37.500 0.00 0.00 0.00 2.24
592 630 5.989777 AGCTCGTCACATAACAAACTAAGTT 59.010 36.000 0.00 0.00 0.00 2.66
593 631 6.482308 AGCTCGTCACATAACAAACTAAGTTT 59.518 34.615 0.00 0.00 36.05 2.66
594 632 7.012044 AGCTCGTCACATAACAAACTAAGTTTT 59.988 33.333 0.00 0.00 33.10 2.43
595 633 7.642586 GCTCGTCACATAACAAACTAAGTTTTT 59.357 33.333 0.00 0.00 33.10 1.94
617 655 1.772182 TTTTGCAAAATACGTGCCCG 58.228 45.000 20.46 0.00 41.49 6.13
618 656 0.952280 TTTGCAAAATACGTGCCCGA 59.048 45.000 10.02 0.00 41.49 5.14
619 657 1.169577 TTGCAAAATACGTGCCCGAT 58.830 45.000 0.00 0.00 41.49 4.18
620 658 1.169577 TGCAAAATACGTGCCCGATT 58.830 45.000 0.00 0.00 41.49 3.34
621 659 2.357075 TGCAAAATACGTGCCCGATTA 58.643 42.857 0.00 0.00 41.49 1.75
622 660 2.096174 TGCAAAATACGTGCCCGATTAC 59.904 45.455 0.00 0.00 41.49 1.89
623 661 2.353579 GCAAAATACGTGCCCGATTACT 59.646 45.455 0.00 0.00 35.91 2.24
624 662 3.556775 GCAAAATACGTGCCCGATTACTA 59.443 43.478 0.00 0.00 35.91 1.82
625 663 4.318546 GCAAAATACGTGCCCGATTACTAG 60.319 45.833 0.00 0.00 35.91 2.57
626 664 4.660789 AAATACGTGCCCGATTACTAGT 57.339 40.909 0.00 0.00 37.88 2.57
627 665 3.637998 ATACGTGCCCGATTACTAGTG 57.362 47.619 5.39 0.00 37.88 2.74
628 666 1.466856 ACGTGCCCGATTACTAGTGA 58.533 50.000 5.39 0.00 37.88 3.41
629 667 1.404391 ACGTGCCCGATTACTAGTGAG 59.596 52.381 5.39 0.00 37.88 3.51
630 668 1.674441 CGTGCCCGATTACTAGTGAGA 59.326 52.381 5.39 0.00 35.63 3.27
631 669 2.287069 CGTGCCCGATTACTAGTGAGAG 60.287 54.545 5.39 0.00 35.63 3.20
632 670 2.950309 GTGCCCGATTACTAGTGAGAGA 59.050 50.000 5.39 0.00 0.00 3.10
633 671 3.003897 GTGCCCGATTACTAGTGAGAGAG 59.996 52.174 5.39 0.00 0.00 3.20
634 672 3.118000 TGCCCGATTACTAGTGAGAGAGA 60.118 47.826 5.39 0.00 0.00 3.10
635 673 3.884091 GCCCGATTACTAGTGAGAGAGAA 59.116 47.826 5.39 0.00 0.00 2.87
636 674 4.338682 GCCCGATTACTAGTGAGAGAGAAA 59.661 45.833 5.39 0.00 0.00 2.52
637 675 5.163540 GCCCGATTACTAGTGAGAGAGAAAA 60.164 44.000 5.39 0.00 0.00 2.29
638 676 6.267070 CCCGATTACTAGTGAGAGAGAAAAC 58.733 44.000 5.39 0.00 0.00 2.43
639 677 6.095720 CCCGATTACTAGTGAGAGAGAAAACT 59.904 42.308 5.39 0.00 0.00 2.66
640 678 6.970043 CCGATTACTAGTGAGAGAGAAAACTG 59.030 42.308 5.39 0.00 0.00 3.16
641 679 7.362229 CCGATTACTAGTGAGAGAGAAAACTGT 60.362 40.741 5.39 0.00 0.00 3.55
642 680 8.666573 CGATTACTAGTGAGAGAGAAAACTGTA 58.333 37.037 5.39 0.00 0.00 2.74
645 683 7.584122 ACTAGTGAGAGAGAAAACTGTAACA 57.416 36.000 0.00 0.00 0.00 2.41
646 684 8.184304 ACTAGTGAGAGAGAAAACTGTAACAT 57.816 34.615 0.00 0.00 0.00 2.71
647 685 8.643324 ACTAGTGAGAGAGAAAACTGTAACATT 58.357 33.333 0.00 0.00 0.00 2.71
648 686 7.954788 AGTGAGAGAGAAAACTGTAACATTC 57.045 36.000 0.00 0.00 0.00 2.67
649 687 6.642950 AGTGAGAGAGAAAACTGTAACATTCG 59.357 38.462 0.00 0.00 0.00 3.34
650 688 6.421202 GTGAGAGAGAAAACTGTAACATTCGT 59.579 38.462 0.00 0.00 0.00 3.85
651 689 6.984474 TGAGAGAGAAAACTGTAACATTCGTT 59.016 34.615 0.00 0.00 39.24 3.85
652 690 7.042725 TGAGAGAGAAAACTGTAACATTCGTTG 60.043 37.037 0.00 0.00 36.52 4.10
653 691 6.761714 AGAGAGAAAACTGTAACATTCGTTGT 59.238 34.615 0.00 0.00 41.53 3.32
655 693 7.758495 AGAGAAAACTGTAACATTCGTTGTTT 58.242 30.769 10.80 0.00 46.51 2.83
656 694 7.908601 AGAGAAAACTGTAACATTCGTTGTTTC 59.091 33.333 10.80 7.46 46.51 2.78
657 695 7.758495 AGAAAACTGTAACATTCGTTGTTTCT 58.242 30.769 10.80 4.76 46.51 2.52
658 696 7.696453 AGAAAACTGTAACATTCGTTGTTTCTG 59.304 33.333 10.80 11.51 46.51 3.02
659 697 6.671614 AACTGTAACATTCGTTGTTTCTGA 57.328 33.333 16.78 0.18 46.51 3.27
660 698 6.287107 ACTGTAACATTCGTTGTTTCTGAG 57.713 37.500 16.78 8.86 46.51 3.35
661 699 6.046593 ACTGTAACATTCGTTGTTTCTGAGA 58.953 36.000 16.78 0.00 46.51 3.27
662 700 6.537301 ACTGTAACATTCGTTGTTTCTGAGAA 59.463 34.615 16.78 0.00 46.51 2.87
663 701 7.065324 ACTGTAACATTCGTTGTTTCTGAGAAA 59.935 33.333 3.02 3.02 46.51 2.52
664 702 7.184106 TGTAACATTCGTTGTTTCTGAGAAAC 58.816 34.615 26.59 26.59 46.51 2.78
665 703 5.169836 ACATTCGTTGTTTCTGAGAAACC 57.830 39.130 29.10 16.92 33.74 3.27
666 704 4.036380 ACATTCGTTGTTTCTGAGAAACCC 59.964 41.667 29.10 20.20 33.74 4.11
667 705 3.553828 TCGTTGTTTCTGAGAAACCCT 57.446 42.857 29.10 0.00 0.00 4.34
668 706 4.675976 TCGTTGTTTCTGAGAAACCCTA 57.324 40.909 29.10 15.41 0.00 3.53
669 707 5.026038 TCGTTGTTTCTGAGAAACCCTAA 57.974 39.130 29.10 17.37 0.00 2.69
670 708 4.812626 TCGTTGTTTCTGAGAAACCCTAAC 59.187 41.667 29.10 24.44 0.00 2.34
671 709 4.573201 CGTTGTTTCTGAGAAACCCTAACA 59.427 41.667 29.10 12.38 0.00 2.41
672 710 5.238650 CGTTGTTTCTGAGAAACCCTAACAT 59.761 40.000 29.10 0.00 0.00 2.71
673 711 6.238648 CGTTGTTTCTGAGAAACCCTAACATT 60.239 38.462 29.10 0.00 0.00 2.71
674 712 7.489160 GTTGTTTCTGAGAAACCCTAACATTT 58.511 34.615 29.10 0.00 0.00 2.32
675 713 7.654022 TGTTTCTGAGAAACCCTAACATTTT 57.346 32.000 29.10 0.00 0.00 1.82
676 714 8.073467 TGTTTCTGAGAAACCCTAACATTTTT 57.927 30.769 29.10 0.00 0.00 1.94
725 763 8.970859 AGAGAAACCCTAACATTATGAATCAG 57.029 34.615 0.00 0.00 0.00 2.90
726 764 8.552296 AGAGAAACCCTAACATTATGAATCAGT 58.448 33.333 0.00 0.00 0.00 3.41
733 803 7.492669 CCCTAACATTATGAATCAGTATAGGCG 59.507 40.741 0.00 0.00 0.00 5.52
735 805 7.891183 AACATTATGAATCAGTATAGGCGTC 57.109 36.000 0.00 0.00 0.00 5.19
739 809 8.651588 CATTATGAATCAGTATAGGCGTCTTTC 58.348 37.037 0.00 0.00 0.00 2.62
745 815 6.032956 TCAGTATAGGCGTCTTTCTTTTCA 57.967 37.500 0.00 0.00 0.00 2.69
746 816 5.867716 TCAGTATAGGCGTCTTTCTTTTCAC 59.132 40.000 0.00 0.00 0.00 3.18
749 819 0.237498 GGCGTCTTTCTTTTCACCCG 59.763 55.000 0.00 0.00 0.00 5.28
750 820 0.385598 GCGTCTTTCTTTTCACCCGC 60.386 55.000 0.00 0.00 0.00 6.13
751 821 0.941542 CGTCTTTCTTTTCACCCGCA 59.058 50.000 0.00 0.00 0.00 5.69
803 873 8.974238 GGGTTAAAAGCATAGGTAATTAGGTTT 58.026 33.333 0.00 0.00 0.00 3.27
828 898 7.925043 TTTTTGAGCGATAAACATAGGGTAA 57.075 32.000 0.00 0.00 0.00 2.85
829 899 8.514330 TTTTTGAGCGATAAACATAGGGTAAT 57.486 30.769 0.00 0.00 0.00 1.89
830 900 8.514330 TTTTGAGCGATAAACATAGGGTAATT 57.486 30.769 0.00 0.00 0.00 1.40
831 901 9.616156 TTTTGAGCGATAAACATAGGGTAATTA 57.384 29.630 0.00 0.00 0.00 1.40
832 902 8.827177 TTGAGCGATAAACATAGGGTAATTAG 57.173 34.615 0.00 0.00 0.00 1.73
833 903 7.383687 TGAGCGATAAACATAGGGTAATTAGG 58.616 38.462 0.00 0.00 0.00 2.69
834 904 7.015877 TGAGCGATAAACATAGGGTAATTAGGT 59.984 37.037 0.00 0.00 0.00 3.08
835 905 8.426569 AGCGATAAACATAGGGTAATTAGGTA 57.573 34.615 0.00 0.00 0.00 3.08
836 906 8.529476 AGCGATAAACATAGGGTAATTAGGTAG 58.471 37.037 0.00 0.00 0.00 3.18
837 907 8.309656 GCGATAAACATAGGGTAATTAGGTAGT 58.690 37.037 0.00 0.00 0.00 2.73
868 938 2.650322 ACTATATGTTTGTTGGGCCGG 58.350 47.619 0.00 0.00 0.00 6.13
876 946 0.969917 TTGTTGGGCCGGAATCCATG 60.970 55.000 5.05 0.00 32.48 3.66
880 950 2.203351 GGCCGGAATCCATGGGTC 60.203 66.667 13.02 9.81 0.00 4.46
881 951 2.595095 GCCGGAATCCATGGGTCA 59.405 61.111 13.02 0.00 0.00 4.02
882 952 1.526917 GCCGGAATCCATGGGTCAG 60.527 63.158 13.02 10.38 0.00 3.51
883 953 1.915228 CCGGAATCCATGGGTCAGT 59.085 57.895 13.02 0.00 0.00 3.41
884 954 0.464373 CCGGAATCCATGGGTCAGTG 60.464 60.000 13.02 4.10 0.00 3.66
885 955 0.541392 CGGAATCCATGGGTCAGTGA 59.459 55.000 13.02 0.00 0.00 3.41
886 956 1.473965 CGGAATCCATGGGTCAGTGAG 60.474 57.143 13.02 0.00 0.00 3.51
887 957 1.673168 GAATCCATGGGTCAGTGAGC 58.327 55.000 13.02 14.04 0.00 4.26
905 979 1.086634 GCTTTCTAGTGAGGCCAGCG 61.087 60.000 5.01 0.00 0.00 5.18
906 980 0.460987 CTTTCTAGTGAGGCCAGCGG 60.461 60.000 5.01 0.00 0.00 5.52
922 1003 2.495409 CGGCCAGCCCATACGAGTA 61.495 63.158 2.24 0.00 0.00 2.59
939 1020 0.745845 GTACGTCTCCCTGCGGTCTA 60.746 60.000 0.00 0.00 0.00 2.59
940 1021 0.463295 TACGTCTCCCTGCGGTCTAG 60.463 60.000 0.00 0.00 0.00 2.43
941 1022 1.749638 CGTCTCCCTGCGGTCTAGT 60.750 63.158 0.00 0.00 0.00 2.57
942 1023 0.463295 CGTCTCCCTGCGGTCTAGTA 60.463 60.000 0.00 0.00 0.00 1.82
943 1024 1.310904 GTCTCCCTGCGGTCTAGTAG 58.689 60.000 0.00 0.00 0.00 2.57
944 1025 0.183014 TCTCCCTGCGGTCTAGTAGG 59.817 60.000 0.00 0.00 42.62 3.18
945 1026 0.106619 CTCCCTGCGGTCTAGTAGGT 60.107 60.000 0.00 0.00 41.61 3.08
946 1027 0.106819 TCCCTGCGGTCTAGTAGGTC 60.107 60.000 0.00 0.00 41.61 3.85
947 1028 0.106619 CCCTGCGGTCTAGTAGGTCT 60.107 60.000 0.00 0.00 41.61 3.85
948 1029 1.310904 CCTGCGGTCTAGTAGGTCTC 58.689 60.000 0.00 0.00 38.88 3.36
949 1030 1.310904 CTGCGGTCTAGTAGGTCTCC 58.689 60.000 0.00 0.00 0.00 3.71
950 1031 0.463295 TGCGGTCTAGTAGGTCTCCG 60.463 60.000 14.69 14.69 40.72 4.63
994 1075 0.178843 AACCCTACCCCACATCCACT 60.179 55.000 0.00 0.00 0.00 4.00
1038 1119 3.148279 GACGAGATGGCCCTCCGT 61.148 66.667 19.06 19.06 34.14 4.69
1707 1860 2.508751 GGTCTACCATCTCCCCGGC 61.509 68.421 0.00 0.00 35.64 6.13
1770 1923 0.106268 ACTGGTTGTTGCATGGGTCA 60.106 50.000 0.00 0.00 0.00 4.02
1812 1974 4.412796 TGATTTGGATAGCCAGAGACTG 57.587 45.455 0.00 0.00 46.91 3.51
1916 2078 4.025979 CCTCGCTGTATTTTTGTATCCGAC 60.026 45.833 0.00 0.00 0.00 4.79
1950 2112 2.150397 AACGCAAGGTCAGTAGTCAC 57.850 50.000 0.00 0.00 46.39 3.67
2301 2550 4.671377 TGTGCTTTGAAGTGTTTGCTAAG 58.329 39.130 0.00 0.00 0.00 2.18
2850 3361 7.151976 ACAAATATGTCAAACAAACCTTAGCC 58.848 34.615 0.00 0.00 33.41 3.93
3469 4066 2.666022 GCAATCGCCAATGGTAAACAAC 59.334 45.455 0.00 0.00 0.00 3.32
3523 4120 4.421479 CGCTCACGCTCCTTCCGT 62.421 66.667 0.00 0.00 39.91 4.69
3698 4314 1.214305 TTGGGGAGCTATGCCAAGGT 61.214 55.000 0.00 0.00 39.08 3.50
3821 4437 3.251016 AGATCGATCCTTCCCATCTCA 57.749 47.619 21.66 0.00 0.00 3.27
3824 4440 3.595190 TCGATCCTTCCCATCTCACTA 57.405 47.619 0.00 0.00 0.00 2.74
3834 4450 1.135257 CCATCTCACTATCCGCGGATC 60.135 57.143 42.11 0.00 36.17 3.36
4055 4727 2.028020 GCTTAGAACTGTGCTACCCACT 60.028 50.000 0.00 0.00 44.92 4.00
4076 4748 1.800315 CTGGGACGTGCGTTAGTCG 60.800 63.158 0.00 0.00 38.20 4.18
4106 4778 6.494146 CCCTACCTGTAACTTATCTCTTAGGG 59.506 46.154 0.00 0.00 36.93 3.53
4118 4790 1.755380 CTCTTAGGGGGACTGTAACCG 59.245 57.143 0.00 0.00 0.00 4.44
4130 4802 4.022155 GGACTGTAACCGAAAACTCTCTCT 60.022 45.833 0.00 0.00 0.00 3.10
4146 4818 9.962783 AAACTCTCTCTTTTCAATGAAATGAAG 57.037 29.630 20.00 17.18 40.21 3.02
4174 4846 4.266714 AGGTCCTTCGTGTTTTCTCAAAA 58.733 39.130 0.00 0.00 0.00 2.44
4175 4847 4.335594 AGGTCCTTCGTGTTTTCTCAAAAG 59.664 41.667 0.00 0.00 0.00 2.27
4272 4949 3.742433 ATTTCATTTGTCGTTTGGCCA 57.258 38.095 0.00 0.00 0.00 5.36
4523 5605 4.159377 TGCTGCTGCATTACTTTAACAC 57.841 40.909 14.93 0.00 45.31 3.32
4792 5903 6.730960 TTAATTCGGTGATGGTGAAGTTAC 57.269 37.500 0.00 0.00 0.00 2.50
4897 6397 1.270550 GCCAACACAGCAGCAAAGTAT 59.729 47.619 0.00 0.00 0.00 2.12
5076 6576 2.778299 AGCCTTGCGACTTTGTCAATA 58.222 42.857 0.00 0.00 32.09 1.90
5291 6798 6.876257 GCTATCCCTATCATAAGACAAGTTGG 59.124 42.308 7.96 0.00 0.00 3.77
5449 6957 6.378848 GGGTAAATTAAACCAGGCAATAGTCA 59.621 38.462 11.03 0.00 38.87 3.41
5655 7228 3.688694 ATCGGTACTGGCTGTTTGTTA 57.311 42.857 1.31 0.00 0.00 2.41
5755 7343 5.850653 CGATTTTCATCACGTCATGTTTTGA 59.149 36.000 0.00 0.00 0.00 2.69
5866 7457 2.192664 TTGGTAGAAATGCCGCTTCA 57.807 45.000 0.00 0.00 0.00 3.02
5982 7701 6.580791 GCTTATTTGCTTGTGTCGATGTTTAA 59.419 34.615 0.00 0.00 0.00 1.52
6016 7735 0.031178 CTTTGCTTTTCCGCACAGCT 59.969 50.000 0.00 0.00 40.09 4.24
6017 7736 0.248990 TTTGCTTTTCCGCACAGCTG 60.249 50.000 13.48 13.48 40.09 4.24
6018 7737 2.429739 GCTTTTCCGCACAGCTGC 60.430 61.111 15.27 0.00 40.38 5.25
6130 7857 0.696501 TTTCCACTGGGCCCTAGTTC 59.303 55.000 25.70 0.00 0.00 3.01
6144 7875 0.914417 TAGTTCCTCTTGGGCCCAGG 60.914 60.000 27.81 27.81 34.39 4.45
6187 7918 3.181493 GGTAAGAACCGATCAAGCGAGTA 60.181 47.826 0.00 0.00 35.62 2.59
6253 7984 0.683973 CCCAACTCTCTGTGCACTCT 59.316 55.000 19.41 0.00 0.00 3.24
6289 8023 0.951040 GCGCCTTGTCAAGCTACTGT 60.951 55.000 7.09 0.00 0.00 3.55
6325 8062 4.932789 CCATGGTAGTCGTGGTGG 57.067 61.111 2.57 0.00 45.36 4.61
6513 8446 7.337436 ACGTCTCCCATCTATAGTTTAGCTATC 59.663 40.741 0.00 0.00 40.61 2.08
6924 8857 4.557205 CTTCTGTTAGTTTGTCGGCTAGT 58.443 43.478 0.00 0.00 0.00 2.57
6943 8876 0.527113 TGGCACAAATCAGGATTGCG 59.473 50.000 0.00 0.00 31.92 4.85
7230 9163 9.307121 CGTACATGAAGACTAGAGAAAATGAAT 57.693 33.333 0.00 0.00 0.00 2.57
7316 9249 7.988904 AATTGCGTCTAACTAGTTATCTCAC 57.011 36.000 15.57 9.22 0.00 3.51
7337 9270 6.671190 TCACTGCTTCTAAAATTCATGTGTG 58.329 36.000 0.00 0.00 0.00 3.82
7390 9323 1.975660 TTGGTGGTTTTCCCTTCTCG 58.024 50.000 0.00 0.00 39.73 4.04
7545 9478 6.336842 AGCACTACGTAGTAAGAAAAAGGA 57.663 37.500 26.95 0.00 45.13 3.36
7944 9909 4.141756 ACAAGGTGAGATCTTATGCTCTGG 60.142 45.833 0.00 0.00 32.44 3.86
7978 9943 7.989416 TCAACCAGTTCGTTATTTTTCCTAT 57.011 32.000 0.00 0.00 0.00 2.57
8107 10072 5.896678 AGTTCTCCAGCTCATATCAGTAGTT 59.103 40.000 0.00 0.00 0.00 2.24
8155 10120 3.983344 CAGAAGTTGGAAAATTTGGCTCG 59.017 43.478 0.00 0.00 32.38 5.03
8156 10121 3.005791 AGAAGTTGGAAAATTTGGCTCGG 59.994 43.478 0.00 0.00 32.38 4.63
8157 10122 1.000843 AGTTGGAAAATTTGGCTCGGC 59.999 47.619 0.00 0.00 0.00 5.54
8158 10123 1.000843 GTTGGAAAATTTGGCTCGGCT 59.999 47.619 0.00 0.00 0.00 5.52
8159 10124 2.208132 TGGAAAATTTGGCTCGGCTA 57.792 45.000 0.00 0.00 0.00 3.93
8160 10125 2.091541 TGGAAAATTTGGCTCGGCTAG 58.908 47.619 0.00 0.00 0.00 3.42
8169 10134 4.919653 CTCGGCTAGCTGCAAGAA 57.080 55.556 19.27 0.00 45.15 2.52
8170 10135 3.376218 CTCGGCTAGCTGCAAGAAT 57.624 52.632 19.27 0.00 45.15 2.40
8171 10136 1.661341 CTCGGCTAGCTGCAAGAATT 58.339 50.000 19.27 0.00 45.15 2.17
8188 10153 5.573337 AGAATTGCACTAGAATGGAAAGC 57.427 39.130 0.00 0.00 33.29 3.51
8192 10157 2.305635 TGCACTAGAATGGAAAGCTGGA 59.694 45.455 0.00 0.00 0.00 3.86
8202 10259 2.165998 GGAAAGCTGGAGAAGTTGCAT 58.834 47.619 0.00 0.00 0.00 3.96
8234 10291 3.066203 GTGTGTTTGGTTCAGGAACGAAT 59.934 43.478 9.83 0.00 42.02 3.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
265 292 0.620700 GGGACTAAAGGCCTCCTCCA 60.621 60.000 5.23 0.00 30.89 3.86
471 509 1.068541 GGTTCGCAAAGGCCTTTAGTG 60.069 52.381 29.94 26.21 36.38 2.74
540 578 2.622942 GCAAACATTCCACTGAACTGGA 59.377 45.455 0.00 0.00 38.66 3.86
541 579 2.624838 AGCAAACATTCCACTGAACTGG 59.375 45.455 0.00 0.00 32.13 4.00
542 580 3.996150 AGCAAACATTCCACTGAACTG 57.004 42.857 0.00 0.00 32.13 3.16
543 581 3.003689 CGAAGCAAACATTCCACTGAACT 59.996 43.478 0.00 0.00 32.13 3.01
544 582 3.003275 TCGAAGCAAACATTCCACTGAAC 59.997 43.478 0.00 0.00 32.13 3.18
545 583 3.210227 TCGAAGCAAACATTCCACTGAA 58.790 40.909 0.00 0.00 34.33 3.02
546 584 2.844946 TCGAAGCAAACATTCCACTGA 58.155 42.857 0.00 0.00 0.00 3.41
547 585 3.624326 TTCGAAGCAAACATTCCACTG 57.376 42.857 0.00 0.00 0.00 3.66
548 586 4.228912 CTTTCGAAGCAAACATTCCACT 57.771 40.909 0.00 0.00 0.00 4.00
561 599 3.673338 TGTTATGTGACGAGCTTTCGAAG 59.327 43.478 1.98 0.00 36.85 3.79
562 600 3.644823 TGTTATGTGACGAGCTTTCGAA 58.355 40.909 1.98 0.00 36.85 3.71
563 601 3.291809 TGTTATGTGACGAGCTTTCGA 57.708 42.857 1.98 0.00 36.85 3.71
564 602 4.084537 AGTTTGTTATGTGACGAGCTTTCG 60.085 41.667 0.00 0.00 39.31 3.46
565 603 5.344207 AGTTTGTTATGTGACGAGCTTTC 57.656 39.130 0.00 0.00 0.00 2.62
566 604 6.482308 ACTTAGTTTGTTATGTGACGAGCTTT 59.518 34.615 0.00 0.00 0.00 3.51
567 605 5.989777 ACTTAGTTTGTTATGTGACGAGCTT 59.010 36.000 0.00 0.00 0.00 3.74
568 606 5.539048 ACTTAGTTTGTTATGTGACGAGCT 58.461 37.500 0.00 0.00 0.00 4.09
569 607 5.840940 ACTTAGTTTGTTATGTGACGAGC 57.159 39.130 0.00 0.00 0.00 5.03
597 635 2.128035 CGGGCACGTATTTTGCAAAAA 58.872 42.857 27.10 14.23 42.12 1.94
598 636 1.337071 TCGGGCACGTATTTTGCAAAA 59.663 42.857 25.76 25.76 42.12 2.44
599 637 0.952280 TCGGGCACGTATTTTGCAAA 59.048 45.000 8.89 8.05 42.12 3.68
600 638 1.169577 ATCGGGCACGTATTTTGCAA 58.830 45.000 8.89 0.00 42.12 4.08
601 639 1.169577 AATCGGGCACGTATTTTGCA 58.830 45.000 8.89 0.00 42.12 4.08
602 640 2.353579 AGTAATCGGGCACGTATTTTGC 59.646 45.455 8.89 2.20 41.85 3.68
603 641 4.807304 ACTAGTAATCGGGCACGTATTTTG 59.193 41.667 8.89 0.00 41.85 2.44
604 642 4.807304 CACTAGTAATCGGGCACGTATTTT 59.193 41.667 8.89 0.81 41.85 1.82
605 643 4.098349 TCACTAGTAATCGGGCACGTATTT 59.902 41.667 8.89 3.57 41.85 1.40
606 644 3.633525 TCACTAGTAATCGGGCACGTATT 59.366 43.478 8.89 9.72 41.85 1.89
607 645 3.216800 TCACTAGTAATCGGGCACGTAT 58.783 45.455 8.89 0.09 41.85 3.06
608 646 2.615447 CTCACTAGTAATCGGGCACGTA 59.385 50.000 8.89 0.00 41.85 3.57
609 647 1.404391 CTCACTAGTAATCGGGCACGT 59.596 52.381 8.89 0.00 41.85 4.49
610 648 1.674441 TCTCACTAGTAATCGGGCACG 59.326 52.381 0.00 0.00 42.74 5.34
611 649 2.950309 TCTCTCACTAGTAATCGGGCAC 59.050 50.000 0.00 0.00 0.00 5.01
612 650 3.118000 TCTCTCTCACTAGTAATCGGGCA 60.118 47.826 0.00 0.00 0.00 5.36
613 651 3.478509 TCTCTCTCACTAGTAATCGGGC 58.521 50.000 0.00 0.00 0.00 6.13
614 652 6.095720 AGTTTTCTCTCTCACTAGTAATCGGG 59.904 42.308 0.00 0.00 0.00 5.14
615 653 6.970043 CAGTTTTCTCTCTCACTAGTAATCGG 59.030 42.308 0.00 0.00 0.00 4.18
616 654 7.531716 ACAGTTTTCTCTCTCACTAGTAATCG 58.468 38.462 0.00 0.00 0.00 3.34
619 657 9.128404 TGTTACAGTTTTCTCTCTCACTAGTAA 57.872 33.333 0.00 0.00 0.00 2.24
620 658 8.687292 TGTTACAGTTTTCTCTCTCACTAGTA 57.313 34.615 0.00 0.00 0.00 1.82
621 659 7.584122 TGTTACAGTTTTCTCTCTCACTAGT 57.416 36.000 0.00 0.00 0.00 2.57
622 660 9.134734 GAATGTTACAGTTTTCTCTCTCACTAG 57.865 37.037 0.00 0.00 0.00 2.57
623 661 7.808381 CGAATGTTACAGTTTTCTCTCTCACTA 59.192 37.037 0.00 0.00 0.00 2.74
624 662 6.642950 CGAATGTTACAGTTTTCTCTCTCACT 59.357 38.462 0.00 0.00 0.00 3.41
625 663 6.421202 ACGAATGTTACAGTTTTCTCTCTCAC 59.579 38.462 0.00 0.00 0.00 3.51
626 664 6.513180 ACGAATGTTACAGTTTTCTCTCTCA 58.487 36.000 0.00 0.00 0.00 3.27
627 665 7.042658 ACAACGAATGTTACAGTTTTCTCTCTC 60.043 37.037 0.00 0.00 40.06 3.20
628 666 6.761714 ACAACGAATGTTACAGTTTTCTCTCT 59.238 34.615 0.00 0.00 40.06 3.10
629 667 6.945072 ACAACGAATGTTACAGTTTTCTCTC 58.055 36.000 0.00 0.00 40.06 3.20
630 668 6.920569 ACAACGAATGTTACAGTTTTCTCT 57.079 33.333 0.00 0.00 40.06 3.10
643 681 4.036380 GGGTTTCTCAGAAACAACGAATGT 59.964 41.667 27.69 0.00 46.82 2.71
644 682 4.275936 AGGGTTTCTCAGAAACAACGAATG 59.724 41.667 27.69 0.00 32.04 2.67
645 683 4.461198 AGGGTTTCTCAGAAACAACGAAT 58.539 39.130 27.69 7.30 32.04 3.34
646 684 3.881220 AGGGTTTCTCAGAAACAACGAA 58.119 40.909 27.69 0.00 32.04 3.85
647 685 3.553828 AGGGTTTCTCAGAAACAACGA 57.446 42.857 27.69 0.00 32.04 3.85
648 686 4.573201 TGTTAGGGTTTCTCAGAAACAACG 59.427 41.667 27.69 0.00 32.04 4.10
649 687 6.635030 ATGTTAGGGTTTCTCAGAAACAAC 57.365 37.500 27.69 22.63 32.04 3.32
650 688 7.654022 AAATGTTAGGGTTTCTCAGAAACAA 57.346 32.000 27.69 13.62 32.04 2.83
651 689 7.654022 AAAATGTTAGGGTTTCTCAGAAACA 57.346 32.000 27.69 10.74 32.04 2.83
708 746 8.035394 ACGCCTATACTGATTCATAATGTTAGG 58.965 37.037 0.00 0.00 0.00 2.69
722 760 5.867716 GTGAAAAGAAAGACGCCTATACTGA 59.132 40.000 0.00 0.00 0.00 3.41
723 761 5.063564 GGTGAAAAGAAAGACGCCTATACTG 59.936 44.000 0.00 0.00 0.00 2.74
724 762 5.176592 GGTGAAAAGAAAGACGCCTATACT 58.823 41.667 0.00 0.00 0.00 2.12
725 763 4.331992 GGGTGAAAAGAAAGACGCCTATAC 59.668 45.833 0.00 0.00 33.98 1.47
726 764 4.510571 GGGTGAAAAGAAAGACGCCTATA 58.489 43.478 0.00 0.00 33.98 1.31
733 803 3.430333 TTTGCGGGTGAAAAGAAAGAC 57.570 42.857 0.00 0.00 0.00 3.01
776 846 7.645002 ACCTAATTACCTATGCTTTTAACCCA 58.355 34.615 0.00 0.00 0.00 4.51
805 875 8.514330 AATTACCCTATGTTTATCGCTCAAAA 57.486 30.769 0.00 0.00 0.00 2.44
806 876 9.268268 CTAATTACCCTATGTTTATCGCTCAAA 57.732 33.333 0.00 0.00 0.00 2.69
808 878 7.015877 ACCTAATTACCCTATGTTTATCGCTCA 59.984 37.037 0.00 0.00 0.00 4.26
810 880 7.312415 ACCTAATTACCCTATGTTTATCGCT 57.688 36.000 0.00 0.00 0.00 4.93
811 881 8.309656 ACTACCTAATTACCCTATGTTTATCGC 58.690 37.037 0.00 0.00 0.00 4.58
839 909 9.209175 GCCCAACAAACATATAGTAGAAGATAG 57.791 37.037 0.00 0.00 0.00 2.08
840 910 8.154856 GGCCCAACAAACATATAGTAGAAGATA 58.845 37.037 0.00 0.00 0.00 1.98
841 911 6.998673 GGCCCAACAAACATATAGTAGAAGAT 59.001 38.462 0.00 0.00 0.00 2.40
842 912 6.354130 GGCCCAACAAACATATAGTAGAAGA 58.646 40.000 0.00 0.00 0.00 2.87
843 913 5.236478 CGGCCCAACAAACATATAGTAGAAG 59.764 44.000 0.00 0.00 0.00 2.85
844 914 5.120399 CGGCCCAACAAACATATAGTAGAA 58.880 41.667 0.00 0.00 0.00 2.10
845 915 4.443739 CCGGCCCAACAAACATATAGTAGA 60.444 45.833 0.00 0.00 0.00 2.59
846 916 3.813166 CCGGCCCAACAAACATATAGTAG 59.187 47.826 0.00 0.00 0.00 2.57
847 917 3.455177 TCCGGCCCAACAAACATATAGTA 59.545 43.478 0.00 0.00 0.00 1.82
848 918 2.240160 TCCGGCCCAACAAACATATAGT 59.760 45.455 0.00 0.00 0.00 2.12
849 919 2.925724 TCCGGCCCAACAAACATATAG 58.074 47.619 0.00 0.00 0.00 1.31
850 920 3.367646 TTCCGGCCCAACAAACATATA 57.632 42.857 0.00 0.00 0.00 0.86
851 921 2.223803 TTCCGGCCCAACAAACATAT 57.776 45.000 0.00 0.00 0.00 1.78
868 938 1.211457 AGCTCACTGACCCATGGATTC 59.789 52.381 15.22 9.91 0.00 2.52
876 946 2.563179 TCACTAGAAAGCTCACTGACCC 59.437 50.000 0.00 0.00 0.00 4.46
880 950 2.615869 GCCTCACTAGAAAGCTCACTG 58.384 52.381 0.00 0.00 0.00 3.66
881 951 1.552792 GGCCTCACTAGAAAGCTCACT 59.447 52.381 0.00 0.00 0.00 3.41
882 952 1.276421 TGGCCTCACTAGAAAGCTCAC 59.724 52.381 3.32 0.00 0.00 3.51
883 953 1.552337 CTGGCCTCACTAGAAAGCTCA 59.448 52.381 3.32 0.00 0.00 4.26
884 954 1.742071 GCTGGCCTCACTAGAAAGCTC 60.742 57.143 3.32 0.00 0.00 4.09
885 955 0.251634 GCTGGCCTCACTAGAAAGCT 59.748 55.000 3.32 0.00 0.00 3.74
886 956 1.086634 CGCTGGCCTCACTAGAAAGC 61.087 60.000 3.32 0.00 0.00 3.51
887 957 0.460987 CCGCTGGCCTCACTAGAAAG 60.461 60.000 3.32 0.00 0.00 2.62
905 979 1.069258 GTACTCGTATGGGCTGGCC 59.931 63.158 14.23 14.23 0.00 5.36
906 980 1.299926 CGTACTCGTATGGGCTGGC 60.300 63.158 0.00 0.00 0.00 4.85
932 1013 2.319219 CGGAGACCTACTAGACCGC 58.681 63.158 0.00 0.00 34.36 5.68
939 1020 2.279408 GGGGAGCGGAGACCTACT 59.721 66.667 0.00 0.00 0.00 2.57
940 1021 2.838693 GGGGGAGCGGAGACCTAC 60.839 72.222 0.00 0.00 0.00 3.18
994 1075 1.900351 CCTCGTGGCTCATCTGGAA 59.100 57.895 0.00 0.00 0.00 3.53
1341 1482 1.234615 ACGAATTGAACGGGCCACAG 61.235 55.000 4.39 0.00 34.93 3.66
1707 1860 0.909623 AGGGGAGACGGTTAACCATG 59.090 55.000 24.14 11.39 35.14 3.66
1770 1923 3.895232 AACTCGAGTATGCCATTGTCT 57.105 42.857 20.39 0.00 0.00 3.41
1812 1974 1.618343 GAAGGCCTCTCTATCAGAGCC 59.382 57.143 5.23 0.00 46.90 4.70
1816 1978 3.740764 GCACTTGAAGGCCTCTCTATCAG 60.741 52.174 5.23 2.69 0.00 2.90
1916 2078 4.414852 CTTGCGTTTCCACATATTGAAGG 58.585 43.478 0.00 0.00 0.00 3.46
1950 2112 2.034066 ACCCATGAGGCAACACCG 59.966 61.111 0.00 0.00 46.52 4.94
2726 2994 7.579726 CATAAGAAACCTGCTACATAGAATGC 58.420 38.462 0.00 0.00 0.00 3.56
2788 3056 3.940852 TGTCAGCAACTTAGCCATATGTG 59.059 43.478 1.24 0.00 34.23 3.21
2850 3361 1.736126 AGCAGCACGATCATGAAACAG 59.264 47.619 0.00 0.00 0.00 3.16
3306 3867 0.608130 TTGAGTATGAGCCGCACAGT 59.392 50.000 0.00 0.00 0.00 3.55
3351 3912 2.546789 GGTGAGTAAAACCAAGACACGG 59.453 50.000 0.00 0.00 37.65 4.94
3405 3969 3.885724 TCGCCATATCAAACACAGAGA 57.114 42.857 0.00 0.00 0.00 3.10
3406 3970 4.025396 GTGATCGCCATATCAAACACAGAG 60.025 45.833 0.00 0.00 37.61 3.35
3523 4120 2.942604 AGGTCAGGCTAGGAAGGTAA 57.057 50.000 0.00 0.00 0.00 2.85
3611 4227 1.523258 CAAGAGCCAGAGGATGCCG 60.523 63.158 0.00 0.00 0.00 5.69
3698 4314 1.361204 ACTGTGGTGACATGGGATCA 58.639 50.000 0.00 0.00 46.14 2.92
3821 4437 1.099295 TCACGTGATCCGCGGATAGT 61.099 55.000 39.08 32.16 41.96 2.12
3824 4440 1.007271 GATCACGTGATCCGCGGAT 60.007 57.895 39.64 39.64 43.85 4.18
3834 4450 0.441533 GCAGCTTCAGTGATCACGTG 59.558 55.000 19.85 17.14 36.20 4.49
4055 4727 0.895100 ACTAACGCACGTCCCAGGTA 60.895 55.000 0.00 0.00 0.00 3.08
4076 4748 4.650131 AGATAAGTTACAGGTAGGGAGCAC 59.350 45.833 0.00 0.00 0.00 4.40
4106 4778 3.006644 AGAGAGTTTTCGGTTACAGTCCC 59.993 47.826 0.00 0.00 0.00 4.46
4118 4790 9.956720 TCATTTCATTGAAAAGAGAGAGTTTTC 57.043 29.630 15.34 2.10 42.06 2.29
4130 4802 5.050227 CCTTTGCGCTTCATTTCATTGAAAA 60.050 36.000 15.34 0.00 35.11 2.29
4146 4818 1.782028 AACACGAAGGACCTTTGCGC 61.782 55.000 19.92 0.00 0.00 6.09
4174 4846 6.966637 ATTTAGGGGCATATGAGAGATTCT 57.033 37.500 6.97 0.00 0.00 2.40
4175 4847 7.170965 TGAATTTAGGGGCATATGAGAGATTC 58.829 38.462 6.97 6.73 0.00 2.52
4272 4949 6.718454 ACATGAGAATTTTGTCCTCTTCACAT 59.282 34.615 0.00 0.00 31.82 3.21
4378 5068 4.135747 ACTCAATTTGTTTTGGTGGGTG 57.864 40.909 0.00 0.00 0.00 4.61
4523 5605 5.293079 GGAAGCTGCTAACAATACTCTCAAG 59.707 44.000 0.90 0.00 0.00 3.02
4660 5751 9.233232 CCCTAACATTGCTAAAATACGAAATTC 57.767 33.333 0.00 0.00 0.00 2.17
4667 5758 5.451381 GGCCACCCTAACATTGCTAAAATAC 60.451 44.000 0.00 0.00 0.00 1.89
4897 6397 1.340889 GTGGCTCAATTGCTGGAACAA 59.659 47.619 0.00 0.00 38.70 2.83
5291 6798 2.600470 GCCCCAACACCCAGGAAC 60.600 66.667 0.00 0.00 0.00 3.62
5449 6957 5.597182 GGAAAAACTCTACTTTTGGTTCCCT 59.403 40.000 0.00 0.00 0.00 4.20
5496 7004 5.518865 ACATCCCATTTTTACTGTAGCCAT 58.481 37.500 0.00 0.00 0.00 4.40
5560 7068 3.118531 AGCTCTCCCACAATTACCATCT 58.881 45.455 0.00 0.00 0.00 2.90
5562 7070 3.136626 GGTAGCTCTCCCACAATTACCAT 59.863 47.826 0.00 0.00 31.61 3.55
5563 7071 2.504175 GGTAGCTCTCCCACAATTACCA 59.496 50.000 0.00 0.00 31.61 3.25
5564 7072 2.158798 GGGTAGCTCTCCCACAATTACC 60.159 54.545 18.56 3.98 44.05 2.85
5565 7073 3.195471 GGGTAGCTCTCCCACAATTAC 57.805 52.381 18.56 0.00 44.05 1.89
5655 7228 3.834489 AAGTCCATCAGCTTCGATGAT 57.166 42.857 14.09 0.00 44.67 2.45
5755 7343 2.207590 GGTGAAAACGAAGTCGAACCT 58.792 47.619 7.87 0.00 45.00 3.50
5890 7481 4.164796 ACCTCTTGGATAATGACATCAGCA 59.835 41.667 0.00 0.00 37.04 4.41
5982 7701 5.728637 AAGCAAAGGCAAATAAGCTAACT 57.271 34.783 0.00 0.00 44.61 2.24
6016 7735 3.205338 CACATCAAACGAGGATATGGCA 58.795 45.455 0.00 0.00 0.00 4.92
6017 7736 3.002656 CACACATCAAACGAGGATATGGC 59.997 47.826 0.00 0.00 0.00 4.40
6018 7737 4.191544 ACACACATCAAACGAGGATATGG 58.808 43.478 0.00 0.00 0.00 2.74
6130 7857 4.120755 GCTCCTGGGCCCAAGAGG 62.121 72.222 39.58 31.01 35.62 3.69
6150 7881 2.009774 CTTACCATGGAAAGGAGCACG 58.990 52.381 21.47 0.00 0.00 5.34
6187 7918 2.906389 TCATGAGGTGTAGGCTTTGACT 59.094 45.455 0.00 0.00 0.00 3.41
6253 7984 0.105964 CGCCGGATACCATGGAGAAA 59.894 55.000 21.47 0.56 0.00 2.52
6308 8045 1.220749 CCCACCACGACTACCATGG 59.779 63.158 11.19 11.19 39.57 3.66
6319 8056 1.000359 CCCCTTTCCATCCCACCAC 60.000 63.158 0.00 0.00 0.00 4.16
6325 8062 0.394899 CAGTGAGCCCCTTTCCATCC 60.395 60.000 0.00 0.00 0.00 3.51
6831 8764 5.403558 TTCTATGTCATCTACTCCCTCCA 57.596 43.478 0.00 0.00 0.00 3.86
6924 8857 0.527113 CGCAATCCTGATTTGTGCCA 59.473 50.000 0.00 0.00 0.00 4.92
7148 9081 4.634184 ATGACTCTGCAATTGATGAAGC 57.366 40.909 10.34 0.00 34.27 3.86
7193 9126 5.635280 AGTCTTCATGTACGAGACAAATGTG 59.365 40.000 16.00 0.00 42.78 3.21
7316 9249 8.752766 AAATCACACATGAATTTTAGAAGCAG 57.247 30.769 0.00 0.00 38.69 4.24
7337 9270 8.837788 AAGAGAACCAAATCCAAATGAAAATC 57.162 30.769 0.00 0.00 0.00 2.17
7390 9323 7.544622 TCTTACACCACATTACAGTCAGATAC 58.455 38.462 0.00 0.00 0.00 2.24
7760 9693 8.132362 ACGTCAAAAACTGCTTCATAAACATTA 58.868 29.630 0.00 0.00 0.00 1.90
7781 9714 5.654603 ACTGATAATCTGTTACCACGTCA 57.345 39.130 0.00 0.00 0.00 4.35
7923 9887 4.036518 ACCAGAGCATAAGATCTCACCTT 58.963 43.478 0.00 0.00 38.74 3.50
8107 10072 3.513515 CCAAAAGCTAAATGGTGGCCTAA 59.486 43.478 3.32 0.00 0.00 2.69
8152 10117 1.329906 CAATTCTTGCAGCTAGCCGAG 59.670 52.381 12.13 6.50 44.83 4.63
8153 10118 1.372582 CAATTCTTGCAGCTAGCCGA 58.627 50.000 12.13 0.00 44.83 5.54
8154 10119 3.911989 CAATTCTTGCAGCTAGCCG 57.088 52.632 12.13 1.20 44.83 5.52
8164 10129 5.803967 GCTTTCCATTCTAGTGCAATTCTTG 59.196 40.000 0.00 0.00 0.00 3.02
8165 10130 5.713861 AGCTTTCCATTCTAGTGCAATTCTT 59.286 36.000 0.00 0.00 0.00 2.52
8166 10131 5.125097 CAGCTTTCCATTCTAGTGCAATTCT 59.875 40.000 0.00 0.00 0.00 2.40
8167 10132 5.338365 CAGCTTTCCATTCTAGTGCAATTC 58.662 41.667 0.00 0.00 0.00 2.17
8168 10133 4.159135 CCAGCTTTCCATTCTAGTGCAATT 59.841 41.667 0.00 0.00 0.00 2.32
8169 10134 3.698040 CCAGCTTTCCATTCTAGTGCAAT 59.302 43.478 0.00 0.00 0.00 3.56
8170 10135 3.084039 CCAGCTTTCCATTCTAGTGCAA 58.916 45.455 0.00 0.00 0.00 4.08
8171 10136 2.305635 TCCAGCTTTCCATTCTAGTGCA 59.694 45.455 0.00 0.00 0.00 4.57
8172 10137 2.941720 CTCCAGCTTTCCATTCTAGTGC 59.058 50.000 0.00 0.00 0.00 4.40
8173 10138 4.478206 TCTCCAGCTTTCCATTCTAGTG 57.522 45.455 0.00 0.00 0.00 2.74
8174 10139 4.534103 ACTTCTCCAGCTTTCCATTCTAGT 59.466 41.667 0.00 0.00 0.00 2.57
8175 10140 5.096443 ACTTCTCCAGCTTTCCATTCTAG 57.904 43.478 0.00 0.00 0.00 2.43
8176 10141 5.248640 CAACTTCTCCAGCTTTCCATTCTA 58.751 41.667 0.00 0.00 0.00 2.10
8177 10142 4.077822 CAACTTCTCCAGCTTTCCATTCT 58.922 43.478 0.00 0.00 0.00 2.40
8178 10143 3.366781 GCAACTTCTCCAGCTTTCCATTC 60.367 47.826 0.00 0.00 0.00 2.67
8179 10144 2.560105 GCAACTTCTCCAGCTTTCCATT 59.440 45.455 0.00 0.00 0.00 3.16
8180 10145 2.165998 GCAACTTCTCCAGCTTTCCAT 58.834 47.619 0.00 0.00 0.00 3.41
8181 10146 1.133823 TGCAACTTCTCCAGCTTTCCA 60.134 47.619 0.00 0.00 0.00 3.53
8182 10147 1.609208 TGCAACTTCTCCAGCTTTCC 58.391 50.000 0.00 0.00 0.00 3.13
8183 10148 3.080319 AGATGCAACTTCTCCAGCTTTC 58.920 45.455 0.00 0.00 0.00 2.62
8184 10149 3.151912 AGATGCAACTTCTCCAGCTTT 57.848 42.857 0.00 0.00 0.00 3.51
8202 10259 4.080243 TGAACCAAACACACCCTAAGAAGA 60.080 41.667 0.00 0.00 0.00 2.87
8234 10291 3.680937 GGAACGACGACATTCCATTACAA 59.319 43.478 7.83 0.00 43.40 2.41
8373 10433 7.207383 TGACTGAAAACGAATCTAACTCAAGA 58.793 34.615 0.00 0.00 0.00 3.02


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

AutoCloner maintained by Alex Coulton.